praneet1988/inferring-and-visualizing-rna-velocity-in-bulk-rna-seq

Analysis steps to calculate RNA Velocity in Bulk RNA-Seq samples. Step by Step Guide.

Inferring RNA-Velocity in Bulk RNA-Seq samples

What is RNA-Velocity?

RNA-Velocity in simple words the ratio of spliced vs unspliced transcripts. mRNA splicing kinetics: Transcriptional induction for a particular gene results in an increase of (newly transcribed) precursor unspliced mRNAs while, conversely, repression or absence of transcription results in a decrease of unspliced mRNAs. Please see: https://www.nature.com/articles/s41586-018-0414-6)

Source: https://scvelo.readthedocs.io/

Please suggest improvements by forking a branch and report bugs on Issues section.

Software/Tool Requirements:

STAR [version 2.6.1 =>] [https://github.com/alexdobin/STAR]

python3 [version 3.7.1] [https://www.python.org/downloads/]

R [version 3.5.0 =>] [https://www.r-project.org/]

simplesam - a python module [https://simplesam.readthedocs.io/en/latest/#]

samtools [version 1.8.0 =>] [http://www.htslib.org/]

velocyto [http://velocyto.org/velocyto.py/install/index.html]

scVelo [https://scvelo.readthedocs.io/]

loompy - a python module [http://linnarssonlab.org/loompy/installation/index.html]

scanpy [https://scanpy.readthedocs.io/en/stable/installation.html]

pandas - a python module [https://pandas.pydata.org/]

numpy - a python module [https://numpy.org/]

matplotlib - a python module [https://matplotlib.org/]

Major Steps for inferring RNA-Velocity in Bulk RNA-Seq samples:

1. Map the raw RNA-Seq reads to genome of interest using STAR
2. Sort and Index the Bam file resulting from Step1 using samtools
3. Run simplesam module in python to add UMI and Barcode tags
4. Remove reads mapped to chr's (tagged as random) or short scaffolds using samtools
5. Run Velocyto on the bam resulting from Step4 with -U option
6. Run scVelo on the loom file resulting from Step5

Steps in Detail:

Step 1:

STAR --genomeDir STAR-Genome-Index --readFilesIn FASTQ-FILES --readFilesCommand gunzip -c
 --outFileNamePrefix OUTbam --runThreadN 4 --outSAMstrandField intronMotif --outSAMtype BAM Unsorted 
 --sjdbGTFfile Genome-GTF

Step 2:

samtools sort OUTbamAligned.out.bam -o OUTbamAligned.out.sorted.bam

samtools index OUTbamAligned.out.sorted.bam

Step 3:

Please see SimpleSam.py is available in the repository for download

python3 SimpleSam.py OUTbamAligned.out.sorted.bam OUTbamAligned.simplesam.sam

samtools view -b -o OUTbamAligned.simplesam.bam OUTbamAligned.simplesam.sam

samtools sort OUTbamAligned.simplesam.bam -o OUTbamAligned.simplesam.sorted.bam

Step 4:

samtools view -b OUTbamAligned.simplesam.sorted.bam chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18
chr19 chr20 chr21 chr22 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chrM chrX chrY > OUTbamAligned.velocyto.temp.bam

samtools view -b -F 4 OUTbamAligned.velocyto.temp.bam > OUTbamAligned.velocyto.mapped.bam

samtools sort OUTbamAligned.velocyto.mapped.bam -o OUTbamAligned.velocyto.sorted.bam

samtools index OUTbamAligned.velocyto.sorted.bam

Step 5:

velocyto run -U -m GENOME-MASKED-GTF --outputfolder VELOCYTO_OUT OUTbamAligned.velocyto.sorted.bam Genome-GTF

Step 6:

If Multiple samples please combine .loom files using command -- python3 LoomCombine.py
Please see LoomCombine.py is available in the repository for download

python3 scVelo.py VELOCYTO_OUT.loom OUTFILE-PREFIX

scVelo.py has a requirement of Annotations.txt file to back-map sample information in case of multiple samples processed using combined loom file

Example graphs

inferring-and-visualizing-rna-velocity-in-bulk-rna-seq's Issues

Velocyto doesn't write a cellsorted intermediate file before loom generation

Hello! I'm trying to run Velocyto on bulk RNA-seq from multiple samples, and while all of the upstream processing from your README file has worked beautifully, the cellsorted intermediate file is not populated, and therefore a loom file is not generated for any samples. Here is the bam file for input:

(RNAVelocity) [eed13@compute-a-16-60 CA1_0.25h_EE_rep1.dir]$ samtools view CA1_0.25h_EE_rep1Aligned.velocyto.sorted.bam | head
A00354:959:HKL37DSX5:4:1472:19551:16125 99 chr1 3069478 255 1S149M = 3069486 155 TGGGGCATGTATGGTGTGTTATGTTAGCTTTAAATATTGGCATTCCATGATACAGAAAAAAAATAAATCATGGTACTTTTGGCAGTGTTGCTTTAATTTAGGGATTAAGTTATACTAGAAAATATTAGGTTCCCACAGAGAGTAATAACT F:F,,F:FF:FFF:,FFF:FF::FFFFFFFF:FFFFFFF:F:FFFFFFFF,FFFFF:FFFFFFFF:FFFFFFFFFFF,:,FFFF,FFFFFFF:FFFFFFF:,,F::F:F:::FFF:F,FFFF:FF,F,:FF:,FFF:,FFFFFF:,FF,, AS:i:294 CB:Z:959 HI:i:1 NH:i:1 UB:Z:HKL37DSX5 nM:i:0
A00354:959:HKL37DSX5:4:1472:19551:16125 147 chr1 3069486 255 147M3S = 3069478 -155 TATGGTGTGTTATGTTAGCTTTAAATATTGGCATTCCATGATACAGAAAAAAAATAAATCATGGTACTTTTGGCAGTGTTGCTTTAATTTAGGGATTAAGTTATACTAGAAAATATTAGGTTCCCACAGAGAGTAATAACTGTCTTCCCC FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF,FFF,FFFFFFFFFFF,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF,: AS:i:294 CB:Z:959 HI:i:1 NH:i:1 UB:Z:HKL37DSX5 nM:i:0
A00354:959:HKL37DSX5:4:1620:32750:30217 99 chr1 3072876 255 150M = 3073020 1241 GGCCAGAGTACTCTCTACAGGCAAGCTCTCCTCTTGCAGGGAAGGTGCACAGATATCTGGCATTCAGACCTGCCTCCTTGCTGAATATGAAGACCTGAAACAGGGCCTGTCCCAGAAGATGGGTTGCTTCTGCAATTTGCGCACTCATCT FFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:295 CB:Z:959 HI:i:1 NH:i:1 UB:Z:HKL37DSX5 XS:Z:- nM:i:0
A00354:959:HKL37DSX5:4:1620:32750:30217 147 chr1 3073020 255 94M949N54M2S = 3072876 -1241 TCATCTGCACAGACTGGTCTCCTGTTGTGGCCACCAGCTGCTCGCAACATGAACGGTTCGACTGAGAAGGCTACTCGAGCTGTAAGAGAGGAATCTGCTCTGGGGGTCAAAGCCCTCCTTGGCAGCCACCTTTTTCAGGCGGAGAAGGCC FF:FFFFFFF,FFFFFFFFF::FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FF,:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFF:FFFF:FFFFFFF,:FFFFFFFFFFFFFFFFFF:FFFFFFFFFF, AS:i:295 CB:Z:959 HI:i:1 NH:i:1 UB:Z:HKL37DSX5 XS:Z:- nM:i:0
A00354:959:HKL37DSX5:4:2374:26594:10786 99 chr1 3088616 0 137M13S = 3088616 137 TGTGGCTTCATTTTCATTAAACTCTAGAAAGTCCTTAATTTCTTTCTTTATTCCTTCCTTGACCAAGGTATCATTGAGAAGAGTGTTGTTCAGTTTCCACGTGAATGTTGGCTTTCTATTATTTATGTTGTTATTGACCCAGATCGGAAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFF AS:i:264 CB:Z:959 HI:i:1 NH:i:5 UB:Z:HKL37DSX5 nM:i:4
A00354:959:HKL37DSX5:4:2374:26594:10786 147 chr1 3088616 0 10S137M3S = 3088616 -137 CTTCCGATCTTGTGGCTTCATTTTCATTAAACTCTAGAAAGTCCTTAATTTCTTTCTTTATTCCTTCCTTGACCAAGGTATCATTGAGAAGAGTGTTGTTCAGTTTCCACGTGAATGTTGGCTTTCTATTATTTATGTTGTTATTGACCC FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFF,FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, AS:i:264 CB:Z:959 HI:i:1 NH:i:5 UB:Z:HKL37DSX5 nM:i:4
A00354:959:HKL37DSX5:4:1535:11776:6793 355 chr1 3113090 3 150M = 3378315 265321 CCCTGAGATTCCACCTCACACCAGTCAGAATGGCTAAGATCAAAAATTCAGGTGACAGCAGATGCTGGCGTGGATGTGGAGAAAGAGGAACACTCCTCCATTGTTGGTGGGATTGCAGGCTTGTACAAACACTATGGAAATCAGTCTGGC ,FF,:F:F,FFFF,FF,FFFF:F,,:FFFFFF:,FFF:FFFFFFF,F:FFFFFFFFF,FF:F,FFF,FFF:FFFF,:FFFFFFFFFFFFFFFFFF,FFFFF,,,::FFFF:FF:F:FFF,F,FFFFF:,FFFFF,F,:FF,FFFFFF:,: AS:i:223 CB:Z:959 HI:i:2 NH:i:2 UB:Z:HKL37DSX5 nM:i:9
A00354:959:HKL37DSX5:4:2565:20925:2660 99 chr1 3116985 255 8M104457N142M = 3221608 104767 TAATAGAGGTGTGAGAAAAGAAAGGGTATATTAAAAGGAATAGGCGGATTGCCCCAGTTAATACAAAATGCATCAAAAGGGAGGAAAATGTCCCAAAAAGCAGAGAGTACTCACTCTCTGGGCCTTATAGCAGGAGTACTCTGTTACCTT F,FF,:FFFF:FFF:FFFFFFFFF::F,:F,F,F:FFF::FFF:FF,F:F::FF,F:F,FF,FF:,FF,F,F,FF,FF::FFF:FFFFF,FFFFFFFFFFFFFFFF:,,,F,,FF,,FF,F,::F,FF:,FF::FFF:FFFFFFFF,F:, AS:i:270 CB:Z:959 HI:i:1 NH:i:1 UB:Z:HKL37DSX5 XS:Z:+ nM:i:10
A00354:959:HKL37DSX5:4:1133:19651:24940 99 chr1 3145199 255 150M = 3171237 26185 CCTCCAAAGTAGCCGATCACTTCTTTACTTTTCTGACATTTTGACAATATTTTTTTTCTTTCTCTTACTTTGCCACTGTTGTAATTGTGCATTTCCTGATGCACGTGGGACGGCTCAGGATGTTGGTATGATGAATTACTAACTCAAGAT FFFFFFFFFFFFFFF:FFFF:,,:,FFF,::FFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFF,:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:293 CB:Z:959 HI:i:1 NH:i:1 UB:Z:HKL37DSX5 nM:i:0
A00354:959:HKL37DSX5:4:2457:18801:13041 99 chr1 3147361 3 150M = 3245963 98734 GTCCTTATATTGTCTCCAGCAGAAGGTGGAGCCCAGATTAAAGGTGTGATCCACCACACCTTTAATCCCAGATGAAAGGCGTAGCCCAGATTAAAGGTGTGTTCCTTAAACTCGGAGATTCAATCTTCTGGAATCCATAGCCACTATGGC FFFFF:FFFFFFFFFFFFFFFFFFFFFF:F,FFFFFFFFFFF::FFFF,FFFFF,FFF:FFFFFFF,FFFFFFFFFF::F,FFF:FFF:FFFFFF::,FFFFFFFFFFFFFFF:FFFFFFFFFF:FF,F,,FFFFFF:F:F:FFFFFF:F AS:i:230 CB:Z:959 HI:i:1 NH:i:2 UB:Z:HKL37DSX5 nM:i:6

And the command along with the log/error:
(RNAVelocity) [eed13@compute-a-16-60 CA1_0.25h_EE_rep1.dir]$ velocyto run -U -vvv --outputfolder . CA1_0.25h_EE_rep1Aligned.velocyto.sorted.bam /n/groups/neuroduo/Erin/reference_files.dir/GRCm39.dir/Mus_musculus.GRCm39.111.chr.gtf
2024-05-31 16:26:27,915 - INFO - No SAMPLEID specified, the sample will be called CA1_0_PBMV3 (last 5 digits are a random-id to avoid overwriting some other file by mistake)
2024-05-31 16:26:27,915 - DEBUG - Using logic: Default
2024-05-31 16:26:27,916 - DEBUG - Cell barcodes will be determined while reading the .bam file
2024-05-31 16:26:27,952 - DEBUG - Peeking into /n/scratch/users/e/eed13/RNAVelocity/CA1_0.25h_EE_rep1.dir/CA1_0.25h_EE_rep1Aligned.velocyto.sorted.bam
2024-05-31 16:26:27,970 - WARNING - The file /n/scratch/users/e/eed13/RNAVelocity/CA1_0.25h_EE_rep1.dir/cellsorted_CA1_0.25h_EE_rep1Aligned.velocyto.sorted.bam already exists. The sorting step will be skipped and the existing file will be used.
2024-05-31 16:26:27,970 - INFO - Load the annotation from /n/groups/neuroduo/Erin/reference_files.dir/GRCm39.dir/Mus_musculus.GRCm39.111.chr.gtf
2024-05-31 16:26:33,710 - DEBUG - Parsing Chromosome 1 strand - [line 0]
2024-05-31 16:26:34,185 - DEBUG - Done with 1- [line 59575]
2024-05-31 16:26:34,185 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:34,195 - DEBUG - Seen 1747 genes until now
2024-05-31 16:26:34,195 - DEBUG - Parsing Chromosome 1 strand + [line 59576]
2024-05-31 16:26:34,659 - DEBUG - Done with 1+ [line 118661]
2024-05-31 16:26:34,660 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:34,670 - DEBUG - Seen 3557 genes until now
2024-05-31 16:26:34,670 - DEBUG - Parsing Chromosome 10 strand - [line 118662]
2024-05-31 16:26:34,858 - DEBUG - Done with 10- [line 160609]
2024-05-31 16:26:34,858 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:34,866 - DEBUG - Seen 4860 genes until now
2024-05-31 16:26:34,866 - DEBUG - Parsing Chromosome 10 strand + [line 160610]
2024-05-31 16:26:35,371 - DEBUG - Done with 10+ [line 205967]
2024-05-31 16:26:35,372 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:35,380 - DEBUG - Seen 6264 genes until now
2024-05-31 16:26:35,380 - DEBUG - Parsing Chromosome 11 strand - [line 205968]
2024-05-31 16:26:35,668 - DEBUG - Done with 11- [line 270664]
2024-05-31 16:26:35,668 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:35,680 - DEBUG - Seen 7870 genes until now
2024-05-31 16:26:35,680 - DEBUG - Parsing Chromosome 11 strand + [line 270665]
2024-05-31 16:26:36,222 - DEBUG - Done with 11+ [line 335655]
2024-05-31 16:26:36,222 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:36,233 - DEBUG - Seen 9385 genes until now
2024-05-31 16:26:36,233 - DEBUG - Parsing Chromosome 12 strand - [line 335656]
2024-05-31 16:26:36,357 - DEBUG - Done with 12- [line 363365]
2024-05-31 16:26:36,357 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:36,364 - DEBUG - Seen 10739 genes until now
2024-05-31 16:26:36,365 - DEBUG - Parsing Chromosome 12 strand + [line 363366]
2024-05-31 16:26:36,534 - DEBUG - Done with 12+ [line 401151]
2024-05-31 16:26:36,534 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:36,542 - DEBUG - Seen 11949 genes until now
2024-05-31 16:26:36,542 - DEBUG - Parsing Chromosome 13 strand - [line 401152]
2024-05-31 16:26:36,708 - DEBUG - Done with 13- [line 438444]
2024-05-31 16:26:36,708 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:36,716 - DEBUG - Seen 13251 genes until now
2024-05-31 16:26:36,716 - DEBUG - Parsing Chromosome 13 strand + [line 438445]
2024-05-31 16:26:37,138 - DEBUG - Done with 13+ [line 467860]
2024-05-31 16:26:37,138 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:37,145 - DEBUG - Seen 14528 genes until now
2024-05-31 16:26:37,145 - DEBUG - Parsing Chromosome 14 strand - [line 467861]
2024-05-31 16:26:37,323 - DEBUG - Done with 14- [line 507798]
2024-05-31 16:26:37,323 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:37,331 - DEBUG - Seen 15755 genes until now
2024-05-31 16:26:37,331 - DEBUG - Parsing Chromosome 14 strand + [line 507799]
2024-05-31 16:26:37,480 - DEBUG - Done with 14+ [line 542074]
2024-05-31 16:26:37,481 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:37,488 - DEBUG - Seen 17117 genes until now
2024-05-31 16:26:37,488 - DEBUG - Parsing Chromosome 15 strand - [line 542075]
2024-05-31 16:26:37,660 - DEBUG - Done with 15- [line 580501]
2024-05-31 16:26:37,660 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:37,668 - DEBUG - Seen 18096 genes until now
2024-05-31 16:26:37,668 - DEBUG - Parsing Chromosome 15 strand + [line 580502]
2024-05-31 16:26:37,820 - DEBUG - Done with 15+ [line 614251]
2024-05-31 16:26:37,820 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:37,827 - DEBUG - Seen 19059 genes until now
2024-05-31 16:26:37,827 - DEBUG - Parsing Chromosome 16 strand - [line 614252]
2024-05-31 16:26:37,956 - DEBUG - Done with 16- [line 643286]
2024-05-31 16:26:37,956 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:37,962 - DEBUG - Seen 19879 genes until now
2024-05-31 16:26:37,962 - DEBUG - Parsing Chromosome 16 strand + [line 643287]
2024-05-31 16:26:38,439 - DEBUG - Done with 16+ [line 675700]
2024-05-31 16:26:38,439 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:38,445 - DEBUG - Seen 20711 genes until now
2024-05-31 16:26:38,445 - DEBUG - Parsing Chromosome 17 strand - [line 675701]
2024-05-31 16:26:38,658 - DEBUG - Done with 17- [line 723378]
2024-05-31 16:26:38,658 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:38,668 - DEBUG - Seen 21938 genes until now
2024-05-31 16:26:38,669 - DEBUG - Parsing Chromosome 17 strand + [line 723379]
2024-05-31 16:26:38,889 - DEBUG - Done with 17+ [line 773931]
2024-05-31 16:26:38,889 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:38,898 - DEBUG - Seen 23126 genes until now
2024-05-31 16:26:38,898 - DEBUG - Parsing Chromosome 18 strand - [line 773932]
2024-05-31 16:26:38,991 - DEBUG - Done with 18- [line 794411]
2024-05-31 16:26:38,992 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:38,996 - DEBUG - Seen 23786 genes until now
2024-05-31 16:26:38,996 - DEBUG - Parsing Chromosome 18 strand + [line 794412]
2024-05-31 16:26:39,112 - DEBUG - Done with 18+ [line 821511]
2024-05-31 16:26:39,113 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:39,118 - DEBUG - Seen 24565 genes until now
2024-05-31 16:26:39,118 - DEBUG - Parsing Chromosome 19 strand - [line 821512]
2024-05-31 16:26:39,266 - DEBUG - Done with 19- [line 854981]
2024-05-31 16:26:39,267 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:39,272 - DEBUG - Seen 25279 genes until now
2024-05-31 16:26:39,272 - DEBUG - Parsing Chromosome 19 strand + [line 854982]
2024-05-31 16:26:39,789 - DEBUG - Done with 19+ [line 884581]
2024-05-31 16:26:39,789 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:39,794 - DEBUG - Seen 26023 genes until now
2024-05-31 16:26:39,795 - DEBUG - Parsing Chromosome 2 strand - [line 884582]
2024-05-31 16:26:40,149 - DEBUG - Done with 2- [line 964481]
2024-05-31 16:26:40,149 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:40,162 - DEBUG - Seen 27882 genes until now
2024-05-31 16:26:40,163 - DEBUG - Parsing Chromosome 2 strand + [line 964482]
2024-05-31 16:26:40,491 - DEBUG - Done with 2+ [line 1039751]
2024-05-31 16:26:40,491 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:40,505 - DEBUG - Seen 29899 genes until now
2024-05-31 16:26:40,506 - DEBUG - Parsing Chromosome 3 strand - [line 1039752]
2024-05-31 16:26:40,685 - DEBUG - Done with 3- [line 1081512]
2024-05-31 16:26:40,686 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:40,695 - DEBUG - Seen 31394 genes until now
2024-05-31 16:26:40,696 - DEBUG - Parsing Chromosome 3 strand + [line 1081513]
2024-05-31 16:26:40,899 - DEBUG - Done with 3+ [line 1127702]
2024-05-31 16:26:40,900 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:40,909 - DEBUG - Seen 32855 genes until now
2024-05-31 16:26:40,909 - DEBUG - Parsing Chromosome 4 strand - [line 1127703]
2024-05-31 16:26:41,595 - DEBUG - Done with 4- [line 1181103]
2024-05-31 16:26:41,595 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:41,605 - DEBUG - Seen 34286 genes until now
2024-05-31 16:26:41,606 - DEBUG - Parsing Chromosome 4 strand + [line 1181104]
2024-05-31 16:26:41,837 - DEBUG - Done with 4+ [line 1233607]
2024-05-31 16:26:41,837 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:41,848 - DEBUG - Seen 35795 genes until now
2024-05-31 16:26:41,849 - DEBUG - Parsing Chromosome 5 strand - [line 1233608]
2024-05-31 16:26:42,123 - DEBUG - Done with 5- [line 1294653]
2024-05-31 16:26:42,124 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:42,135 - DEBUG - Seen 37429 genes until now
2024-05-31 16:26:42,135 - DEBUG - Parsing Chromosome 5 strand + [line 1294654]
2024-05-31 16:26:42,406 - DEBUG - Done with 5+ [line 1356593]
2024-05-31 16:26:42,406 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:42,418 - DEBUG - Seen 39151 genes until now
2024-05-31 16:26:42,418 - DEBUG - Parsing Chromosome 6 strand - [line 1356594]
2024-05-31 16:26:42,625 - DEBUG - Done with 6- [line 1404907]
2024-05-31 16:26:42,626 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:42,637 - DEBUG - Seen 40734 genes until now
2024-05-31 16:26:42,637 - DEBUG - Parsing Chromosome 6 strand + [line 1404908]
2024-05-31 16:26:42,859 - DEBUG - Done with 6+ [line 1456670]
2024-05-31 16:26:42,859 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:42,870 - DEBUG - Seen 42381 genes until now
2024-05-31 16:26:42,870 - DEBUG - Parsing Chromosome 7 strand - [line 1456671]
2024-05-31 16:26:43,834 - DEBUG - Done with 7- [line 1534606]
2024-05-31 16:26:43,834 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:43,856 - DEBUG - Seen 44966 genes until now
2024-05-31 16:26:43,856 - DEBUG - Parsing Chromosome 7 strand + [line 1534607]
2024-05-31 16:26:44,175 - DEBUG - Done with 7+ [line 1610002]
2024-05-31 16:26:44,176 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:44,190 - DEBUG - Seen 47216 genes until now
2024-05-31 16:26:44,190 - DEBUG - Parsing Chromosome 8 strand - [line 1610003]
2024-05-31 16:26:44,362 - DEBUG - Done with 8- [line 1648479]
2024-05-31 16:26:44,362 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:44,370 - DEBUG - Seen 48489 genes until now
2024-05-31 16:26:44,370 - DEBUG - Parsing Chromosome 8 strand + [line 1648480]
2024-05-31 16:26:44,588 - DEBUG - Done with 8+ [line 1698120]
2024-05-31 16:26:44,588 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:44,597 - DEBUG - Seen 49842 genes until now
2024-05-31 16:26:44,597 - DEBUG - Parsing Chromosome 9 strand - [line 1698121]
2024-05-31 16:26:44,835 - DEBUG - Done with 9- [line 1752034]
2024-05-31 16:26:44,835 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:44,844 - DEBUG - Seen 51248 genes until now
2024-05-31 16:26:44,845 - DEBUG - Parsing Chromosome 9 strand + [line 1752035]
2024-05-31 16:26:45,087 - DEBUG - Done with 9+ [line 1807833]
2024-05-31 16:26:45,087 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:45,097 - DEBUG - Seen 52764 genes until now
2024-05-31 16:26:45,098 - DEBUG - Parsing Chromosome MT strand - [line 1807834]
2024-05-31 16:26:45,098 - DEBUG - Done with MT- [line 1807863]
2024-05-31 16:26:45,098 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:45,098 - DEBUG - Seen 52773 genes until now
2024-05-31 16:26:45,098 - DEBUG - Parsing Chromosome MT strand + [line 1807864]
2024-05-31 16:26:45,099 - DEBUG - Done with MT+ [line 1807980]
2024-05-31 16:26:45,099 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:45,099 - DEBUG - Seen 52801 genes until now
2024-05-31 16:26:45,099 - DEBUG - Parsing Chromosome X strand - [line 1807981]
2024-05-31 16:26:45,232 - DEBUG - Done with X- [line 1838889]
2024-05-31 16:26:45,233 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:45,239 - DEBUG - Seen 54099 genes until now
2024-05-31 16:26:45,239 - DEBUG - Parsing Chromosome X strand + [line 1838890]
2024-05-31 16:26:45,384 - DEBUG - Done with X+ [line 1872954]
2024-05-31 16:26:45,385 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:45,392 - DEBUG - Seen 55489 genes until now
2024-05-31 16:26:45,392 - DEBUG - Parsing Chromosome Y strand - [line 1872955]
2024-05-31 16:26:45,426 - DEBUG - Done with Y- [line 1880111]
2024-05-31 16:26:45,426 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:45,430 - DEBUG - Seen 56412 genes until now
2024-05-31 16:26:45,430 - DEBUG - Parsing Chromosome Y strand + [line 1880112]
2024-05-31 16:26:45,462 - DEBUG - Assigning indexes to genes
2024-05-31 16:26:45,465 - DEBUG - Done with Y+ [line 1887001]
2024-05-31 16:26:45,466 - DEBUG - Fixing corner cases of transcript models containg intron longer than 1000Kbp
2024-05-31 16:26:46,738 - DEBUG - Generated 1577210 features corresponding to 149076 transcript models from /n/groups/neuroduo/Erin/reference_files.dir/GRCm39.dir/Mus_musculus.GRCm39.111.chr.gtf
2024-05-31 16:26:46,766 - INFO - Scan /n/scratch/users/e/eed13/RNAVelocity/CA1_0.25h_EE_rep1.dir/CA1_0.25h_EE_rep1Aligned.velocyto.sorted.bam to validate intron intervals
2024-05-31 16:26:48,527 - DEBUG - Reading /n/scratch/users/e/eed13/RNAVelocity/CA1_0.25h_EE_rep1.dir/CA1_0.25h_EE_rep1Aligned.velocyto.sorted.bam
2024-05-31 16:26:48,538 - DEBUG - Read first 0 million reads
2024-05-31 16:26:48,538 - DEBUG - Marking up chromosome 1
2024-05-31 16:28:12,824 - DEBUG - Marking up chromosome 2
2024-05-31 16:30:05,801 - DEBUG - Marking up chromosome 3
2024-05-31 16:30:12,449 - DEBUG - Read first 10 million reads
2024-05-31 16:31:09,175 - DEBUG - Marking up chromosome 4
2024-05-31 16:32:16,762 - DEBUG - Marking up chromosome 5
2024-05-31 16:33:39,411 - DEBUG - Marking up chromosome 6
2024-05-31 16:33:44,662 - DEBUG - Read first 20 million reads
2024-05-31 16:34:48,414 - DEBUG - Marking up chromosome 7
2024-05-31 16:36:07,371 - DEBUG - Marking up chromosome 8
2024-05-31 16:37:07,164 - DEBUG - Marking up chromosome 9
2024-05-31 16:37:16,758 - DEBUG - Read first 30 million reads
2024-05-31 16:38:23,534 - DEBUG - Marking up chromosome 10
2024-05-31 16:39:28,547 - DEBUG - Marking up chromosome 11
2024-05-31 16:40:51,023 - DEBUG - Read first 40 million reads
2024-05-31 16:41:04,040 - DEBUG - Marking up chromosome 12
2024-05-31 16:42:15,777 - DEBUG - Marking up chromosome 13
2024-05-31 16:43:04,504 - DEBUG - Marking up chromosome 14
2024-05-31 16:43:42,807 - DEBUG - Read first 50 million reads
2024-05-31 16:43:56,867 - DEBUG - Marking up chromosome 15
2024-05-31 16:44:47,074 - DEBUG - Marking up chromosome 16
2024-05-31 16:45:54,381 - DEBUG - Marking up chromosome 17
2024-05-31 16:46:31,659 - DEBUG - Read first 60 million reads
2024-05-31 16:46:55,002 - DEBUG - Marking up chromosome 18
2024-05-31 16:47:37,391 - DEBUG - Marking up chromosome 19
2024-05-31 16:48:38,023 - DEBUG - Marking up chromosome X
2024-05-31 16:49:17,595 - DEBUG - Marking up chromosome Y
2024-05-31 16:49:18,225 - DEBUG - Marking up chromosome MT
2024-05-31 16:50:17,496 - DEBUG - Read first 70 million reads
2024-05-31 16:52:10,803 - DEBUG - End of file. Reset index: start scanning from initial position.
2024-05-31 16:52:10,804 - DEBUG - 0 reads were skipped because no apropiate cell or umi barcode was found
2024-05-31 16:52:10,804 - DEBUG - Start molecule counting!
2024-05-31 16:52:12,650 - DEBUG - Features available for chromosomes : ['1-', '1+', '10-', '10+', '11-', '11+', '12-', '12+', '13-', '13+', '14-', '14+', '15-', '15+', '16-', '16+', '17-', '17+', '18-', '18+', '19-', '19+', '2-', '2+', '3-', '3+', '4-', '4+', '5-', '5+', '6-', '6+', '7-', '7+', '8-', '8+', '9-', '9+', 'MT-', 'MT+', 'X-', 'X+', 'Y-', 'Y+']
2024-05-31 16:52:12,650 - DEBUG - Mask available for chromosomes : []
2024-05-31 16:52:12,650 - DEBUG - Summarizing the results of intron validation.
2024-05-31 16:52:13,231 - DEBUG - Validated 391425 introns (of which unique intervals 141734) out of 714067 total possible introns (considering each possible transcript models).
2024-05-31 16:52:13,232 - DEBUG - Reading /n/scratch/users/e/eed13/RNAVelocity/CA1_0.25h_EE_rep1.dir/cellsorted_CA1_0.25h_EE_rep1Aligned.velocyto.sorted.bam
2024-05-31 16:52:13,236 - DEBUG - Counting for batch 1, containing 0 cells and 0 reads
2024-05-31 16:52:13,236 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
2024-05-31 16:52:13,236 - WARNING - The barcode selection mode is off, no cell events will be identified by <80 counts
2024-05-31 16:52:13,237 - WARNING - 0 of the barcodes where without cell
2024-05-31 16:52:13,237 - DEBUG - 0 reads were skipped because no apropiate cell or umi barcode was found
2024-05-31 16:52:13,237 - DEBUG - Counting done!
2024-05-31 16:52:13,274 - DEBUG - Example of barcode: 959 and cell_id: CA1_0_PBMV3:959
2024-05-31 16:52:13,274 - DEBUG - Generating output file ./CA1_0_PBMV3.loom
2024-05-31 16:52:13,274 - DEBUG - Collecting row attributes
2024-05-31 16:52:13,606 - DEBUG - Generating data table
2024-05-31 16:52:13,607 - DEBUG - Writing loom file
Traceback (most recent call last):
File "/n/groups/neuroduo/Erin/runscripts/RNAVelocity/bin/velocyto", line 8, in
sys.exit(cli())
File "/n/groups/neuroduo/Erin/runscripts/RNAVelocity/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/n/groups/neuroduo/Erin/runscripts/RNAVelocity/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/n/groups/neuroduo/Erin/runscripts/RNAVelocity/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/n/groups/neuroduo/Erin/runscripts/RNAVelocity/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/n/groups/neuroduo/Erin/runscripts/RNAVelocity/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/n/groups/neuroduo/Erin/runscripts/RNAVelocity/lib/python3.10/site-packages/velocyto/commands/run.py", line 113, in run
return _run(bamfile=bamfile, gtffile=gtffile, bcfile=bcfile, outputfolder=outputfolder,
File "/n/groups/neuroduo/Erin/runscripts/RNAVelocity/lib/python3.10/site-packages/velocyto/commands/_run.py", line 287, in _run
ds = loompy.create(filename=outfile, layers=total, row_attrs=ra, col_attrs=ca)
File "/n/groups/neuroduo/Erin/runscripts/RNAVelocity/lib/python3.10/site-packages/loompy/loompy.py", line 1053, in create
raise ValueError("Main matrix cannot be empty")
ValueError: Main matrix cannot be empty

Velocyto run error

Hi,

I use the pipeline you provide. But When I use Velocyto, error occurred.

2022-05-06 09:27:43,140 - INFO - No SAMPLEID specified, the sample will be called CD133_vesicle_from_PLC_1_S37_L002_Aligned_HDXSQ (last 5 digits are a random-id to avoid overwriting some other file by mistake)
2022-05-06 09:27:43,140 - DEBUG - Using logic: Default
2022-05-06 09:27:43,140 - DEBUG - Cell barcodes will be determined while reading the .bam file
2022-05-06 09:27:43,162 - WARNING - Your system does not support calling grep MemAvailable /proc/meminfo so the memory effort for the samtools command could not be chosen appropriately. 32Gb will be assumed
2022-05-06 09:27:43,162 - DEBUG - Peeking into /mnt/dell4/Kota/CD133_vesicle_from_PLC_1_S37_L002_Aligned.velocyto.sorted.bam
2022-05-06 09:27:43,267 - WARNING - The file /mnt/dell4/Kota/cellsorted_CD133_vesicle_from_PLC_1_S37_L002_Aligned.velocyto.sorted.bam already exists. The sorting step will be skipped and the existing file will be used.
2022-05-06 09:27:43,267 - INFO - Load the annotation from /mnt/dell4/Homo_sapiens/UCSC/hg19/Annotation/Archives/archive-2015-07-17-14-32-32/Genes/genes.gtf
2022-05-06 09:27:44,108 - WARNING - The entry exon_number was not present in the gtf file. It will be infferred from the position.
2022-05-06 09:27:53,719 - DEBUG - Parsing Chromosome 1 strand - [line 0]
2022-05-06 09:27:54,212 - DEBUG - Done with 1- [line 23050]
2022-05-06 09:27:54,212 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:54,224 - DEBUG - Seen 1305 genes until now
2022-05-06 09:27:54,225 - DEBUG - Parsing Chromosome 1 strand + [line 23051]
2022-05-06 09:27:54,754 - DEBUG - Done with 1+ [line 48458]
2022-05-06 09:27:54,754 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:54,770 - DEBUG - Seen 2631 genes until now
2022-05-06 09:27:54,770 - DEBUG - Parsing Chromosome 10 strand - [line 48459]
2022-05-06 09:27:55,313 - DEBUG - Done with 10- [line 59341]
2022-05-06 09:27:55,313 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:55,319 - DEBUG - Seen 3136 genes until now
2022-05-06 09:27:55,319 - DEBUG - Parsing Chromosome 10 strand + [line 59342]
2022-05-06 09:27:55,544 - DEBUG - Done with 10+ [line 69777]
2022-05-06 09:27:55,544 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:55,550 - DEBUG - Seen 3662 genes until now
2022-05-06 09:27:55,550 - DEBUG - Parsing Chromosome 11 strand - [line 69778]
2022-05-06 09:27:55,820 - DEBUG - Done with 11- [line 82401]
2022-05-06 09:27:55,820 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:55,828 - DEBUG - Seen 4446 genes until now
2022-05-06 09:27:55,828 - DEBUG - Parsing Chromosome 11 strand + [line 82402]
2022-05-06 09:27:56,133 - DEBUG - Done with 11+ [line 96727]
2022-05-06 09:27:56,134 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:56,142 - DEBUG - Seen 5254 genes until now
2022-05-06 09:27:56,142 - DEBUG - Parsing Chromosome 12 strand - [line 96728]
2022-05-06 09:27:56,803 - DEBUG - Done with 12- [line 109880]
2022-05-06 09:27:56,803 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:56,811 - DEBUG - Seen 5919 genes until now
2022-05-06 09:27:56,811 - DEBUG - Parsing Chromosome 12 strand + [line 109881]
2022-05-06 09:27:57,103 - DEBUG - Done with 12+ [line 123770]
2022-05-06 09:27:57,104 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:57,110 - DEBUG - Seen 6563 genes until now
2022-05-06 09:27:57,110 - DEBUG - Parsing Chromosome 13 strand - [line 123771]
2022-05-06 09:27:57,206 - DEBUG - Done with 13- [line 128367]
2022-05-06 09:27:57,207 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:57,209 - DEBUG - Seen 6857 genes until now
2022-05-06 09:27:57,209 - DEBUG - Parsing Chromosome 13 strand + [line 128368]
2022-05-06 09:27:57,297 - DEBUG - Done with 13+ [line 132480]
2022-05-06 09:27:57,297 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:57,299 - DEBUG - Seen 7149 genes until now
2022-05-06 09:27:57,300 - DEBUG - Parsing Chromosome 14 strand - [line 132481]
2022-05-06 09:27:57,444 - DEBUG - Done with 14- [line 139278]
2022-05-06 09:27:57,445 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:57,448 - DEBUG - Seen 7528 genes until now
2022-05-06 09:27:57,449 - DEBUG - Parsing Chromosome 14 strand + [line 139279]
2022-05-06 09:27:57,612 - DEBUG - Done with 14+ [line 147015]
2022-05-06 09:27:57,612 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:57,617 - DEBUG - Seen 8010 genes until now
2022-05-06 09:27:57,617 - DEBUG - Parsing Chromosome 15 strand - [line 147016]
2022-05-06 09:27:58,251 - DEBUG - Done with 15- [line 156162]
2022-05-06 09:27:58,251 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:58,255 - DEBUG - Seen 8426 genes until now
2022-05-06 09:27:58,255 - DEBUG - Parsing Chromosome 15 strand + [line 156163]
2022-05-06 09:27:58,421 - DEBUG - Done with 15+ [line 164141]
2022-05-06 09:27:58,422 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:58,426 - DEBUG - Seen 8925 genes until now
2022-05-06 09:27:58,426 - DEBUG - Parsing Chromosome 16 strand - [line 164142]
2022-05-06 09:27:58,604 - DEBUG - Done with 16- [line 172634]
2022-05-06 09:27:58,605 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:58,609 - DEBUG - Seen 9435 genes until now
2022-05-06 09:27:58,609 - DEBUG - Parsing Chromosome 16 strand + [line 172635]
2022-05-06 09:27:58,843 - DEBUG - Done with 16+ [line 183783]
2022-05-06 09:27:58,843 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:58,854 - DEBUG - Seen 9991 genes until now
2022-05-06 09:27:58,855 - DEBUG - Parsing Chromosome 17 strand - [line 183784]
2022-05-06 09:27:59,154 - DEBUG - Done with 17- [line 197972]
2022-05-06 09:27:59,154 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:59,161 - DEBUG - Seen 10784 genes until now
2022-05-06 09:27:59,162 - DEBUG - Parsing Chromosome 17 strand + [line 197973]
2022-05-06 09:27:59,438 - DEBUG - Done with 17+ [line 211354]
2022-05-06 09:27:59,439 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:59,446 - DEBUG - Seen 11471 genes until now
2022-05-06 09:27:59,446 - DEBUG - Parsing Chromosome 17_ctg5_hap1 strand - [line 211355]
2022-05-06 09:27:59,454 - DEBUG - Done with 17_ctg5_hap1- [line 211728]
2022-05-06 09:27:59,454 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:59,455 - DEBUG - Seen 11471 genes until now
2022-05-06 09:27:59,455 - DEBUG - Parsing Chromosome 17_ctg5_hap1 strand + [line 211729]
2022-05-06 09:27:59,457 - DEBUG - Done with 17_ctg5_hap1+ [line 211823]
2022-05-06 09:27:59,457 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:59,457 - DEBUG - Seen 11471 genes until now
2022-05-06 09:27:59,457 - DEBUG - Parsing Chromosome 17_gl000205_random strand + [line 211824]
2022-05-06 09:27:59,457 - DEBUG - Done with 17_gl000205_random+ [line 211824]
2022-05-06 09:27:59,457 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:59,458 - DEBUG - Seen 11472 genes until now
2022-05-06 09:27:59,458 - DEBUG - Parsing Chromosome 18 strand - [line 211825]
2022-05-06 09:27:59,531 - DEBUG - Done with 18- [line 215288]
2022-05-06 09:27:59,531 - DEBUG - Assigning indexes to genes
2022-05-06 09:27:59,533 - DEBUG - Seen 11659 genes until now
2022-05-06 09:27:59,533 - DEBUG - Parsing Chromosome 18 strand + [line 215289]
2022-05-06 09:28:00,179 - DEBUG - Done with 18+ [line 219231]
2022-05-06 09:28:00,179 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:00,181 - DEBUG - Seen 11864 genes until now
2022-05-06 09:28:00,181 - DEBUG - Parsing Chromosome 19 strand - [line 219232]
2022-05-06 09:28:00,437 - DEBUG - Done with 19- [line 231523]
2022-05-06 09:28:00,437 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:00,444 - DEBUG - Seen 12678 genes until now
2022-05-06 09:28:00,445 - DEBUG - Parsing Chromosome 19 strand + [line 231524]
2022-05-06 09:28:00,720 - DEBUG - Done with 19+ [line 244758]
2022-05-06 09:28:00,720 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:00,728 - DEBUG - Seen 13577 genes until now
2022-05-06 09:28:00,728 - DEBUG - Parsing Chromosome 19_gl000209_random strand + [line 244759]
2022-05-06 09:28:00,731 - DEBUG - Done with 19_gl000209_random+ [line 244895]
2022-05-06 09:28:00,731 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:00,731 - DEBUG - Seen 13585 genes until now
2022-05-06 09:28:00,731 - DEBUG - Parsing Chromosome 1_gl000191_random strand - [line 244896]
2022-05-06 09:28:00,733 - DEBUG - Done with 1_gl000191_random- [line 244950]
2022-05-06 09:28:00,733 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:00,733 - DEBUG - Seen 13585 genes until now
2022-05-06 09:28:00,733 - DEBUG - Parsing Chromosome 1_gl000192_random strand - [line 244951]
2022-05-06 09:28:00,734 - DEBUG - Done with 1_gl000192_random- [line 245001]
2022-05-06 09:28:00,735 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:00,735 - DEBUG - Seen 13587 genes until now
2022-05-06 09:28:00,735 - DEBUG - Parsing Chromosome 2 strand - [line 245002]
2022-05-06 09:28:01,121 - DEBUG - Done with 2- [line 263870]
2022-05-06 09:28:01,122 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:01,131 - DEBUG - Seen 14417 genes until now
2022-05-06 09:28:01,131 - DEBUG - Parsing Chromosome 2 strand + [line 263871]
2022-05-06 09:28:01,502 - DEBUG - Done with 2+ [line 281952]
2022-05-06 09:28:01,502 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:01,510 - DEBUG - Seen 15266 genes until now
2022-05-06 09:28:01,510 - DEBUG - Parsing Chromosome 20 strand - [line 281953]
2022-05-06 09:28:01,630 - DEBUG - Done with 20- [line 287676]
2022-05-06 09:28:01,631 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:01,634 - DEBUG - Seen 15615 genes until now
2022-05-06 09:28:01,634 - DEBUG - Parsing Chromosome 20 strand + [line 287677]
2022-05-06 09:28:01,771 - DEBUG - Done with 20+ [line 294332]
2022-05-06 09:28:01,771 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:01,775 - DEBUG - Seen 16002 genes until now
2022-05-06 09:28:01,775 - DEBUG - Parsing Chromosome 21 strand - [line 294333]
2022-05-06 09:28:01,835 - DEBUG - Done with 21- [line 297176]
2022-05-06 09:28:01,836 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:01,837 - DEBUG - Seen 16185 genes until now
2022-05-06 09:28:01,838 - DEBUG - Parsing Chromosome 21 strand + [line 297177]
2022-05-06 09:28:02,541 - DEBUG - Done with 21+ [line 300102]
2022-05-06 09:28:02,541 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:02,543 - DEBUG - Seen 16341 genes until now
2022-05-06 09:28:02,543 - DEBUG - Parsing Chromosome 22 strand - [line 300103]
2022-05-06 09:28:02,641 - DEBUG - Done with 22- [line 304874]
2022-05-06 09:28:02,641 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:02,644 - DEBUG - Seen 16635 genes until now
2022-05-06 09:28:02,644 - DEBUG - Parsing Chromosome 22 strand + [line 304875]
2022-05-06 09:28:02,760 - DEBUG - Done with 22+ [line 310536]
2022-05-06 09:28:02,761 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:02,763 - DEBUG - Seen 16929 genes until now
2022-05-06 09:28:02,764 - DEBUG - Parsing Chromosome 3 strand - [line 310537]
2022-05-06 09:28:03,048 - DEBUG - Done with 3- [line 324266]
2022-05-06 09:28:03,049 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:03,055 - DEBUG - Seen 17642 genes until now
2022-05-06 09:28:03,055 - DEBUG - Parsing Chromosome 3 strand + [line 324267]
2022-05-06 09:28:03,344 - DEBUG - Done with 3+ [line 338415]
2022-05-06 09:28:03,344 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:03,353 - DEBUG - Seen 18372 genes until now
2022-05-06 09:28:03,354 - DEBUG - Parsing Chromosome 4 strand - [line 338416]
2022-05-06 09:28:03,544 - DEBUG - Done with 4- [line 347712]
2022-05-06 09:28:03,544 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:03,549 - DEBUG - Seen 18851 genes until now
2022-05-06 09:28:03,549 - DEBUG - Parsing Chromosome 4 strand + [line 347713]
2022-05-06 09:28:03,739 - DEBUG - Done with 4+ [line 356946]
2022-05-06 09:28:03,739 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:03,744 - DEBUG - Seen 19363 genes until now
2022-05-06 09:28:03,744 - DEBUG - Parsing Chromosome 4_ctg9_hap1 strand - [line 356947]
2022-05-06 09:28:03,746 - DEBUG - Done with 4_ctg9_hap1- [line 357014]
2022-05-06 09:28:03,746 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:03,746 - DEBUG - Seen 19363 genes until now
2022-05-06 09:28:03,746 - DEBUG - Parsing Chromosome 4_ctg9_hap1 strand + [line 357015]
2022-05-06 09:28:03,747 - DEBUG - Done with 4_ctg9_hap1+ [line 357042]
2022-05-06 09:28:03,747 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:03,747 - DEBUG - Seen 19363 genes until now
2022-05-06 09:28:03,747 - DEBUG - Parsing Chromosome 4_gl000193_random strand - [line 357043]
2022-05-06 09:28:03,747 - DEBUG - Done with 4_gl000193_random- [line 357048]
2022-05-06 09:28:03,747 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:03,747 - DEBUG - Seen 19364 genes until now
2022-05-06 09:28:03,747 - DEBUG - Parsing Chromosome 4_gl000194_random strand - [line 357049]
2022-05-06 09:28:03,748 - DEBUG - Done with 4_gl000194_random- [line 357067]
2022-05-06 09:28:03,748 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:03,748 - DEBUG - Seen 19365 genes until now
2022-05-06 09:28:03,748 - DEBUG - Parsing Chromosome 5 strand - [line 357068]
2022-05-06 09:28:03,955 - DEBUG - Done with 5- [line 367035]
2022-05-06 09:28:03,955 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:03,961 - DEBUG - Seen 19944 genes until now
2022-05-06 09:28:03,962 - DEBUG - Parsing Chromosome 5 strand + [line 367036]
2022-05-06 09:28:04,200 - DEBUG - Done with 5+ [line 378629]
2022-05-06 09:28:04,200 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:04,206 - DEBUG - Seen 20560 genes until now
2022-05-06 09:28:04,206 - DEBUG - Parsing Chromosome 6 strand - [line 378630]
2022-05-06 09:28:04,463 - DEBUG - Done with 6- [line 391139]
2022-05-06 09:28:04,464 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:04,470 - DEBUG - Seen 21237 genes until now
2022-05-06 09:28:04,470 - DEBUG - Parsing Chromosome 6 strand + [line 391140]
2022-05-06 09:28:05,438 - DEBUG - Done with 6+ [line 402242]
2022-05-06 09:28:05,439 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,447 - DEBUG - Seen 21905 genes until now
2022-05-06 09:28:05,447 - DEBUG - Parsing Chromosome 6_apd_hap1 strand - [line 402243]
2022-05-06 09:28:05,465 - DEBUG - Done with 6_apd_hap1- [line 403104]
2022-05-06 09:28:05,465 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,465 - DEBUG - Seen 21905 genes until now
2022-05-06 09:28:05,466 - DEBUG - Parsing Chromosome 6_apd_hap1 strand + [line 403105]
2022-05-06 09:28:05,477 - DEBUG - Done with 6_apd_hap1+ [line 403638]
2022-05-06 09:28:05,477 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,477 - DEBUG - Seen 21905 genes until now
2022-05-06 09:28:05,477 - DEBUG - Parsing Chromosome 6_cox_hap2 strand - [line 403639]
2022-05-06 09:28:05,521 - DEBUG - Done with 6_cox_hap2- [line 405640]
2022-05-06 09:28:05,521 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,522 - DEBUG - Seen 21906 genes until now
2022-05-06 09:28:05,522 - DEBUG - Parsing Chromosome 6_cox_hap2 strand + [line 405641]
2022-05-06 09:28:05,557 - DEBUG - Done with 6_cox_hap2+ [line 407389]
2022-05-06 09:28:05,557 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,558 - DEBUG - Seen 21906 genes until now
2022-05-06 09:28:05,558 - DEBUG - Parsing Chromosome 6_dbb_hap3 strand - [line 407390]
2022-05-06 09:28:05,597 - DEBUG - Done with 6_dbb_hap3- [line 409192]
2022-05-06 09:28:05,597 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,598 - DEBUG - Seen 21906 genes until now
2022-05-06 09:28:05,598 - DEBUG - Parsing Chromosome 6_dbb_hap3 strand + [line 409193]
2022-05-06 09:28:05,633 - DEBUG - Done with 6_dbb_hap3+ [line 410913]
2022-05-06 09:28:05,633 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,634 - DEBUG - Seen 21906 genes until now
2022-05-06 09:28:05,634 - DEBUG - Parsing Chromosome 6_mann_hap4 strand - [line 410914]
2022-05-06 09:28:05,663 - DEBUG - Done with 6_mann_hap4- [line 412381]
2022-05-06 09:28:05,663 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,664 - DEBUG - Seen 21906 genes until now
2022-05-06 09:28:05,664 - DEBUG - Parsing Chromosome 6_mann_hap4 strand + [line 412382]
2022-05-06 09:28:05,693 - DEBUG - Done with 6_mann_hap4+ [line 413693]
2022-05-06 09:28:05,694 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,694 - DEBUG - Seen 21906 genes until now
2022-05-06 09:28:05,695 - DEBUG - Parsing Chromosome 6_mcf_hap5 strand - [line 413694]
2022-05-06 09:28:05,734 - DEBUG - Done with 6_mcf_hap5- [line 415624]
2022-05-06 09:28:05,734 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,735 - DEBUG - Seen 21907 genes until now
2022-05-06 09:28:05,735 - DEBUG - Parsing Chromosome 6_mcf_hap5 strand + [line 415625]
2022-05-06 09:28:05,768 - DEBUG - Done with 6_mcf_hap5+ [line 417121]
2022-05-06 09:28:05,768 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,769 - DEBUG - Seen 21907 genes until now
2022-05-06 09:28:05,769 - DEBUG - Parsing Chromosome 6_qbl_hap6 strand - [line 417122]
2022-05-06 09:28:05,807 - DEBUG - Done with 6_qbl_hap6- [line 419021]
2022-05-06 09:28:05,807 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,808 - DEBUG - Seen 21907 genes until now
2022-05-06 09:28:05,808 - DEBUG - Parsing Chromosome 6_qbl_hap6 strand + [line 419022]
2022-05-06 09:28:05,845 - DEBUG - Done with 6_qbl_hap6+ [line 420751]
2022-05-06 09:28:05,845 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,846 - DEBUG - Seen 21907 genes until now
2022-05-06 09:28:05,846 - DEBUG - Parsing Chromosome 6_ssto_hap7 strand - [line 420752]
2022-05-06 09:28:05,879 - DEBUG - Done with 6_ssto_hap7- [line 422384]
2022-05-06 09:28:05,880 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,880 - DEBUG - Seen 21907 genes until now
2022-05-06 09:28:05,880 - DEBUG - Parsing Chromosome 6_ssto_hap7 strand + [line 422385]
2022-05-06 09:28:05,911 - DEBUG - Done with 6_ssto_hap7+ [line 423880]
2022-05-06 09:28:05,911 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:05,912 - DEBUG - Seen 21907 genes until now
2022-05-06 09:28:05,912 - DEBUG - Parsing Chromosome 7 strand - [line 423881]
2022-05-06 09:28:06,133 - DEBUG - Done with 7- [line 434605]
2022-05-06 09:28:06,133 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:06,138 - DEBUG - Seen 22517 genes until now
2022-05-06 09:28:06,139 - DEBUG - Parsing Chromosome 7 strand + [line 434606]
2022-05-06 09:28:06,391 - DEBUG - Done with 7+ [line 446945]
2022-05-06 09:28:06,392 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:06,397 - DEBUG - Seen 23150 genes until now
2022-05-06 09:28:06,398 - DEBUG - Parsing Chromosome 7_gl000195_random strand - [line 446946]
2022-05-06 09:28:06,398 - DEBUG - Done with 7_gl000195_random- [line 446949]
2022-05-06 09:28:06,398 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:06,398 - DEBUG - Seen 23151 genes until now
2022-05-06 09:28:06,398 - DEBUG - Parsing Chromosome 8 strand - [line 446950]
2022-05-06 09:28:06,572 - DEBUG - Done with 8- [line 455414]
2022-05-06 09:28:06,572 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:06,576 - DEBUG - Seen 23667 genes until now
2022-05-06 09:28:06,577 - DEBUG - Parsing Chromosome 8 strand + [line 455415]
2022-05-06 09:28:06,728 - DEBUG - Done with 8+ [line 462748]
2022-05-06 09:28:06,728 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:06,732 - DEBUG - Seen 24095 genes until now
2022-05-06 09:28:06,732 - DEBUG - Parsing Chromosome 9 strand - [line 462749]
2022-05-06 09:28:06,924 - DEBUG - Done with 9- [line 471970]
2022-05-06 09:28:06,925 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:06,929 - DEBUG - Seen 24659 genes until now
2022-05-06 09:28:06,930 - DEBUG - Parsing Chromosome 9 strand + [line 471971]
2022-05-06 09:28:07,141 - DEBUG - Done with 9+ [line 482378]
2022-05-06 09:28:07,142 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,146 - DEBUG - Seen 25145 genes until now
2022-05-06 09:28:07,146 - DEBUG - Parsing Chromosome Un_gl000211 strand + [line 482379]
2022-05-06 09:28:07,147 - DEBUG - Done with Un_gl000211+ [line 482385]
2022-05-06 09:28:07,147 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,147 - DEBUG - Seen 25146 genes until now
2022-05-06 09:28:07,147 - DEBUG - Parsing Chromosome Un_gl000212 strand + [line 482386]
2022-05-06 09:28:07,147 - DEBUG - Done with Un_gl000212+ [line 482393]
2022-05-06 09:28:07,147 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,147 - DEBUG - Seen 25147 genes until now
2022-05-06 09:28:07,147 - DEBUG - Parsing Chromosome Un_gl000213 strand - [line 482394]
2022-05-06 09:28:07,148 - DEBUG - Done with Un_gl000213- [line 482406]
2022-05-06 09:28:07,148 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,148 - DEBUG - Seen 25148 genes until now
2022-05-06 09:28:07,148 - DEBUG - Parsing Chromosome Un_gl000213 strand + [line 482407]
2022-05-06 09:28:07,148 - DEBUG - Done with Un_gl000213+ [line 482407]
2022-05-06 09:28:07,148 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,148 - DEBUG - Seen 25148 genes until now
2022-05-06 09:28:07,148 - DEBUG - Parsing Chromosome Un_gl000215 strand + [line 482408]
2022-05-06 09:28:07,148 - DEBUG - Done with Un_gl000215+ [line 482409]
2022-05-06 09:28:07,148 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,149 - DEBUG - Seen 25148 genes until now
2022-05-06 09:28:07,149 - DEBUG - Parsing Chromosome Un_gl000218 strand - [line 482410]
2022-05-06 09:28:07,149 - DEBUG - Done with Un_gl000218- [line 482419]
2022-05-06 09:28:07,149 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,149 - DEBUG - Seen 25150 genes until now
2022-05-06 09:28:07,149 - DEBUG - Parsing Chromosome Un_gl000219 strand - [line 482420]
2022-05-06 09:28:07,149 - DEBUG - Done with Un_gl000219- [line 482426]
2022-05-06 09:28:07,149 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,150 - DEBUG - Seen 25151 genes until now
2022-05-06 09:28:07,150 - DEBUG - Parsing Chromosome Un_gl000220 strand + [line 482427]
2022-05-06 09:28:07,150 - DEBUG - Done with Un_gl000220+ [line 482444]
2022-05-06 09:28:07,150 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,151 - DEBUG - Seen 25158 genes until now
2022-05-06 09:28:07,151 - DEBUG - Parsing Chromosome Un_gl000222 strand - [line 482445]
2022-05-06 09:28:07,151 - DEBUG - Done with Un_gl000222- [line 482464]
2022-05-06 09:28:07,151 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,151 - DEBUG - Seen 25158 genes until now
2022-05-06 09:28:07,151 - DEBUG - Parsing Chromosome Un_gl000223 strand - [line 482465]
2022-05-06 09:28:07,152 - DEBUG - Done with Un_gl000223- [line 482496]
2022-05-06 09:28:07,152 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,152 - DEBUG - Seen 25158 genes until now
2022-05-06 09:28:07,152 - DEBUG - Parsing Chromosome Un_gl000223 strand + [line 482497]
2022-05-06 09:28:07,153 - DEBUG - Done with Un_gl000223+ [line 482499]
2022-05-06 09:28:07,153 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,153 - DEBUG - Seen 25158 genes until now
2022-05-06 09:28:07,153 - DEBUG - Parsing Chromosome Un_gl000227 strand - [line 482500]
2022-05-06 09:28:07,153 - DEBUG - Done with Un_gl000227- [line 482502]
2022-05-06 09:28:07,153 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,153 - DEBUG - Seen 25158 genes until now
2022-05-06 09:28:07,153 - DEBUG - Parsing Chromosome Un_gl000228 strand - [line 482503]
2022-05-06 09:28:07,153 - DEBUG - Done with Un_gl000228- [line 482510]
2022-05-06 09:28:07,154 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,154 - DEBUG - Seen 25158 genes until now
2022-05-06 09:28:07,154 - DEBUG - Parsing Chromosome Un_gl000228 strand + [line 482511]
2022-05-06 09:28:07,154 - DEBUG - Done with Un_gl000228+ [line 482515]
2022-05-06 09:28:07,154 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,154 - DEBUG - Seen 25159 genes until now
2022-05-06 09:28:07,154 - DEBUG - Parsing Chromosome X strand - [line 482516]
2022-05-06 09:28:07,349 - DEBUG - Done with X- [line 491920]
2022-05-06 09:28:07,350 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,355 - DEBUG - Seen 25719 genes until now
2022-05-06 09:28:07,355 - DEBUG - Parsing Chromosome X strand + [line 491921]
2022-05-06 09:28:07,556 - DEBUG - Done with X+ [line 501736]
2022-05-06 09:28:07,556 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,561 - DEBUG - Seen 26258 genes until now
2022-05-06 09:28:07,562 - DEBUG - Parsing Chromosome Y strand - [line 501737]
2022-05-06 09:28:07,623 - DEBUG - Done with Y- [line 504685]
2022-05-06 09:28:07,624 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,625 - DEBUG - Seen 26337 genes until now
2022-05-06 09:28:07,625 - DEBUG - Parsing Chromosome Y strand + [line 504686]
2022-05-06 09:28:07,650 - DEBUG - Assigning indexes to genes
2022-05-06 09:28:07,651 - DEBUG - Done with Y+ [line 505972]
2022-05-06 09:28:07,651 - DEBUG - Fixing corner cases of transcript models containg intron longer than 1000Kbp
2022-05-06 09:28:09,073 - DEBUG - Generated 957406 features corresponding to 54070 transcript models from /mnt/dell4/Homo_sapiens/UCSC/hg19/Annotation/Archives/archive-2015-07-17-14-32-32/Genes/genes.gtf
2022-05-06 09:28:09,095 - INFO - Load the repeat masking annotation from /mnt/dell4/Kota/GRCh38_rmsk.gtf
2022-05-06 09:28:09,095 - DEBUG - Reading /mnt/dell4/Kota/GRCh38_rmsk.gtf, the file will be sorted in memory
2022-05-06 09:29:23,793 - DEBUG - Processed masked annotation .gtf and generated 4545598 intervals to mask!
2022-05-06 09:29:24,686 - INFO - Scan /mnt/dell4/Kota/CD133_vesicle_from_PLC_1_S37_L002_Aligned.velocyto.sorted.bam to validate intron intervals
2022-05-06 09:29:27,456 - DEBUG - Reading /mnt/dell4/Kota/CD133_vesicle_from_PLC_1_S37_L002_Aligned.velocyto.sorted.bam
2022-05-06 09:29:27,472 - DEBUG - Read first 0 million reads
2022-05-06 09:29:27,473 - DEBUG - Marking up chromosome MT
2022-05-06 09:29:27,473 - WARNING - The .bam file refers to a chromosome 'MT+' not present in the annotation (.gtf) file
2022-05-06 09:29:27,473 - WARNING - The .bam file refers to a chromosome 'MT-' not present in the annotation (.gtf) file
2022-05-06 09:29:33,510 - DEBUG - Marking up chromosome 1
2022-05-06 09:36:27,453 - DEBUG - Marking up chromosome 2
2022-05-06 09:39:27,247 - DEBUG - Read first 10 million reads
2022-05-06 09:40:51,953 - DEBUG - Marking up chromosome 3
2022-05-06 09:44:08,252 - DEBUG - Marking up chromosome 4
2022-05-06 09:46:04,300 - DEBUG - Marking up chromosome 5
2022-05-06 09:48:35,946 - DEBUG - Read first 20 million reads
2022-05-06 09:49:34,299 - DEBUG - Marking up chromosome 6
2022-05-06 09:54:07,622 - DEBUG - Marking up chromosome 7
2022-05-06 09:58:27,385 - DEBUG - Read first 30 million reads
2022-05-06 09:59:16,124 - DEBUG - Marking up chromosome 8
2022-05-06 10:01:33,193 - DEBUG - Marking up chromosome 9
2022-05-06 10:04:11,369 - DEBUG - Marking up chromosome 10
2022-05-06 10:06:48,166 - DEBUG - Marking up chromosome 11
2022-05-06 10:08:17,138 - DEBUG - Read first 40 million reads
2022-05-06 10:11:10,313 - DEBUG - Marking up chromosome 12
2022-05-06 10:16:27,883 - DEBUG - Marking up chromosome 13
2022-05-06 10:17:36,592 - DEBUG - Marking up chromosome 14
2022-05-06 10:18:30,474 - DEBUG - Read first 50 million reads
2022-05-06 10:22:20,385 - DEBUG - Marking up chromosome 15
2022-05-06 10:24:48,630 - DEBUG - Marking up chromosome 16
2022-05-06 10:25:57,510 - DEBUG - Read first 60 million reads
2022-05-06 10:27:21,617 - DEBUG - Marking up chromosome 17
2022-05-06 10:32:39,165 - DEBUG - Marking up chromosome 18
2022-05-06 10:33:38,379 - DEBUG - Marking up chromosome 19
2022-05-06 10:36:17,952 - DEBUG - Read first 70 million reads
2022-05-06 10:38:55,659 - DEBUG - Marking up chromosome 20
2022-05-06 10:40:43,239 - DEBUG - Marking up chromosome 21
2022-05-06 10:41:52,243 - DEBUG - Marking up chromosome 22
2022-05-06 10:43:20,304 - DEBUG - Marking up chromosome X
2022-05-06 10:45:34,489 - DEBUG - Marking up chromosome Y
2022-05-06 10:45:41,570 - DEBUG - End of file. Reset index: start scanning from initial position.
2022-05-06 10:45:41,571 - DEBUG - 0 reads were skipped because no apropiate cell or umi barcode was found
2022-05-06 10:45:41,572 - DEBUG - Start molecule counting!
2022-05-06 10:45:48,024 - DEBUG - Features available for chromosomes : ['1-', '1+', '10-', '10+', '11-', '11+', '12-', '12+', '13-', '13+', '14-', '14+', '15-', '15+', '16-', '16+', '17-', '17+', '17_ctg5_hap1-', '17_ctg5_hap1+', '17_gl000205_random+', '18-', '18+', '19-', '19+', '19_gl000209_random+', '1_gl000191_random-', '1_gl000192_random-', '2-', '2+', '20-', '20+', '21-', '21+', '22-', '22+', '3-', '3+', '4-', '4+', '4_ctg9_hap1-', '4_ctg9_hap1+', '4_gl000193_random-', '4_gl000194_random-', '5-', '5+', '6-', '6+', '6_apd_hap1-', '6_apd_hap1+', '6_cox_hap2-', '6_cox_hap2+', '6_dbb_hap3-', '6_dbb_hap3+', '6_mann_hap4-', '6_mann_hap4+', '6_mcf_hap5-', '6_mcf_hap5+', '6_qbl_hap6-', '6_qbl_hap6+', '6_ssto_hap7-', '6_ssto_hap7+', '7-', '7+', '7_gl000195_random-', '8-', '8+', '9-', '9+', 'Un_gl000211+', 'Un_gl000212+', 'Un_gl000213-', 'Un_gl000213+', 'Un_gl000215+', 'Un_gl000218-', 'Un_gl000219-', 'Un_gl000220+', 'Un_gl000222-', 'Un_gl000223-', 'Un_gl000223+', 'Un_gl000227-', 'Un_gl000228-', 'Un_gl000228+', 'X-', 'X+', 'Y-', 'Y+']
2022-05-06 10:45:48,025 - DEBUG - Mask available for chromosomes : ['1-', '1+', '10-', '10+', '10_GL383545v1_alt-', '10_GL383545v1_alt+', '10_GL383546v1_alt-', '10_GL383546v1_alt+', '10_KI270824v1_alt-', '10_KI270824v1_alt+', '10_KI270825v1_alt-', '10_KI270825v1_alt+', '10_KN196480v1_fix-', '10_KN196480v1_fix+', '10_KN538365v1_fix-', '10_KN538365v1_fix+', '10_KN538366v1_fix-', '10_KN538366v1_fix+', '10_KN538367v1_fix-', '10_KN538367v1_fix+', '10_KQ090020v1_alt-', '10_KQ090020v1_alt+', '10_KQ090021v1_fix-', '10_KQ090021v1_fix+', '10_ML143354v1_fix-', '10_ML143354v1_fix+', '10_ML143355v1_fix-', '10_ML143355v1_fix+', '11-', '11+', '11_GL383547v1_alt-', '11_GL383547v1_alt+', '11_JH159136v1_alt-', '11_JH159136v1_alt+', '11_JH159137v1_alt-', '11_JH159137v1_alt+', '11_KI270721v1_random-', '11_KI270721v1_random+', '11_KI270826v1_alt-', '11_KI270826v1_alt+', '11_KI270827v1_alt-', '11_KI270827v1_alt+', '11_KI270829v1_alt-', '11_KI270829v1_alt+', '11_KI270830v1_alt-', '11_KI270830v1_alt+', '11_KI270831v1_alt-', '11_KI270831v1_alt+', '11_KI270832v1_alt-', '11_KI270832v1_alt+', '11_KI270902v1_alt-', '11_KI270902v1_alt+', '11_KI270903v1_alt-', '11_KI270903v1_alt+', '11_KI270927v1_alt-', '11_KI270927v1_alt+', '11_KN196481v1_fix-', '11_KN196481v1_fix+', '11_KN538368v1_alt-', '11_KN538368v1_alt+', '11_KQ090022v1_fix-', '11_KQ090022v1_fix+', '11_KQ759759v1_fix-', '11_KQ759759v1_fix+', '11_KV766195v1_fix-', '11_KV766195v1_fix+', '11_KZ559108v1_fix-', '11_KZ559108v1_fix+', '11_KZ559109v1_fix-', '11_KZ559109v1_fix+', '11_KZ559110v1_alt-', '11_KZ559110v1_alt+', '11_KZ559111v1_alt-', '11_KZ559111v1_alt+', '11_ML143356v1_fix-', '11_ML143356v1_fix+', '11_ML143357v1_fix-', '11_ML143357v1_fix+', '11_ML143358v1_fix-', '11_ML143358v1_fix+', '11_ML143359v1_fix-', '11_ML143359v1_fix+', '11_ML143360v1_fix-', '11_ML143360v1_fix+', '12-', '12+', '12_GL383549v1_alt-', '12_GL383549v1_alt+', '12_GL383550v2_alt-', '12_GL383550v2_alt+', '12_GL383551v1_alt-', '12_GL383551v1_alt+', '12_GL383552v1_alt-', '12_GL383552v1_alt+', '12_GL383553v2_alt-', '12_GL383553v2_alt+', '12_GL877875v1_alt-', '12_GL877875v1_alt+', '12_GL877876v1_alt-', '12_GL877876v1_alt+', '12_KI270833v1_alt-', '12_KI270833v1_alt+', '12_KI270834v1_alt-', '12_KI270834v1_alt+', '12_KI270835v1_alt-', '12_KI270835v1_alt+', '12_KI270836v1_alt-', '12_KI270836v1_alt+', '12_KI270837v1_alt-', '12_KI270837v1_alt+', '12_KI270904v1_alt-', '12_KI270904v1_alt+', '12_KN196482v1_fix-', '12_KN196482v1_fix+', '12_KN538369v1_fix-', '12_KN538369v1_fix+', '12_KN538370v1_fix-', '12_KN538370v1_fix+', '12_KQ090023v1_alt-', '12_KQ090023v1_alt+', '12_KQ759760v1_fix-', '12_KQ759760v1_fix+', '12_KZ208916v1_fix-', '12_KZ208916v1_fix+', '12_KZ208917v1_fix-', '12_KZ208917v1_fix+', '12_KZ208918v1_alt-', '12_KZ208918v1_alt+', '12_KZ559112v1_alt-', '12_KZ559112v1_alt+', '12_ML143361v1_fix-', '12_ML143361v1_fix+', '12_ML143362v1_fix-', '12_ML143362v1_fix+', '13-', '13+', '13_KI270838v1_alt-', '13_KI270838v1_alt+', '13_KI270839v1_alt-', '13_KI270839v1_alt+', '13_KI270840v1_alt-', '13_KI270840v1_alt+', '13_KI270841v1_alt-', '13_KI270841v1_alt+', '13_KI270842v1_alt-', '13_KI270842v1_alt+', '13_KI270843v1_alt-', '13_KI270843v1_alt+', '13_KN196483v1_fix-', '13_KN196483v1_fix+', '13_KN538371v1_fix-', '13_KN538371v1_fix+', '13_KN538372v1_fix-', '13_KN538372v1_fix+', '13_KN538373v1_fix-', '13_KN538373v1_fix+', '13_KQ090024v1_alt-', '13_KQ090024v1_alt+', '13_KQ090025v1_alt-', '13_KQ090025v1_alt+', '13_ML143363v1_fix+', '13_ML143364v1_fix-', '13_ML143364v1_fix+', '13_ML143365v1_fix-', '13_ML143365v1_fix+', '13_ML143366v1_fix-', '13_ML143366v1_fix+', '14-', '14+', '14_GL000009v2_random-', '14_GL000009v2_random+', '14_GL000194v1_random-', '14_GL000194v1_random+', '14_GL000225v1_random-', '14_GL000225v1_random+', '14_KI270722v1_random-', '14_KI270722v1_random+', '14_KI270723v1_random-', '14_KI270723v1_random+', '14_KI270724v1_random-', '14_KI270724v1_random+', '14_KI270725v1_random-', '14_KI270725v1_random+', '14_KI270726v1_random-', '14_KI270726v1_random+', '14_KI270844v1_alt-', '14_KI270844v1_alt+', '14_KI270845v1_alt-', '14_KI270845v1_alt+', '14_KI270846v1_alt-', '14_KI270846v1_alt+', '14_KI270847v1_alt-', '14_KI270847v1_alt+', '14_KZ208919v1_alt-', '14_KZ208919v1_alt+', '14_KZ208920v1_fix-', '14_KZ208920v1_fix+', '14_ML143367v1_fix-', '14_ML143367v1_fix+', '14_ML143368v1_alt-', '14_ML143368v1_alt+', '15-', '15+', '15_GL383554v1_alt-', '15_GL383554v1_alt+', '15_GL383555v2_alt-', '15_GL383555v2_alt+', '15_KI270727v1_random-', '15_KI270727v1_random+', '15_KI270848v1_alt-', '15_KI270848v1_alt+', '15_KI270849v1_alt-', '15_KI270849v1_alt+', '15_KI270850v1_alt-', '15_KI270850v1_alt+', '15_KI270851v1_alt-', '15_KI270851v1_alt+', '15_KI270852v1_alt-', '15_KI270852v1_alt+', '15_KI270905v1_alt-', '15_KI270905v1_alt+', '15_KI270906v1_alt-', '15_KI270906v1_alt+', '15_KN538374v1_fix-', '15_KN538374v1_fix+', '15_KQ031389v1_alt-', '15_KQ031389v1_alt+', '15_ML143369v1_fix-', '15_ML143369v1_fix+', '15_ML143370v1_fix-', '15_ML143370v1_fix+', '15_ML143371v1_fix-', '15_ML143371v1_fix+', '15_ML143372v1_fix-', '15_ML143372v1_fix+', '16-', '16+', '16_GL383556v1_alt-', '16_GL383556v1_alt+', '16_GL383557v1_alt-', '16_GL383557v1_alt+', '16_KI270728v1_random-', '16_KI270728v1_random+', '16_KI270853v1_alt-', '16_KI270853v1_alt+', '16_KI270854v1_alt-', '16_KI270854v1_alt+', '16_KI270855v1_alt-', '16_KI270855v1_alt+', '16_KI270856v1_alt-', '16_KI270856v1_alt+', '16_KQ031390v1_alt-', '16_KQ031390v1_alt+', '16_KQ090026v1_alt-', '16_KQ090026v1_alt+', '16_KQ090027v1_alt-', '16_KQ090027v1_alt+', '16_KV880768v1_fix-', '16_KV880768v1_fix+', '16_KZ208921v1_alt-', '16_KZ208921v1_alt+', '16_KZ559113v1_fix-', '16_KZ559113v1_fix+', '16_ML143373v1_fix-', '16_ML143373v1_fix+', '17-', '17+', '17_GL000205v2_random-', '17_GL000205v2_random+', '17_GL000258v2_alt-', '17_GL000258v2_alt+', '17_GL383563v3_alt-', '17_GL383563v3_alt+', '17_GL383564v2_alt-', '17_GL383564v2_alt+', '17_GL383565v1_alt-', '17_GL383565v1_alt+', '17_GL383566v1_alt-', '17_GL383566v1_alt+', '17_JH159146v1_alt-', '17_JH159146v1_alt+', '17_JH159147v1_alt-', '17_JH159147v1_alt+', '17_JH159148v1_alt-', '17_JH159148v1_alt+', '17_KI270729v1_random-', '17_KI270729v1_random+', '17_KI270730v1_random-', '17_KI270730v1_random+', '17_KI270857v1_alt-', '17_KI270857v1_alt+', '17_KI270858v1_alt-', '17_KI270858v1_alt+', '17_KI270859v1_alt-', '17_KI270859v1_alt+', '17_KI270860v1_alt-', '17_KI270860v1_alt+', '17_KI270861v1_alt-', '17_KI270861v1_alt+', '17_KI270862v1_alt-', '17_KI270862v1_alt+', '17_KI270907v1_alt-', '17_KI270907v1_alt+', '17_KI270908v1_alt-', '17_KI270908v1_alt+', '17_KI270909v1_alt-', '17_KI270909v1_alt+', '17_KI270910v1_alt-', '17_KI270910v1_alt+', '17_KV575245v1_fix-', '17_KV575245v1_fix+', '17_KV766196v1_fix-', '17_KV766196v1_fix+', '17_KV766197v1_alt-', '17_KV766197v1_alt+', '17_KV766198v1_alt-', '17_KV766198v1_alt+', '17_KZ559114v1_alt-', '17_KZ559114v1_alt+', '17_ML143374v1_fix-', '17_ML143374v1_fix+', '17_ML143375v1_fix-', '17_ML143375v1_fix+', '18-', '18+', '18_GL383567v1_alt-', '18_GL383567v1_alt+', '18_GL383568v1_alt-', '18_GL383568v1_alt+', '18_GL383569v1_alt-', '18_GL383569v1_alt+', '18_GL383570v1_alt-', '18_GL383570v1_alt+', '18_GL383571v1_alt-', '18_GL383571v1_alt+', '18_GL383572v1_alt-', '18_GL383572v1_alt+', '18_KI270863v1_alt-', '18_KI270863v1_alt+', '18_KI270864v1_alt-', '18_KI270864v1_alt+', '18_KI270911v1_alt-', '18_KI270911v1_alt+', '18_KI270912v1_alt-', '18_KI270912v1_alt+', '18_KQ090028v1_fix-', '18_KQ090028v1_fix+', '18_KQ458385v1_alt-', '18_KQ458385v1_alt+', '18_KZ208922v1_fix-', '18_KZ208922v1_fix+', '18_KZ559115v1_fix-', '18_KZ559115v1_fix+', '18_KZ559116v1_alt-', '18_KZ559116v1_alt+', '19-', '19+', '19_GL000209v2_alt-', '19_GL000209v2_alt+', '19_GL383573v1_alt-', '19_GL383573v1_alt+', '19_GL383574v1_alt-', '19_GL383574v1_alt+', '19_GL383575v2_alt-', '19_GL383575v2_alt+', '19_GL383576v1_alt-', '19_GL383576v1_alt+', '19_GL949746v1_alt-', '19_GL949746v1_alt+', '19_GL949747v2_alt-', '19_GL949747v2_alt+', '19_GL949748v2_alt-', '19_GL949748v2_alt+', '19_GL949749v2_alt-', '19_GL949749v2_alt+', '19_GL949750v2_alt-', '19_GL949750v2_alt+', '19_GL949751v2_alt-', '19_GL949751v2_alt+', '19_GL949752v1_alt-', '19_GL949752v1_alt+', '19_GL949753v2_alt-', '19_GL949753v2_alt+', '19_KI270865v1_alt-', '19_KI270865v1_alt+', '19_KI270866v1_alt-', '19_KI270866v1_alt+', '19_KI270867v1_alt-', '19_KI270867v1_alt+', '19_KI270868v1_alt-', '19_KI270868v1_alt+', '19_KI270882v1_alt-', '19_KI270882v1_alt+', '19_KI270883v1_alt-', '19_KI270883v1_alt+', '19_KI270884v1_alt-', '19_KI270884v1_alt+', '19_KI270885v1_alt-', '19_KI270885v1_alt+', '19_KI270886v1_alt-', '19_KI270886v1_alt+', '19_KI270887v1_alt-', '19_KI270887v1_alt+', '19_KI270888v1_alt-', '19_KI270888v1_alt+', '19_KI270889v1_alt-', '19_KI270889v1_alt+', '19_KI270890v1_alt-', '19_KI270890v1_alt+', '19_KI270891v1_alt-', '19_KI270891v1_alt+', '19_KI270914v1_alt-', '19_KI270914v1_alt+', '19_KI270915v1_alt-', '19_KI270915v1_alt+', '19_KI270916v1_alt-', '19_KI270916v1_alt+', '19_KI270917v1_alt-', '19_KI270917v1_alt+', '19_KI270918v1_alt-', '19_KI270918v1_alt+', '19_KI270919v1_alt-', '19_KI270919v1_alt+', '19_KI270920v1_alt-', '19_KI270920v1_alt+', '19_KI270921v1_alt-', '19_KI270921v1_alt+', '19_KI270922v1_alt-', '19_KI270922v1_alt+', '19_KI270923v1_alt-', '19_KI270923v1_alt+', '19_KI270929v1_alt-', '19_KI270929v1_alt+', '19_KI270930v1_alt-', '19_KI270930v1_alt+', '19_KI270931v1_alt-', '19_KI270931v1_alt+', '19_KI270932v1_alt-', '19_KI270932v1_alt+', '19_KI270933v1_alt-', '19_KI270933v1_alt+', '19_KI270938v1_alt-', '19_KI270938v1_alt+', '19_KN196484v1_fix-', '19_KN196484v1_fix+', '19_KQ458386v1_fix-', '19_KQ458386v1_fix+', '19_KV575246v1_alt-', '19_KV575246v1_alt+', '19_KV575247v1_alt-', '19_KV575247v1_alt+', '19_KV575248v1_alt-', '19_KV575248v1_alt+', '19_KV575249v1_alt-', '19_KV575249v1_alt+', '19_KV575250v1_alt-', '19_KV575250v1_alt+', '19_KV575251v1_alt-', '19_KV575251v1_alt+', '19_KV575252v1_alt-', '19_KV575252v1_alt+', '19_KV575253v1_alt-', '19_KV575253v1_alt+', '19_KV575254v1_alt-', '19_KV575254v1_alt+', '19_KV575255v1_alt-', '19_KV575255v1_alt+', '19_KV575256v1_alt-', '19_KV575256v1_alt+', '19_KV575257v1_alt-', '19_KV575257v1_alt+', '19_KV575258v1_alt-', '19_KV575258v1_alt+', '19_KV575259v1_alt-', '19_KV575259v1_alt+', '19_KV575260v1_alt-', '19_KV575260v1_alt+', '19_ML143376v1_fix-', '19_ML143376v1_fix+', '1_GL383518v1_alt-', '1_GL383518v1_alt+', '1_GL383519v1_alt-', '1_GL383519v1_alt+', '1_GL383520v2_alt-', '1_GL383520v2_alt+', '1_KI270706v1_random-', '1_KI270706v1_random+', '1_KI270707v1_random-', '1_KI270707v1_random+', '1_KI270708v1_random-', '1_KI270708v1_random+', '1_KI270709v1_random-', '1_KI270709v1_random+', '1_KI270710v1_random-', '1_KI270710v1_random+', '1_KI270711v1_random-', '1_KI270711v1_random+', '1_KI270712v1_random-', '1_KI270712v1_random+', '1_KI270713v1_random-', '1_KI270713v1_random+', '1_KI270714v1_random-', '1_KI270714v1_random+', '1_KI270759v1_alt-', '1_KI270759v1_alt+', '1_KI270760v1_alt-', '1_KI270760v1_alt+', '1_KI270761v1_alt-', '1_KI270761v1_alt+', '1_KI270762v1_alt-', '1_KI270762v1_alt+', '1_KI270763v1_alt-', '1_KI270763v1_alt+', '1_KI270764v1_alt-', '1_KI270764v1_alt+', '1_KI270765v1_alt-', '1_KI270765v1_alt+', '1_KI270766v1_alt-', '1_KI270766v1_alt+', '1_KI270892v1_alt-', '1_KI270892v1_alt+', '1_KN196472v1_fix-', '1_KN196472v1_fix+', '1_KN196473v1_fix-', '1_KN196473v1_fix+', '1_KN196474v1_fix-', '1_KN196474v1_fix+', '1_KN538360v1_fix-', '1_KN538360v1_fix+', '1_KN538361v1_fix-', '1_KN538361v1_fix+', '1_KQ031383v1_fix-', '1_KQ031383v1_fix+', '1_KQ458382v1_alt-', '1_KQ458382v1_alt+', '1_KQ458383v1_alt-', '1_KQ458383v1_alt+', '1_KQ458384v1_alt-', '1_KQ458384v1_alt+', '1_KQ983255v1_alt-', '1_KQ983255v1_alt+', '1_KV880763v1_alt-', '1_KV880763v1_alt+', '1_KZ208904v1_alt-', '1_KZ208904v1_alt+', '1_KZ208905v1_alt-', '1_KZ208905v1_alt+', '1_KZ208906v1_fix-', '1_KZ208906v1_fix+', '1_KZ559100v1_fix-', '1_KZ559100v1_fix+', '2-', '2+', '20-', '20+', '20_GL383577v2_alt-', '20_GL383577v2_alt+', '20_KI270869v1_alt-', '20_KI270869v1_alt+', '20_KI270870v1_alt-', '20_KI270870v1_alt+', '20_KI270871v1_alt-', '20_KI270871v1_alt+', '21-', '21+', '21_GL383578v2_alt-', '21_GL383578v2_alt+', '21_GL383579v2_alt-', '21_GL383579v2_alt+', '21_GL383580v2_alt-', '21_GL383580v2_alt+', '21_GL383581v2_alt-', '21_GL383581v2_alt+', '21_KI270872v1_alt-', '21_KI270872v1_alt+', '21_KI270873v1_alt-', '21_KI270873v1_alt+', '21_KI270874v1_alt-', '21_KI270874v1_alt+', '21_ML143377v1_fix-', '21_ML143377v1_fix+', '22-', '22+', '22_GL383582v2_alt-', '22_GL383582v2_alt+', '22_GL383583v2_alt-', '22_GL383583v2_alt+', '22_KB663609v1_alt-', '22_KB663609v1_alt+', '22_KI270731v1_random-', '22_KI270731v1_random+', '22_KI270732v1_random-', '22_KI270732v1_random+', '22_KI270733v1_random-', '22_KI270733v1_random+', '22_KI270734v1_random-', '22_KI270734v1_random+', '22_KI270735v1_random-', '22_KI270735v1_random+', '22_KI270736v1_random-', '22_KI270736v1_random+', '22_KI270737v1_random-', '22_KI270737v1_random+', '22_KI270738v1_random-', '22_KI270738v1_random+', '22_KI270739v1_random-', '22_KI270739v1_random+', '22_KI270875v1_alt-', '22_KI270875v1_alt+', '22_KI270876v1_alt-', '22_KI270876v1_alt+', '22_KI270877v1_alt-', '22_KI270877v1_alt+', '22_KI270878v1_alt-', '22_KI270878v1_alt+', '22_KI270879v1_alt-', '22_KI270879v1_alt+', '22_KI270928v1_alt-', '22_KI270928v1_alt+', '22_KN196485v1_alt-', '22_KN196485v1_alt+', '22_KN196486v1_alt-', '22_KN196486v1_alt+', '22_KQ458387v1_alt-', '22_KQ458387v1_alt+', '22_KQ458388v1_alt-', '22_KQ458388v1_alt+', '22_KQ759761v1_alt-', '22_KQ759761v1_alt+', '22_KQ759762v1_fix-', '22_KQ759762v1_fix+', '22_ML143378v1_fix-', '22_ML143378v1_fix+', '22_ML143379v1_fix-', '22_ML143379v1_fix+', '22_ML143380v1_fix-', '22_ML143380v1_fix+', '2_GL383521v1_alt-', '2_GL383521v1_alt+', '2_GL383522v1_alt-', '2_GL383522v1_alt+', '2_GL582966v2_alt-', '2_GL582966v2_alt+', '2_KI270715v1_random+', '2_KI270716v1_random+', '2_KI270767v1_alt-', '2_KI270767v1_alt+', '2_KI270768v1_alt-', '2_KI270768v1_alt+', '2_KI270769v1_alt-', '2_KI270769v1_alt+', '2_KI270770v1_alt-', '2_KI270770v1_alt+', '2_KI270771v1_alt-', '2_KI270771v1_alt+', '2_KI270772v1_alt-', '2_KI270772v1_alt+', '2_KI270773v1_alt-', '2_KI270773v1_alt+', '2_KI270774v1_alt-', '2_KI270774v1_alt+', '2_KI270775v1_alt-', '2_KI270775v1_alt+', '2_KI270776v1_alt-', '2_KI270776v1_alt+', '2_KI270893v1_alt-', '2_KI270893v1_alt+', '2_KI270894v1_alt-', '2_KI270894v1_alt+', '2_KN538362v1_fix-', '2_KN538362v1_fix+', '2_KN538363v1_fix-', '2_KN538363v1_fix+', '2_KQ031384v1_fix-', '2_KQ031384v1_fix+', '2_KQ983256v1_alt-', '2_KQ983256v1_alt+', '2_KZ208907v1_alt-', '2_KZ208907v1_alt+', '2_KZ208908v1_alt-', '2_KZ208908v1_alt+', '2_ML143341v1_fix-', '2_ML143341v1_fix+', '2_ML143342v1_fix-', '2_ML143342v1_fix+', '3-', '3+', '3_GL000221v1_random-', '3_GL000221v1_random+', '3_GL383526v1_alt-', '3_GL383526v1_alt+', '3_JH636055v2_alt-', '3_JH636055v2_alt+', '3_KI270777v1_alt-', '3_KI270777v1_alt+', '3_KI270778v1_alt-', '3_KI270778v1_alt+', '3_KI270779v1_alt-', '3_KI270779v1_alt+', '3_KI270780v1_alt-', '3_KI270780v1_alt+', '3_KI270781v1_alt-', '3_KI270781v1_alt+', '3_KI270782v1_alt-', '3_KI270782v1_alt+', '3_KI270783v1_alt-', '3_KI270783v1_alt+', '3_KI270784v1_alt-', '3_KI270784v1_alt+', '3_KI270895v1_alt-', '3_KI270895v1_alt+', '3_KI270924v1_alt-', '3_KI270924v1_alt+', '3_KI270934v1_alt-', '3_KI270934v1_alt+', '3_KI270935v1_alt-', '3_KI270935v1_alt+', '3_KI270936v1_alt-', '3_KI270936v1_alt+', '3_KI270937v1_alt-', '3_KI270937v1_alt+', '3_KN196475v1_fix-', '3_KN196475v1_fix+', '3_KN196476v1_fix-', '3_KN196476v1_fix+', '3_KN538364v1_fix-', '3_KN538364v1_fix+', '3_KQ031385v1_fix-', '3_KQ031385v1_fix+', '3_KQ031386v1_fix-', '3_KQ031386v1_fix+', '3_KV766192v1_fix-', '3_KV766192v1_fix+', '3_KZ208909v1_alt-', '3_KZ208909v1_alt+', '3_KZ559101v1_alt-', '3_KZ559101v1_alt+', '3_KZ559102v1_alt-', '3_KZ559102v1_alt+', '3_KZ559103v1_alt-', '3_KZ559103v1_alt+', '3_KZ559104v1_fix-', '3_KZ559104v1_fix+', '3_KZ559105v1_alt-', '3_KZ559105v1_alt+', '3_ML143343v1_alt-', '3_ML143343v1_alt+', '4-', '4+', '4_GL000008v2_random-', '4_GL000008v2_random+', '4_GL000257v2_alt-', '4_GL000257v2_alt+', '4_GL383527v1_alt-', '4_GL383527v1_alt+', '4_GL383528v1_alt-', '4_GL383528v1_alt+', '4_KI270785v1_alt-', '4_KI270785v1_alt+', '4_KI270786v1_alt-', '4_KI270786v1_alt+', '4_KI270787v1_alt-', '4_KI270787v1_alt+', '4_KI270788v1_alt-', '4_KI270788v1_alt+', '4_KI270789v1_alt-', '4_KI270789v1_alt+', '4_KI270790v1_alt-', '4_KI270790v1_alt+', '4_KI270896v1_alt-', '4_KI270896v1_alt+', '4_KI270925v1_alt-', '4_KI270925v1_alt+', '4_KQ090013v1_alt-', '4_KQ090013v1_alt+', '4_KQ090014v1_alt-', '4_KQ090014v1_alt+', '4_KQ090015v1_alt-', '4_KQ090015v1_alt+', '4_KQ983257v1_fix-', '4_KQ983257v1_fix+', '4_KQ983258v1_alt-', '4_KQ983258v1_alt+', '4_KV766193v1_alt-', '4_KV766193v1_alt+', '4_ML143344v1_fix-', '4_ML143344v1_fix+', '4_ML143345v1_fix-', '4_ML143345v1_fix+', '4_ML143346v1_fix-', '4_ML143346v1_fix+', '4_ML143347v1_fix-', '4_ML143347v1_fix+', '4_ML143348v1_fix-', '4_ML143348v1_fix+', '4_ML143349v1_fix-', '4_ML143349v1_fix+', '5-', '5+', '5_GL000208v1_random-', '5_GL000208v1_random+', '5_GL339449v2_alt-', '5_GL339449v2_alt+', '5_GL383530v1_alt-', '5_GL383530v1_alt+', '5_GL383531v1_alt-', '5_GL383531v1_alt+', '5_GL383532v1_alt-', '5_GL383532v1_alt+', '5_GL949742v1_alt-', '5_GL949742v1_alt+', '5_KI270791v1_alt-', '5_KI270791v1_alt+', '5_KI270792v1_alt-', '5_KI270792v1_alt+', '5_KI270793v1_alt-', '5_KI270793v1_alt+', '5_KI270794v1_alt-', '5_KI270794v1_alt+', '5_KI270795v1_alt-', '5_KI270795v1_alt+', '5_KI270796v1_alt-', '5_KI270796v1_alt+', '5_KI270897v1_alt-', '5_KI270897v1_alt+', '5_KI270898v1_alt-', '5_KI270898v1_alt+', '5_KN196477v1_alt-', '5_KN196477v1_alt+', '5_KV575243v1_alt-', '5_KV575243v1_alt+', '5_KV575244v1_fix-', '5_KV575244v1_fix+', '5_KZ208910v1_alt-', '5_KZ208910v1_alt+', '5_ML143350v1_fix-', '5_ML143350v1_fix+', '6-', '6+', '6_GL000250v2_alt-', '6_GL000250v2_alt+', '6_GL000251v2_alt-', '6_GL000251v2_alt+', '6_GL000252v2_alt-', '6_GL000252v2_alt+', '6_GL000253v2_alt-', '6_GL000253v2_alt+', '6_GL000254v2_alt-', '6_GL000254v2_alt+', '6_GL000255v2_alt-', '6_GL000255v2_alt+', '6_GL000256v2_alt-', '6_GL000256v2_alt+', '6_GL383533v1_alt-', '6_GL383533v1_alt+', '6_KB021644v2_alt-', '6_KB021644v2_alt+', '6_KI270758v1_alt-', '6_KI270758v1_alt+', '6_KI270797v1_alt-', '6_KI270797v1_alt+', '6_KI270798v1_alt-', '6_KI270798v1_alt+', '6_KI270799v1_alt-', '6_KI270799v1_alt+', '6_KI270800v1_alt-', '6_KI270800v1_alt+', '6_KI270801v1_alt-', '6_KI270801v1_alt+', '6_KI270802v1_alt-', '6_KI270802v1_alt+', '6_KN196478v1_fix-', '6_KN196478v1_fix+', '6_KQ031387v1_fix-', '6_KQ031387v1_fix+', '6_KQ090016v1_fix-', '6_KQ090016v1_fix+', '6_KQ090017v1_alt-', '6_KQ090017v1_alt+', '6_KV766194v1_fix-', '6_KV766194v1_fix+', '6_KZ208911v1_fix-', '6_KZ208911v1_fix+', '6_ML143351v1_fix-', '6_ML143351v1_fix+', '7-', '7+', '7_GL383534v2_alt-', '7_GL383534v2_alt+', '7_KI270803v1_alt-', '7_KI270803v1_alt+', '7_KI270804v1_alt-', '7_KI270804v1_alt+', '7_KI270805v1_alt-', '7_KI270805v1_alt+', '7_KI270806v1_alt-', '7_KI270806v1_alt+', '7_KI270807v1_alt-', '7_KI270807v1_alt+', '7_KI270808v1_alt-', '7_KI270808v1_alt+', '7_KI270809v1_alt-', '7_KI270809v1_alt+', '7_KI270899v1_alt-', '7_KI270899v1_alt+', '7_KQ031388v1_fix-', '7_KQ031388v1_fix+', '7_KV880764v1_fix-', '7_KV880764v1_fix+', '7_KV880765v1_fix-', '7_KV880765v1_fix+', '7_KZ208912v1_fix-', '7_KZ208912v1_fix+', '7_KZ208913v1_alt-', '7_KZ208913v1_alt+', '7_KZ559106v1_alt-', '7_KZ559106v1_alt+', '7_ML143352v1_fix-', '7_ML143352v1_fix+', '8-', '8+', '8_KI270810v1_alt-', '8_KI270810v1_alt+', '8_KI270811v1_alt-', '8_KI270811v1_alt+', '8_KI270812v1_alt-', '8_KI270812v1_alt+', '8_KI270813v1_alt-', '8_KI270813v1_alt+', '8_KI270814v1_alt-', '8_KI270814v1_alt+', '8_KI270815v1_alt-', '8_KI270815v1_alt+', '8_KI270816v1_alt-', '8_KI270816v1_alt+', '8_KI270817v1_alt-', '8_KI270817v1_alt+', '8_KI270818v1_alt-', '8_KI270818v1_alt+', '8_KI270819v1_alt-', '8_KI270819v1_alt+', '8_KI270820v1_alt-', '8_KI270820v1_alt+', '8_KI270821v1_alt-', '8_KI270821v1_alt+', '8_KI270822v1_alt-', '8_KI270822v1_alt+', '8_KI270900v1_alt-', '8_KI270900v1_alt+', '8_KI270901v1_alt-', '8_KI270901v1_alt+', '8_KI270926v1_alt-', '8_KI270926v1_alt+', '8_KV880766v1_fix-', '8_KV880766v1_fix+', '8_KV880767v1_fix-', '8_KV880767v1_fix+', '8_KZ208914v1_fix-', '8_KZ208914v1_fix+', '8_KZ208915v1_fix-', '8_KZ208915v1_fix+', '8_KZ559107v1_alt-', '8_KZ559107v1_alt+', '9-', '9+', '9_GL383539v1_alt-', '9_GL383539v1_alt+', '9_GL383540v1_alt-', '9_GL383540v1_alt+', '9_GL383541v1_alt-', '9_GL383541v1_alt+', '9_GL383542v1_alt-', '9_GL383542v1_alt+', '9_KI270717v1_random-', '9_KI270717v1_random+', '9_KI270718v1_random-', '9_KI270718v1_random+', '9_KI270719v1_random-', '9_KI270719v1_random+', '9_KI270720v1_random-', '9_KI270720v1_random+', '9_KI270823v1_alt-', '9_KI270823v1_alt+', '9_KN196479v1_fix-', '9_KN196479v1_fix+', '9_KQ090018v1_alt-', '9_KQ090018v1_alt+', '9_KQ090019v1_alt-', '9_KQ090019v1_alt+', '9_ML143353v1_fix-', '9_ML143353v1_fix+', 'M-', 'M+', 'Un_GL000195v1-', 'Un_GL000195v1+', 'Un_GL000213v1-', 'Un_GL000213v1+', 'Un_GL000214v1-', 'Un_GL000214v1+', 'Un_GL000216v2-', 'Un_GL000216v2+', 'Un_GL000218v1-', 'Un_GL000218v1+', 'Un_GL000219v1-', 'Un_GL000219v1+', 'Un_GL000220v1-', 'Un_GL000220v1+', 'Un_GL000224v1-', 'Un_GL000224v1+', 'Un_GL000226v1+', 'Un_KI270302v1+', 'Un_KI270303v1-', 'Un_KI270304v1-', 'Un_KI270305v1+', 'Un_KI270310v1-', 'Un_KI270311v1+', 'Un_KI270312v1-', 'Un_KI270315v1+', 'Un_KI270316v1+', 'Un_KI270317v1-', 'Un_KI270320v1+', 'Un_KI270322v1-', 'Un_KI270329v1-', 'Un_KI270330v1-', 'Un_KI270330v1+', 'Un_KI270333v1-', 'Un_KI270334v1+', 'Un_KI270335v1+', 'Un_KI270336v1-', 'Un_KI270337v1-', 'Un_KI270338v1+', 'Un_KI270340v1+', 'Un_KI270362v1-', 'Un_KI270363v1-', 'Un_KI270364v1-', 'Un_KI270364v1+', 'Un_KI270366v1-', 'Un_KI270371v1+', 'Un_KI270372v1-', 'Un_KI270372v1+', 'Un_KI270373v1-', 'Un_KI270373v1+', 'Un_KI270374v1-', 'Un_KI270374v1+', 'Un_KI270375v1-', 'Un_KI270376v1-', 'Un_KI270378v1+', 'Un_KI270379v1+', 'Un_KI270381v1-', 'Un_KI270382v1+', 'Un_KI270383v1-', 'Un_KI270384v1-', 'Un_KI270385v1+', 'Un_KI270386v1-', 'Un_KI270387v1+', 'Un_KI270388v1+', 'Un_KI270389v1+', 'Un_KI270390v1+', 'Un_KI270391v1-', 'Un_KI270392v1+', 'Un_KI270393v1-', 'Un_KI270394v1+', 'Un_KI270395v1-', 'Un_KI270396v1-', 'Un_KI270411v1-', 'Un_KI270412v1-', 'Un_KI270414v1+', 'Un_KI270417v1+', 'Un_KI270418v1-', 'Un_KI270419v1+', 'Un_KI270420v1-', 'Un_KI270422v1-', 'Un_KI270423v1+', 'Un_KI270424v1+', 'Un_KI270425v1+', 'Un_KI270429v1+', 'Un_KI270435v1-', 'Un_KI270435v1+', 'Un_KI270438v1-', 'Un_KI270438v1+', 'Un_KI270442v1-', 'Un_KI270442v1+', 'Un_KI270448v1-', 'Un_KI270448v1+', 'Un_KI270465v1-', 'Un_KI270466v1+', 'Un_KI270467v1+', 'Un_KI270468v1+', 'Un_KI270507v1+', 'Un_KI270508v1-', 'Un_KI270509v1-', 'Un_KI270510v1+', 'Un_KI270511v1-', 'Un_KI270512v1-', 'Un_KI270512v1+', 'Un_KI270515v1+', 'Un_KI270516v1+', 'Un_KI270517v1-', 'Un_KI270518v1+', 'Un_KI270519v1-', 'Un_KI270519v1+', 'Un_KI270521v1-', 'Un_KI270521v1+', 'Un_KI270522v1-', 'Un_KI270528v1+', 'Un_KI270529v1-', 'Un_KI270530v1+', 'Un_KI270538v1-', 'Un_KI270538v1+', 'Un_KI270539v1+', 'Un_KI270544v1-', 'Un_KI270548v1+', 'Un_KI270579v1-', 'Un_KI270579v1+', 'Un_KI270580v1-', 'Un_KI270581v1-', 'Un_KI270581v1+', 'Un_KI270582v1-', 'Un_KI270582v1+', 'Un_KI270583v1+', 'Un_KI270584v1-', 'Un_KI270587v1-', 'Un_KI270588v1+', 'Un_KI270589v1-', 'Un_KI270589v1+', 'Un_KI270590v1-', 'Un_KI270591v1-', 'Un_KI270591v1+', 'Un_KI270593v1+', 'Un_KI270741v1-', 'Un_KI270741v1+', 'Un_KI270742v1-', 'Un_KI270742v1+', 'Un_KI270743v1-', 'Un_KI270743v1+', 'Un_KI270744v1-', 'Un_KI270744v1+', 'Un_KI270745v1-', 'Un_KI270745v1+', 'Un_KI270746v1-', 'Un_KI270746v1+', 'Un_KI270747v1-', 'Un_KI270747v1+', 'Un_KI270748v1-', 'Un_KI270748v1+', 'Un_KI270749v1-', 'Un_KI270749v1+', 'Un_KI270750v1-', 'Un_KI270750v1+', 'Un_KI270751v1-', 'Un_KI270751v1+', 'Un_KI270752v1-', 'Un_KI270752v1+', 'Un_KI270753v1-', 'Un_KI270753v1+', 'Un_KI270754v1-', 'Un_KI270754v1+', 'Un_KI270755v1-', 'Un_KI270755v1+', 'Un_KI270756v1+', 'Un_KI270757v1-', 'Un_KI270757v1+', 'X-', 'X+', 'X_KI270880v1_alt-', 'X_KI270880v1_alt+', 'X_KI270881v1_alt-', 'X_KI270881v1_alt+', 'X_KI270913v1_alt-', 'X_KI270913v1_alt+', 'X_KV766199v1_alt-', 'X_KV766199v1_alt+', 'X_ML143381v1_fix-', 'X_ML143381v1_fix+', 'X_ML143382v1_fix-', 'X_ML143382v1_fix+', 'X_ML143383v1_fix-', 'X_ML143383v1_fix+', 'X_ML143384v1_fix-', 'X_ML143384v1_fix+', 'X_ML143385v1_fix-', 'X_ML143385v1_fix+', 'Y-', 'Y+', 'Y_KI270740v1_random-', 'Y_KN196487v1_fix-', 'Y_KN196487v1_fix+', 'Y_KZ208923v1_fix-', 'Y_KZ208923v1_fix+', 'Y_KZ208924v1_fix-']
2022-05-06 10:45:48,025 - DEBUG - Summarizing the results of intron validation.
2022-05-06 10:45:48,613 - DEBUG - Validated 111700 introns (of which unique intervals 58817) out of 451668 total possible introns (considering each possible transcript models).
2022-05-06 10:45:48,614 - DEBUG - Reading /mnt/dell4/Kota/cellsorted_CD133_vesicle_from_PLC_1_S37_L002_Aligned.velocyto.sorted.bam
[E::idx_find_and_load] Could not retrieve index file for '/mnt/dell4/Kota/cellsorted_CD133_vesicle_from_PLC_1_S37_L002_Aligned.velocyto.sorted.bam'
2022-05-06 10:45:48,654 - DEBUG - Read first 0 million reads
2022-05-06 10:56:30,919 - DEBUG - Read first 10 million reads
2022-05-06 11:06:51,637 - DEBUG - Read first 20 million reads
2022-05-06 11:17:12,822 - DEBUG - Read first 30 million reads
2022-05-06 11:28:59,452 - DEBUG - Read first 40 million reads
2022-05-06 11:40:39,679 - DEBUG - Read first 50 million reads
2022-05-06 11:48:04,312 - DEBUG - Read first 60 million reads
2022-05-06 12:00:34,207 - DEBUG - Read first 70 million reads
2022-05-06 12:10:03,753 - DEBUG - Counting for batch 1, containing 1 cells and 71075728 reads
velocyto.sh: line 5: 43000 Killed velocyto run -U -m /mnt/dell4/Kota/GRCh38_rmsk.gtf --outputfolder VELOCYTO_OUT ${id}_Aligned.velocyto.sorted.bam /mnt/dell4/Homo_sapiens/UCSC/hg19/Annotation/Archives/archive-2015-07-17-14-32-32/Genes/genes.gtf

Could you tell me how to solve it?