atram_preprocessor.py error with multiple fastq files

[MareikeJaniak]

Hi! I just updated to the latest version of aTRAM and I tried to build fresh libraries, but I am getting an error when trying to run atram_preprocessor.py that I was not getting before.

When trying to use multiple fastq files as input, either by entering multiple file names after --end-1/--end-2 or by using a wildcard, atram immediately throws the following error:

usage: atram_preprocessor.py [-h] [--version] [--end-1 FASTA/Q] [--end-2 FASTA/Q] [--mixed-ends FASTA/Q] [--single-ends FASTA/Q] [-b DB] [--cpus CPUS] [-t DIR] [--keep-temp-dir] [-l LOG_FILE] [-s SHARDS] [--path PATH] [--fasta] [--fastq] [--gzip] [--bzip] atram_preprocessor.py: error: unrecognized arguments: /home/mcj43/scratch/Foraging_paper/TR_genes/fastq/Alouatta/HGV2KDSXX_2_143UDI-idt-UMI-header_1.fastq.gz /home/mcj43/scratch/Foraging_paper/TR_genes/fastq/Alouatta/HGV2KDSXX_2_143UDI-idt-UMI-header_2.fastq.gz

The files in the "unrecognized arguments" correspond to the second fastq input files. My full command is here:

/home/mcj43/software/aTRAM/atram_preprocessor.py -b /home/mcj43/scratch/Foraging_paper/TR_genes/aTRAM/libraries/Alouatta --end-1 /home/mcj43/scratch/Foraging_paper/TR_genes/fastq/Alouatta/HGV2KDSXX_1_143UDI-idt-UMI-header_1.fastq.gz /home/mcj43/scratch/Foraging_paper/TR_genes/fastq/Alouatta/HGV2KDSXX_2_143UDI-idt-UMI-header_1.fastq.gz --end-2 /home/mcj43/scratch/Foraging_paper/TR_genes/fastq/Alouatta/HGV2KDSXX_1_143UDI-idt-UMI-header_2.fastq.gz /home/mcj43/scratch/Foraging_paper/TR_genes/fastq/Alouatta/HGV2KDSXX_2_143UDI-idt-UMI-header_2.fastq.gz --fastq --gzip

Using wildcards instead of entering two files throws the same error.

[rafelafrance]

The one thing you didn't try is repeating the arguments like: --end-1 file1a.fq --end-1 file1b.fq

This is admittedly confusing. We should either update the help or allow the other forms you tried.

[MareikeJaniak]

Ok, I will try that! Sorry, I miss understood how to enter multiple files.

Was this different in previous versions of aTRAM? I have old scripts in which I (seemingly) used wildcards successfully.

Thanks for your quick response!

[rafelafrance]

It did change, mea culpa.

We're going to accept all 3 forms in the future.

[MareikeJaniak]

No worries! And thanks so much for changing it in future versions!

[rafelafrance]

Is covered by issue #273