Problems with FastQtoSAM
Answered
Hi! I'm running FastQtoSAM on GATK 4.1.8. I submitted 65 parallel tasks and received 19 errors. Why are some but not all of my FastQ files triggering errors? What do the errors mean? Can I avoid the errors by adjusting my command?
Thanks in advance,
Siddharth
If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 4.1.8
b) Exact command used: java -Xmx8g -jar /work/03437/sprakash/lonestar/apps/gatk/gatk-package-4.1.8.0-local.jar FastqToSam -F1 /corral-secure/uth/Sex-Chromosome-Loss/BGI/fastq/514448/V300089406_L02_HUMftlX009687-607_1.fq.gz -F2 /corral-secure/uth/Sex-Chromosome-Loss/BGI/fastq/514448/V300089406_L02_HUMftlX009687-607_2.fq.gz --TMP_DIR /scratch/03437/sprakash -SM 514448 -RG 607 -O/work/03437/sprakash/lonestar/tmp/V300089406_L02_HUMftlX009687-607.unmapped.bam
c) Entire error log:
htsjdk.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields; File /work/03437/sprakash/lonestar/tmp/V300087533_L03_HUMftlX009772-406.aligned.sam; Line 4733423
htsjdk.samtools.SAMFormatException: Error parsing text SAM file. length(QUAL) != length(SEQ); File /work/03437/sprakash/lonestar/tmp/V300089578_L02_HUMftlX009695-403.aligned.sam; Line 4718247
htsjdk.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields in tag 'XS'; File /work/03437/sprakash/lonestar/tmp/V300089390_L01_HUMftlX009695-403.aligned.sam; Line 5361996
Caused by: htsjdk.samtools.SAMFormatException: Not enough fields in tag 'XS'
htsjdk.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields; File /work/03437/sprakash/lonestar/tmp/V300089390_L01_HUMftlX009696-404.aligned.sam; Line 7428488
htsjdk.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields; File /work/03437/sprakash/lonestar/tmp/V300089390_L02_HUMftlX009701-410.aligned.sam; Line 11782775
htsjdk.samtools.SAMFormatException: Error parsing text SAM file. length(QUAL) != length(SEQ); File /work/03437/sprakash/lonestar/tmp/V300087533_L04_HUMftlX009772-406.aligned.sam; Line 11807918
htsjdk.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields; File /work/03437/sprakash/lonestar/tmp/V300089390_L01_HUMftlX009757-694.aligned.sam; Line 10473813
htsjdk.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields; File /work/03437/sprakash/lonestar/tmp/V300089578_L02_HUMftlX009696-404.aligned.sam; Line 11442948
htsjdk.samtools.SAMFormatException: Error parsing text SAM file. Invalid character in read bases; File /work/03437/sprakash/lonestar/tmp/V300089578_L02_HUMftlX009757-694.aligned.sam; Line 18945622
htsjdk.samtools.SAMFormatException: Error parsing text SAM file. length(QUAL) != length(SEQ); File /work/03437/sprakash/lonestar/tmp/V300087533_L03_HUMftlX009765-707.aligned.sam; Line 19252587
htsjdk.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields; File /work/03437/sprakash/lonestar/tmp/V300089578_L04_HUMftlX009710-612.aligned.sam; Line 15170193
htsjdk.samtools.SAMFormatException: Error parsing text SAM file. length(QUAL) != length(SEQ); File /work/03437/sprakash/lonestar/tmp/V300089578_L02_HUMftlX009756-692.aligned.sam; Line 25267897
htsjdk.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields; File /work/03437/sprakash/lonestar/tmp/V300089578_L03_HUMftlX009701-410.aligned.sam; Line 28726860
htsjdk.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields; File /work/03437/sprakash/lonestar/tmp/V300089375_L01_HUMftlX009721-633.aligned.sam; Line 27892398
htsjdk.samtools.SAMFormatException: Error parsing text SAM file. length(QUAL) != length(SEQ); File /work/03437/sprakash/lonestar/tmp/V300089375_L02_HUMftlX009721-633.aligned.sam; Line 31042146
htsjdk.samtools.SAMFormatException: Error parsing text SAM file. length(QUAL) != length(SEQ); File /work/03437/sprakash/lonestar/tmp/V300089578_L02_HUMftlX009697-405.aligned.sam; Line 36141191
htsjdk.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields in tag 'MD'; File /work/03437/sprakash/lonestar/tmp/V300089390_L02_HUMftlX009699-407.aligned.sam; Line 42082387
Caused by: htsjdk.samtools.SAMFormatException: Not enough fields in tag 'MD'
If not an error, choose a category for your question(REQUIRED):
a)How do I (......)?
b) What does (......) mean?
c) Why do I see (......)?
d) Where do I find (......)?
e) Will (......) be in future releases?
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Can you please provide the following:
- Can you please share the entire stack trace for this? You can print the stack by using this java option (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true')
- Please run the command with the stack-trace on one of the failed samples and share the exact command used for it and the entire stack trace
- Also please share a few lines from the fastqs that is ending in the error and a few lines from the fastqs that run successfully without an error. Maybe the first 8 lines from fq1 and fq2
- Please also share the exact command and the entire stack trace for one of the samples that worked without any error.
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I have also this problem please share some solution Thanks Charlie Jacob
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Hi Charlie Jacob, if Siddharth Prakash does not respond with more information, go ahead and provide more information regarding your issue so we can look into it further. Here are our recommendations for a post: https://gatk.broadinstitute.org/hc/en-us/articles/360053845952-Forum-Guidelines#write_a_new_post
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