rvolden/mandalorion-episode-ii

Version II of Mandalorion

mandalorion-episode-ii's Issues

MemoryError during defineAndQuantifyWrapper.py

Dear @christopher-vollmers ,

Hello. I have been trying to run the test-run of your script using the example script you have provided.
Unfortunately I am getting the error shown below, and I cannot get the solution anywhere.

(most recent call last):
File "defineAndQuantifyIsoforms.py", line 245, in
main()
File "defineAndQuantifyIsoforms.py", line 242, in main
define_start_end_sites(start_end_dict, individual_path, subreads)
File "defineAndQuantifyIsoforms.py", line 132, in define_start_end_sites
positions = np.array(start_end_dict[identity])
MemoryError
Traceback (most recent call last):
File "createConsensi.py", line 212, in
for line in open(path + '/isoform_list'):
FileNotFoundError: [Errno 2] No such file or directory: '/data/ONT/Data/PM-AU-0002-N-A1//isoform_list'

I did some research on it and found that it might be because of 32-bit system of python. But I found that we had 64-bit system python installed in our system.
Would there be any suggestion on how I could overcome this issue?

If you could help me with it, I would really appreciate it!

Thank you!

Jungwoo

Apply Mandalorion-Episode-II in regular ONT 1D data

Hi @rvolden ,

It says in README that current Mandalorion only supports data format C3POa produces from R2C2 nanopore data. Is there any way I can modify the scripts or my data to make Mandalorion available for ONT 1D data? For example, is it feasible to edit sequence id in my fasta/fastq file to the same format as C3POa produces?

Error regarding nanopore 1D reads

Hi @rvolden ,

I was trying to used the modified code pulled from yours. But I didnot find to report the issue in that page so reporting it to you.

While I was running the code for MinION 1D reads, I came across the following error.

/u/local/apps/python/3.6.1/lib/python3.6/site-packages/numpy-1.12.1-py3.6-linux-x86_64.egg/numpy/core/fromnumeric.py:2889: RuntimeWarning: Mean of empty slice.
out=out, **kwargs)
/u/local/apps/python/3.6.1/lib/python3.6/site-packages/numpy-1.12.1-py3.6-linux-x86_64.egg/numpy/core/_methods.py:80: RuntimeWarning: invalid value encountered in double_scalars
ret = ret.dtype.type(ret / rcount)
rm: cannot remove `/u/home/a/MinION/Run_04_Part/parsed_reads/*': No such file or directory
Traceback (most recent call last):
File "defineAndQuantifyIsoforms.py", line 245, in
main()
File "defineAndQuantifyIsoforms.py", line 242, in main
define_start_end_sites(start_end_dict, individual_path, subreads)
File "defineAndQuantifyIsoforms.py", line 181, in define_start_end_sites
+ filename + '.fasta', 'a')
OSError: [Errno 31] Too many links: '/u/home/a/MinION/Run_04_Part/parsed_reads/Isoform25001.fasta'
Traceback (most recent call last):
File "createConsensi.py", line 70, in
progs = configReader(args['config'])
File "createConsensi.py", line 50, in configReader
raise Exception('Check config file')
Exception: Check config file
Traceback (most recent call last):
File "filterIsoforms.py", line 42, in
isoforms = read_fasta(infile)
File "filterIsoforms.py", line 24, in read_fasta
for line in open(inFile):
FileNotFoundError: [Errno 2] No such file or directory: '/u/home/a/MinION/Run_04_Part/Isoform_Consensi.fasta'

bed file was generated; parsed_read folder was also generated and I can see the isoform fasta filed in the folder. But I fail to understand what this error is.
Thanks

Can't get Mandalorion-Episode-II working

I have been trying to get Mandalorion-Episode-II working for isoform expression of 1D ONT sequencing data and am having trouble. The command I am running is as follows:

python3 defineAndQuantifyWrapper.py \
-c /data/csijcs/nanopore/K562_cytoplasmic_polyA_cDNA_PCR/Mandalorion_isoform_calling/content.txt \
-f /data/csijcs/nanopore/K562_cytoplasmic_polyA_cDNA_PCR/Mandalorion_isoform_calling/config.txt \
-p /data/csijcs/nanopore/K562_cytoplasmic_polyA_cDNA_PCR/Mandalorion_isoform_calling \
-m /home/csijcs/Mandalorion-Episode-II/NUC.4.4.mat \
-g /data/csijcs/hg38/gencode.v28.primary_assembly.annotation.gtf \
-u 5 -d 30 -s 200 -r 0.05 -R 3 -i 0 -t 0 -I 100 -T 60

The config.txt file contains:

poa	/home/csijcs/anaconda3/envs/py3/bin/poa
water	/home/csijcs/anaconda3/envs/py3/bin/water
minimap2	/home/csijcs/anaconda3/bin/minimap2
consensus	consensus.py
racon	/home/csijcs/anaconda3/bin/racon
blat	/home/csijcs/anaconda3/envs/py3/bin/blat

The content.txt file contains:
/data/csijcs/nanopore/K562_cytoplasmic_polyA_cDNA_PCR/minimap2_alignment/K562_cytoplasmic_polyA_cDNA_PCR_alignment.psl /data/csijcs/nanopore/K562_cytoplasmic_polyA_cDNA_PCR/fastq_20_june_2018/pass/all /data/csijcs/nanopore/K562_cytoplasmic_polyA_cDNA_PCR/fastq_20_june_2018/pass/all /data/csijcs/nanopore/K562_cytoplasmic_polyA_cDNA_PCR/minimap2_alignment/K562_cytoplasmic_polyA_cDNA_PCR_alignment.sam

(I have tried this with and without the .fasta and .fastq extensions and get the same errors)

The errors I receive are:

rm: cannot remove ‘/data/csijcs/nanopore/K562_cytoplasmic_polyA_cDNA_PCR/fastq_20_june_2018/pass/all/parsed_reads/*’: No such file or directory
Traceback (most recent call last):
  File "defineAndQuantifyIsoforms.py", line 245, in <module>
    main()
  File "defineAndQuantifyIsoforms.py", line 239, in main
    splice_dict = splice_dict = collect_splice_events(path)
  File "defineAndQuantifyIsoforms.py", line 33, in collect_splice_events
    for line in open(path + '/SS.bed'):
FileNotFoundError: [Errno 2] No such file or directory: '/data/csijcs/nanopore/K562_cytoplasmic_polyA_cDNA_PCR/Mandalorion_isoform_calling///SS.bed'
Traceback (most recent call last):
  File "createConsensi.py", line 212, in <module>
    for line in open(path + '/isoform_list'):
FileNotFoundError: [Errno 2] No such file or directory: '/data/csijcs/nanopore/K562_cytoplasmic_polyA_cDNA_PCR/fastq_20_june_2018/pass/all/isoform_list'

The pipeline creates a parsed_reads folder, but it is empty. It also creates the files Isoform_Consensi.fasta and Isoform_Consensi_filtered.fasta, but they are both empty. It does not appear to create the SS.bed file or the isofrom_list file.

Can you please tell me what I am doing wrong?

Error

Hi there,

I am trying to quantify my ONT DRS reads with Mandalorion - II.
However, I'm getting this error:

ValueError: invalid literal for int() with base 10: '/media/gsfl/Jessie/First_Run/'

Please let me know why this is happening.

Thank you
Jessie

invalid literal?

Hi,
When running defineAndQuantifyWrapper.py , the call to createConsensi.py generates this error:

Traceback (most recent call last):
File "/usr/local/bin/createConsensi.py", line 221, in
corrected_consensus, repeats = determine_consensus(name, fasta, fastq)
File "/usr/local/bin/createConsensi.py", line 142, in determine_consensus
fastq_reads = read_fastq_file(fastq)
File "/usr/local/bin/createConsensi.py", line 101, in read_fastq_file
name, seed = name_root[0], int(name_root[1])
ValueError: invalid literal for int() with base 10: 'c'

I tried modifying line 101 in createConsensi.py from:
name, seed = name_root[0], int(name_root[1]) to:
name, seed = name_root[0], int(float(name_root[1]))
and got the same error.

Then I tried:
name, seed = name_root[0], int(name_root[1], 16)
and this ran to completion and generated output, however the Isoform_Consensi.fasta and Isoform_Consensi_filtered.fasta files have only the headers, no sequence. e.g.

chr4_5l196242-3r2030945l196244-3r2030955l196245-3r203096~_+_47474642_47483237_40.0_69.0_9

chr12__+_12911985_12912385_39.5_55.0_4

Now I'm not sure whether to continue trying to figure out the problem in createConsensi.py, or perhaps I have generated illegal fasta names somehow in the C3PO pipeline?

Issue with the run

Dear developer,

Hello. First of all, thank you for creating such wonderful tool.
I was trying to run the script you have provided and ended up getting some technical issue.

The script I typed in was shown below:
python3 /data/ONT_RNA/download/mandalorion/Mandalorion-Episode-II-master/defineAndQuantifyWrapper.py -c 20180918_PM_AU_samples.txt -f contig_file.txt -p /data/ONT_RNA/download/mandalorion/Mandalorion-Episode-II-master/ -m /data/ONT_RNA/download/mandalorion/Mandalorion-Episode-II-master/NUC.4.4.mat -u 5 -d 30 -s 200 -g /data/ONT_RNA/reference/gencode.v28.annotation.gtf -r 0.05 -R 3 -i 0 -t 0 -I 100 -T 60

and the result error was shown as below:
python3: can't open file 'spliceSites.py': [Errno 2] No such file or directory python3: can't open file 'defineAndQuantifyIsoforms.py': [Errno 2] No such file or directory python3: can't open file 'createConsensi.py': [Errno 2] No such file or directory python3: can't open file 'filterIsoforms.py': [Errno 2] No such file or directory

I was not quite sure if any installation was needed for these python scripts to run.
Please let me know if any further information needed for troubleshooting.

Thank you very much for your help.

Jungwoo