ERROR: CMD ended with status code 2

[Liyong-Zhang]

Hello there,

I am using Trans-ABySS to assemble a transcriptome for my pair-end RNAseq data (3 replicates x 50 genotypes). I installed Trans-ABySS (v2.0.1) through conda on a Linux server. The commands are following file_list=($(find /liyong_temp/trimmed/ -type f -name "*P.fq.gz" | sort)) out=/transcriptome_assembly/de_novo/transabyss transabyss \ --pe ${file_list[@]} \ --threads 64 \ --length 200 \ --outdir $out

The log file is: /liyong_temp/trimmed/Cs123_trimmed_1P.fq.gz': discarded 5 reads containing non-ACGT characters /liyong_temp/trimmed/Cs123_trimmed_2P.fq.gz': discarded 62 reads containing non-ACGT characters ........................ /liyong_temp/trimmed/Cs133_trimmed_1P.fq.gz': discarded 2 reads containing non-ACGT characters /liyong_temp/trimmed/Cs133_trimmed_2P.fq.gz': discarded 16 reads containing non-ACGT characters

The minimum coverage of single-end contigs is 2. The minimum coverage of merged contigs is 2. The minimum coverage of single-end contigs is 0.652174. The minimum coverage of merged contigs is 2. Consider increasing the coverage threshold parameter, c, to 2. The minimum coverage of single-end contigs is 2. The minimum coverage of merged contigs is 2. warning: the seed-length should be at least twice k: k=32, s=32 Building the suffix array... Building the Burrows-Wheeler transform... Building the character occurrence table... sort: write failed: /tmp/sortUz7aTQ: No space left on device error: `transabyss-3.hist': No such file or directory make: ** [/home/AGR.GC.CA/zhangliy/transabyss_conda/env/bin/abyss-pe.Makefile:559: transabyss-3.dist] Error 1 make: Deleting file 'transabyss-3.dist'**

Any suggestion how I could get this to work? Many thanks.

[kmnip]

Hi,

This part of your log indicates an error:

sort: write failed: /tmp/sortUz7aTQ: No space left on device

This means your temp directory is full and there wasn't enough space for the sort command. You can set TMPDIR to a local directory. For example:

mkdir /transcriptome_assembly/de_novo/transabyss/tmpdir
export TMPDIR=/transcriptome_assembly/de_novo/transabyss/tmpdir
transabyss ...

Hope that helps!

[Liyong-Zhang]

Hi,

Thank you for the quick response. Sounds good, I will give it try after setting the tmpdir.

Thanks!

[Liyong-Zhang]

After I set the tmpdir, it looks all good now. Thanks!