Comments (4)
Hi @PavitaKae, very difficult to tell - looking at the output file you provided, coverage on the class I genes (HLA-A, -B, -C) is very low. This would indicate that either the test file is corrupted, or that something with the read extraction process has gone wrong. Did you modify the reference extraction files in any way? Could you send an md5 of NA12878.mini.cram? And could you capture all of STDOUT and STDERR and post it here?
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This is my MD5sum for NA12878 file -> 45d1769ffed71418571c9a2414465a12
I didn't modify your reference graph, just download and make graph by following manual.
I attach file for .out and .err.
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There is some issue with read extraction - in your output log, it says processBAM::extractSeeds(): getReadIDs 833136 reads, collected 402762 read IDs.
, whereas it should say processBAM::extractSeeds(): getReadIDs 13649900 reads, collected 1373415 read IDs.
.
In your error log, there is a message from Picard: To execute picard run: java -jar $EBROOTPICARD/picard.jar
(also, there are some warning messages about the locale that come from Perl, but I don't think these matter too much).
If you go into the working directory for the sample (e.g. HLA-LA/working/NA12878_mini
), R_1.fastq and R_2.fastq should both be about 500Mb in size (I would expect them to be smaller on your system), and extraction.bam should be a little bit larger than 310Mb (I would expect this to be the case on your system).
I think that there is some issue with Picard - if you execute the extraction command, i.e. /tarafs/biobank/data/modules/.local/easybuild/software/Miniconda3/4.4.10/envs/noon/bin/picard SamToFastq VALIDATION_STRINGENCY=LENIENT I=/tarafs/biobank/data/home/pkaewpro/proj0015/HLA-LA/working/NA_test/extraction.bam F=/tarafs/biobank/data/home/pkaewpro/proj0015/HLA-LA/working/NA_test/R_1.fastq F2=/tarafs/biobank/data/home/pkaewpro/proj0015/HLA-LA/working/NA_test/R_2.fastq FU=/tarafs/biobank/data/home/pkaewpro/proj0015/HLA-LA/working/NA_test/R_U.fastq 2>&1
, manually, do you get an error message?
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Hi, AlexanderDilthey
I back to run again, it look good. Because i choose to install new picard program.
Thank you for your response. :D
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Related Issues (20)
- Error: no compatible reference specifications HOT 1
- HLA*ASM HOT 1
- Error - [main_samview] fail to read the header from "-". HOT 1
- How to generate "reference_HLA_ASM.tar.gz" file
- Proportion of bases with good coverage
- v1.01 and v1.03
- R_1.fastq and R_2.fastq are empty?
- [Help needed] Unable to process a chr6-only BAM file HOT 1
- ont2d not supported by bwa
- Does it support the typing only based on long-read RNA-seq data?
- [M::bwa_idx_load_from_disk] read 0 ALT contigs - empty sam files
- Cannot support DRB3/4/5 ?
- G mean
- the HLA analysis of tumor samples and control samples
- how to specify specific IMGT version ? HOT 1
- how to use the latet IMGT to create PRG_MHC_GRCh38_withIMGT database from HLA-LA typing tool ?
- only for GRCh38? not Hg19?
- HLA-LA file format conversion HOT 3
- No compatible reference HOT 10
- Use of uninitialized value $graph in concatenation (.) or string
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