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Margin-[E::hts_open_format] Failed to open file .bam #161
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Can you please put down the full command you are running? I think the |
Hi, sorry for the late reply.
Note: I also tried without the |
It looks like a permission issue now. Can you please specify the |
Hi,
Hope you are doing well. I am getting an error on the margin step of the pipeline. When I re-run it works. I am sure that my bam file was placed in the actual location. There are no duplicate reads in my bam.
`
Command output:
`
Bam FlagStats output
39637 + 0 in total (QC-passed reads + QC-failed reads)
9767 + 0 secondary |
8658 + 0 supplementary |
0 + 0 duplicates |
39637 + 0 mapped (100.00% : N/A) |
0 + 0 paired in sequencing |
0 + 0 read1 |
0 + 0 read2 |
0 + 0 properly paired (N/A : N/A) |
0 + 0 with itself and mate mapped |
0 + 0 singletons (N/A : N/A) |
0 + 0 with mate mapped to a different chr |
0 + 0 with mate mapped to a different chr (mapQ>=5)
Best Regards
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