I got out of memory errors while running concoct_coverage_table.py if I feed a lot of bam files. The error messages are below. When I feed less bam files (~10), there were no error messages. I was working on cluster so there should have large RAM. In principal I can feed part of the bam files and run multiple times and merge the result to a single coverage_table.tsv file. But is there an easier way to avoid out of memory error?
Cheers, Yun
(concoct_env) [fr_yw50@uc2n996 CONCOCT]$ concoct_coverage_table.py contigs_10K.bed ../metabat2/bam/*sort.bam > coverage_table.tsv
[E::bam_hdr_read] Out of memory
ERROR: failed to read header for '../metabat2/bam/Sample_201418-sort.bam'
Traceback (most recent call last):
File "/home/fr/fr_fr/fr_yw50/anaconda3/envs/concoct_env/bin/concoct_coverage_table.py", line 91, in
generate_input_table(args.bedfile, args.bamfiles, samplenames=samplenames)
File "/home/fr/fr_fr/fr_yw50/anaconda3/envs/concoct_env/bin/concoct_coverage_table.py", line 41, in generate_input_table
sys.stderr.write(out)
TypeError: write() argument must be str, not bytes
Hi CONCOCT team,
I got out of memory errors while running concoct_coverage_table.py if I feed a lot of bam files. The error messages are below. When I feed less bam files (~10), there were no error messages. I was working on cluster so there should have large RAM. In principal I can feed part of the bam files and run multiple times and merge the result to a single coverage_table.tsv file. But is there an easier way to avoid out of memory error?
Cheers, Yun
(concoct_env) [fr_yw50@uc2n996 CONCOCT]$ concoct_coverage_table.py contigs_10K.bed ../metabat2/bam/*sort.bam > coverage_table.tsv [E::bam_hdr_read] Out of memory ERROR: failed to read header for '../metabat2/bam/Sample_201418-sort.bam' Traceback (most recent call last): File "/home/fr/fr_fr/fr_yw50/anaconda3/envs/concoct_env/bin/concoct_coverage_table.py", line 91, in
generate_input_table(args.bedfile, args.bamfiles, samplenames=samplenames)
File "/home/fr/fr_fr/fr_yw50/anaconda3/envs/concoct_env/bin/concoct_coverage_table.py", line 41, in generate_input_table
sys.stderr.write(out)
TypeError: write() argument must be str, not bytes