OverflowError: value too large to convert to uint32_t #5
Comments
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my scripts is : if [ $6 -eq 0 ]; then |
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Hi, Apparently, there is a CIGAR operation larger than 2^32, i.e. larger than 4 GB. Are you analyzing a particularly large genome? If not, can you have a look at your input BAM file to see why there is such a large value in there? Cheers |
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Thank you for your kind reply! the d1.txt contains CIGAR in error regions. d1.txt |
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Thanks for the CIGAR strings. It's a good idea to partition the BAM file to identify the offending line. However, I think you might have taken the CIGAR from column 6 of the alignment record. Instead, you need to check the optional |
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HI: We extracted the cigar string which are upload at https://github.com/jxlabWzZ/TMP_FILES/blob/main/dd1.txt.gz. best wishes |
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Hi WzZ, I cannot find any problem in the CIGAR strings you uploaded. So let's try something else. Can you quickly edit the following file? Please replace line 46 with the following: Now rerun SVIM-asm with Cheers |
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Thanks a lot for your kind response. I can execute the program normally with try/except and continue statements. That code may lead to losing some SV information, i guess. It's now ready to execute. Anyway, thanks again. The latest log file is: 2021-04-13 20:34:14,569 [INFO ] ****************** Start SVIM-asm, version 1.0.2 ****************** |
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oops! best! |
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Hi WzZ, thanks for reporting back about this. It's good to know that SVIM-asm at least exits normally now with the try/except. I now permanently added this with 8836ded. After investigating your log, I found that the shortest CIGAR operation in the problematic strings was 268.445.248 bp long. That number is slightly larger than 2^28=268.435.456. So the maximum value for Cheers |
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Okay, I got a reply from one of the pysam developers. The problem lies in the BAM format specification which reserves 32bits for each CIGAR operation (28 bits for the length and 4 bits for the operation type). So there's not much that can be done about it except ignoring these long CIGAR operations or using another format (maybe PAF instead of BAM). |
Hi
I'm having a problem with the SVIM-asm based on your recommended codes, and I don't know how to solve it.
can you help me ?
the log file is as fellows:
2021-04-12 18:16:38,496 [INFO ] ****************** Start SVIM-asm, version 1.0.2 ******************
2021-04-12 18:16:38,497 [INFO ] CMD: python3 /home/xxx/miniconda3/envs/svimasm_env/bin/svim-asm haploid --min_sv_size 50 --max_sv_size 5000000 /home/xxx/02.syri/02.sus11.1//S
2021-04-12 18:16:38,497 [INFO ] WORKING DIR: /home/xxx/02.syri/02.sus11.1/SVIM/works
2021-04-12 18:16:38,497 [INFO ] PARAMETER: sub, VALUE: haploid
2021-04-12 18:16:38,497 [INFO ] PARAMETER: working_dir, VALUE: /home/xxx/02.syri/02.sus11.1/SVIM/works
2021-04-12 18:16:38,498 [INFO ] PARAMETER: bam_file, VALUE: TMP.sorted.bam
2021-04-12 18:16:38,498 [INFO ] PARAMETER: genome, VALUE: /home/xxx/01.SV_calling/00.Call_SV/00.NGS/drcv8.fa
2021-04-12 18:16:38,498 [INFO ] PARAMETER: verbose, VALUE: False
2021-04-12 18:16:38,498 [INFO ] PARAMETER: min_mapq, VALUE: 20
2021-04-12 18:16:38,498 [INFO ] PARAMETER: min_sv_size, VALUE: 50
2021-04-12 18:16:38,498 [INFO ] PARAMETER: max_sv_size, VALUE: 5000000
2021-04-12 18:16:38,499 [INFO ] PARAMETER: query_gap_tolerance, VALUE: 50
2021-04-12 18:16:38,499 [INFO ] PARAMETER: query_overlap_tolerance, VALUE: 50
2021-04-12 18:16:38,499 [INFO ] PARAMETER: reference_gap_tolerance, VALUE: 50
2021-04-12 18:16:38,499 [INFO ] PARAMETER: reference_overlap_tolerance, VALUE: 50
2021-04-12 18:16:38,499 [INFO ] PARAMETER: sample, VALUE: Sample
2021-04-12 18:16:38,499 [INFO ] PARAMETER: types, VALUE: DEL,INS,INV,DUP:TANDEM,DUP:INT,BND
2021-04-12 18:16:38,500 [INFO ] PARAMETER: symbolic_alleles, VALUE: False
2021-04-12 18:16:38,500 [INFO ] PARAMETER: tandem_duplications_as_insertions, VALUE: False
2021-04-12 18:16:38,500 [INFO ] PARAMETER: interspersed_duplications_as_insertions, VALUE: False
2021-04-12 18:16:38,500 [INFO ] PARAMETER: query_names, VALUE: False
2021-04-12 18:16:38,500 [INFO ] ****************** STEP 1: COLLECT ******************
2021-04-12 18:16:38,500 [INFO ] MODE: haploid
2021-04-12 18:16:38,501 [INFO ] INPUT: /home/xxx/02.syri/02.sus11.1/SVIM/TMP.sorted.bam
2021-04-12 18:16:38,512 [INFO ] Processing chromosome chr1...
2021-04-12 18:16:40,922 [ERROR ] value too large to convert to uint32_t
Traceback (most recent call last):
File "/home/xxx/miniconda3/envs/svimasm_env/bin/svim-asm", line 183, in
sys.exit(main())
File "/home/xxx/miniconda3/envs/svimasm_env/bin/svim-asm", line 74, in main
sv_candidates = analyze_alignment_file_coordsorted(aln_file1, options)
File "/home/xxx/miniconda3/envs/svimasm_env/lib/python3.7/site-packages/svim_asm/SVIM_COLLECT.py", line 72, in analyze_alignment_file_coordsorted
supplementary_alignments = retrieve_other_alignments(current_alignment, bam)
File "/home/xxx/miniconda3/envs/svimasm_env/lib/python3.7/site-packages/svim_asm/SVIM_COLLECT.py", line 46, in retrieve_other_alignments
a.cigarstring = cigar
File "pysam/libcalignedsegment.pyx", line 1298, in pysam.libcalignedsegment.AlignedSegment.cigarstring.set
File "pysam/libcalignedsegment.pyx", line 2220, in pysam.libcalignedsegment.AlignedSegment.cigartuples.set
OverflowError: value too large to convert to uint32_t
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