Hi,
I just installed the latest samtools (0.1.19-44428cd) and now I have an issue with my SAM->BAM->BAM_Sorted Pipeline using the Linux pipe. In samtools version 0.1.18 (r982:295) the following always worked well:
But with the new version I always get the following error:
I also ran the pipeline with version 0.1.18 to check whether the resulting sorted bam files are the same (regardless of the error message). Linux diff command said no. So my first question: Is the error message problematic?
After some testing I realized that there is even a difference (also for version 0.1.18) between a sorted bam that was build with the pipe (like in the command above) or that was build without the pipe via:
So my second question is whether anyone knows the difference and if this can be problematic too?
Sorry, this part was wrong, I made a stupid mistake. The pipe sorting and and direct way of sorting gives the same result!
As the error is not reported in the non-pipeline version, and the resulting file is the same as that of the pipeline version, the error message in version 0.1.19 is negligible. The only question remaining now is the difference in the 0.1.18-sorted file and the 0.1.19-sorted file:
temp_sorted_old_pipe.bam was build using the old samtools version (0.1.18)
Thank you very much
I just installed the latest samtools (0.1.19-44428cd) and now I have an issue with my SAM->BAM->BAM_Sorted Pipeline using the Linux pipe. In samtools version 0.1.18 (r982:295) the following always worked well:
Code:
samtools view -bS -1 temp.sam | samtools sort - temp_sorted
Code:
[bam_header_read] EOF marker is absent. The input is probably truncated
After some testing I realized that there is even a difference (also for version 0.1.18) between a sorted bam that was build with the pipe (like in the command above) or that was build without the pipe via:
Code:
samtools sort temp.bam temp_sorted
Sorry, this part was wrong, I made a stupid mistake. The pipe sorting and and direct way of sorting gives the same result!
As the error is not reported in the non-pipeline version, and the resulting file is the same as that of the pipeline version, the error message in version 0.1.19 is negligible. The only question remaining now is the difference in the 0.1.18-sorted file and the 0.1.19-sorted file:
Code:
diff <(samtools view temp_sorted_pipe.bam) <(samtools view temp_sorted_old_pipe.bam) | head -20 466a467 > DJG6PNM1:223:D1GB7ACXX:2:1101:19332:59581 16 gi|555853|gb|U13369.1|HSU13369 3657 255 19M * 0 0 TACCTGGTTGATCCTGCCA HHIIIIHHHHHFFFFFCCC XA:i:0 MD:Z:19 NM:i:0 474,475d474 < DJG6PNM1:223:D1GB7ACXX:2:1101:19332:59581 16 gi|555853|gb|U13369.1|HSU13369 3657 255 19M * 0 0 TACCTGGTTGATCCTGCCA HHIIIIHHHHHFFFFFCCC XA:i:0 MD:Z:19 NM:i:0 < DJG6PNM1:223:D1GB7ACXX:2:1101:14750:15107 0 gi|555853|gb|U13369.1|HSU13369 3660 255 16M * 0 0 CTGGTTGATCCTGCCA BCCFDFFFHHHHGIII XA:i:0 MD:Z:16 NM:i:0 477c476 < DJG6PNM1:223:D1GB7ACXX:2:1101:15030:64473 0 gi|555853|gb|U13369.1|HSU13369 3661 255 26M * 0 0 TGGTTGATCCTGCCAGTAGCATATGC 4114=?BDHHHGHIIIIIIIIIEIHI XA:i:0 MD:Z:26 NM:i:0 --- > DJG6PNM1:223:D1GB7ACXX:2:1101:14750:15107 0 gi|555853|gb|U13369.1|HSU13369 3660 255 16M * 0 0 CTGGTTGATCCTGCCA BCCFDFFFHHHHGIII XA:i:0 MD:Z:16 NM:i:0 478a478 > DJG6PNM1:223:D1GB7ACXX:2:1101:15030:64473 0 gi|555853|gb|U13369.1|HSU13369 3661 255 26M * 0 0 TGGTTGATCCTGCCAGTAGCATATGC 4114=?BDHHHGHIIIIIIIIIEIHI XA:i:0 MD:Z:26 NM:i:0 492d491 < DJG6PNM1:223:D1GB7ACXX:2:1101:5749:82660 0 gi|555853|gb|U13369.1|HSU13369 3669 255 29M * 0 0 CCTGCCAGTAGCATATGCTTGTCTCAAAG CCCFFFFFHHHHHIIIIIIIIIIIIIIII XA:i:0 MD:Z:29 NM:i:0 495,497c494 < DJG6PNM1:223:D1GB7ACXX:2:1101:17420:15616 0 gi|555853|gb|U13369.1|HSU13369 3670 255 23M * 0 0 CTGCCAGTAGCATATGCTTGTCT CCCFFFFFHHHHHIIIIIIIIII XA:i:0 MD:Z:23 NM:i:0 < DJG6PNM1:223:D1GB7ACXX:2:1101:6026:70596 0 gi|555853|gb|U13369.1|HSU13369 3670 255 23M * 0 0 CTGCCAGTAGCATATGCTTGTCT CCCFFFFFHHHHHIIIIIIIIII XA:i:0 MD:Z:23 NM:i:0 < DJG6PNM1:223:D1GB7ACXX:2:1102:15933:7414 0 gi|555853|gb|U13369.1|HSU13369 3670 255 22M * 0 0 CTGCCAGTAGCATATGCTTGTC BCCFFFFFHHHHHIIIIIIIII XA:i:0 MD:Z:22 NM:i:0 --- > DJG6PNM1:223:D1GB7ACXX:2:1101:5749:82660 0 gi|555853|gb|U13369.1|HSU13369 3669 255 29M * 0 0 CCTGCCAGTAGCATATGCTTGTCTCAAAG CCCFFFFFHHHHHIIIIIIIIIIIIIIII XA:i:0 MD:Z:29 NM:i:0 498a496
Thank you very much
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