Hi to all,
I hope that is the right place where post my issue.
I'm using Cpipe in a qualitative analysis, for a project of my university.
Now, after the installation, I must execute the self-test. The issue is that the test is correct until the point where it starts the "recall precision test". The pipeline executes this piece of code:
[bam_header_read] EOF marker is absent. The input is probably truncated.
[M::main_mem] read 509156 sequences (50000164 bp)...
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!
Cleaned up file align/NA12878CHR22_31fc6a75c408009fd2aaf62076fe0c304fc3931a_L001.bam to .bpipe/trash/NA12878CHR22_31fc6a75c408009fd2aaf62076fe0c304fc3931a_L001.bam
ERROR: Command failed with exit status = 1 :
Samtools gives me this error. [samopen] no @SQ lines in the header. [sam_read1] missing header? Abort! How I can fix that?
I know this isn't a forum about cpipe, but I have read that is a common issue of samtools.
I use Samtools ver. 0.1.19 and WBA ver. 0.7.5a .
Thanks for, futures, answers.
I hope that is the right place where post my issue.
I'm using Cpipe in a qualitative analysis, for a project of my university.
Now, after the installation, I must execute the self-test. The issue is that the test is correct until the point where it starts the "recall precision test". The pipeline executes this piece of code:
[bam_header_read] EOF marker is absent. The input is probably truncated.
[M::main_mem] read 509156 sequences (50000164 bp)...
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!
Cleaned up file align/NA12878CHR22_31fc6a75c408009fd2aaf62076fe0c304fc3931a_L001.bam to .bpipe/trash/NA12878CHR22_31fc6a75c408009fd2aaf62076fe0c304fc3931a_L001.bam
ERROR: Command failed with exit status = 1 :
Samtools gives me this error. [samopen] no @SQ lines in the header. [sam_read1] missing header? Abort! How I can fix that?
I know this isn't a forum about cpipe, but I have read that is a common issue of samtools.
I use Samtools ver. 0.1.19 and WBA ver. 0.7.5a .
Thanks for, futures, answers.
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