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PierreBSC / Viral-Track

MIT License
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[E::hts_open_format] Failed to open file "" : No such file or directory #1

Closed mdeloger closed 4 years ago

mdeloger commented 4 years ago

Hi,

here after what I obtain at the "Viral_Track_scanning" step :

Output directory does not exist ! Creating it ! 1 Fastq files are going to be processed ! Mapping UPN1_S1_L001_R2_001_extracted.fastq file Apr 29 12:58:01 ..... started STAR run Apr 29 12:58:01 ..... loading genome Apr 29 12:59:11 ..... started 1st pass mapping Apr 29 13:04:15 ..... finished 1st pass mapping Apr 29 13:04:15 ..... inserting junctions into the genome indices Apr 29 13:06:05 ..... started mapping Apr 29 13:17:46 ..... finished mapping Apr 29 13:17:47 ..... started sorting BAM Apr 29 13:21:16 ..... finished successfully Mapping ofUPN1_S1_L001_R2_001_extracted.fastq done ! All fastq files have been mapped successfully Starting the BAM file analysis Indexing of the bam file for UPN1_S1_L001_R2_001_extracted is done Computing stat file for the bam file for UPN1_S1_L001_R2_001_extracted is done Checking the mapping quality of each virus... Export of the viral SAM file done for UPN1_S1_L001_R2_001_extracted Exporting QC UPN1_S1_L001_R2_001_extracted ....No viral sequences detected detected Exporting QC table for UPN1_S1_L001_R2_001_extracted .... done !Creating QC plot for UPN1_S1_L001_R2_001_extracted ....QC plot done ! Merging Viral SAM files identified[E::hts_open_format] Failed to open file "" : No such file or directory samtools merge: fail to open "": No such file or directory

It seems that the list of BAM files, that it is supposed to merge, is empty, but in the "Viral_BAM_files" folder there are 52 BAMs files.

Thank you in advance

PierreBSC commented 4 years ago

Hi Jules (if I am not mistaken),

So this is also a mistake I have spotten, it is not really a problem as Viral-Track works perfectly and I just need to remove the useless lines generating this error message. Do you get the correct QC files at the end of the process ?

Best

mdeloger commented 4 years ago

Hi,

yes I obtain a correct QC file at the end of the process (even if it is quite strange to obtain a 100% viral mapping events on the barplot of the second line).

Thank you

PierreBSC commented 4 years ago

Hi,

Great ! For the mistake you mentionned that's weird : can you send me your QC pdf file so I can see ?

Best

mdeloger commented 4 years ago

As in the example one of the github : https://github.com/PierreBSC/Viral-Track/blob/master/QC_report.pdf

image

PierreBSC commented 4 years ago

Ok, I thought I had corrected that mistake. Thank you for pointing this out ! If you don't have any other problem I can close the issue.