IOError: [Errno 28] No space left on device

[AMMMachado]

Dear ,

First of all thanks for the amazing program. Seems to have a lot of potential.

I installed the program from the source, in a centos cluster with 7tb disk and 512GB ram. The test run, runned without problems.

I am working on a highly heterozygous genome which size is estimated to +/- 2.8Gb. When I'm trying to run the program on my datasets, the program give me always the same error, in scaffolding step.

################################################## [Fri Jun 7 15:51:50 2019] Scaffolding... iteration 1.1: ABC_40x_200k_scaffolding_closing_def/contigs.fa 996014 2380224055 41.686 157230 2112069423 24447 678 1763700 396054 File exists: ABC_40x_200k_scaffolding_closing_def/_sspace.1.1.lib1.tab iteration 1.2: ABC_40x_200k_scaffolding_closing_def/_sspace.1.1.fa 994218 2380212360 41.686 156180 2112373614 24589 680 1766560 396054 Traceback (most recent call last): File "/redundans/redundans.py", line 541, in main() File "/redundans/redundans.py", line 536, in main o.norearrangements, o.verbose, o.usebwa, o.log, o.tmp) File "/redundans/redundans.py", line 332, in redundans identity, overlap, minLength, resume) File "/redundans/redundans.py", line 129, in run_scaffolding sspacebin, verbose=0, usebwa=usebwa, log=log) File "/redundans/bin/fastq2sspace.py", line 274, in fastq2sspace cores, mapq, upto, verbose, usebwa, log) File "/redundans/bin/fastq2sspace.py", line 230, in get_tab_files sam2sspace_tab(proc.stdout, out, mapqTh, upto, verbose, log, ref2, cores) # File "/redundans/bin/fastq2sspace.py", line 71, in sam2sspace_tab _tmpfile.write(sam2fastq("%s/1"%i, seq1, qual1, flag1)+sam2fastq("%s/2"%i, seq2, qual2, flag2)) IOError: [Errno 28] No space left on device

I already tried several parameters.. but the error persist.

My command line :

/home/amachado/SW/redundans/redundans.py -v -t 30 -i *.fq -f ABC_40x_180k.fasta -o ABC_40x_180k_scaffolding_closing_def --noreduction --tmp /tmp

/home/amachado/SW/redundans/redundans.py -v -t 20 -i *.fq -f ABC_40x_180k.fasta -o ABC_40x_180k_scaffolding_closing_def_WR --nogapclosing --nocleaning --tmp /tmp

Thank you in advance for your help! Andre

[wuxiaopei0509]

maybe the computer resourecs is not enough

[lpryszcz]

Hi @AMMMachado , thanks for the report! As @wuxiaopei0509 pointed it's likely out of space at /tmp dir.
You can change it by setting TMPDIR / TEMP or TMP environmental variable before running redundans for example

export TMPDIR=/home/YOURUSER/tmp

make sure this TMPDIR exists.