Closed AMMMachado closed 4 years ago
maybe the computer resourecs is not enough
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.
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