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ngs-fzb / MTBseq_source

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.
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TBlist and TBvariants #76

Closed RichardUABC closed 2 years ago

RichardUABC commented 2 years ago

Hi.

I have an error when running the comparative analysis, MTBseq does not detect the output files of TBlist and TBvariant for input to TBjoin, but these are in their corresponding folder, correctly generated. I include the project and the list of sequences, but it marks me that one is not detected, each run is different sequence and to remove them from the list still appear the error another, so for all, it is as if it did not recognize the file.

This is the error message.

[2022-04-27 03:39:52] Could not find files for C068_S21_! Did you run TBlist and TBvariants for C068_S21_? These are the permissions of the folders that MTBseq generated. drwxr-xr-x 1 root root 4096 Apr 26 22:42 Called drwxr-xr-x 1 root root 4096 Apr 27 00:26 Classification drwxr-xr-x 1 root root 4096 Apr 26 05:54 GATK_Bam drwxr-xr-x 1 root root 4096 Apr 26 03:52 Groups drwxr-xr-x 1 root root 4096 Apr 26 03:52 Joint -rw-r--r-- 1 root root 401030 Apr 27 00:57 MTBseq_2022-04-26_.log drwxr-xr-x 1 root root 4096 Apr 26 06:15 Mpileup drwxr-xr-x 1 root root 4096 Apr 26 21:15 Position_Tables drwxr-xr-x 1 root root 4096 Apr 26 22:45 Statistics -rw-r--r-- 1 root root 398 Apr 26 03:50 samples.txt I already tried it on two different computers, installed from conda and as sourse, the result is the same error. What do you think is the problem? Regards I close it, the solution was in #45