I am still proceeding in troubleshooting.
I write to report some information about search closed reference
qiime vsearch cluster-features-closed-reference
hereafter I report the output of verbose option.
I noticed in particular:
vsearch v2.7.0_linux_x86_64, 70.8GB RAM, 12 cores, which I do not understand, in the sense that I do not require those resources. I am running on the cluster in a single node.
7276798 nt in 5088 seqs, min 1258, max 2353, avg 1430
Counting k-mers 100%
Creating k-mer index 100%
Matching query sequences: 7958865 of 8119151 (98.03%)
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: vsearch --sortbysize /lustre2/scratch/tmp/tmp6p2i6yqj --xsize --output /lustre2/scratch/tmp/q2-DNAFASTAFormat-9k_7183q
vsearch v2.7.0_linux_x86_64, 70.8GB RAM, 12 cores
Reading file /lustre2/scratch/tmp/tmp6p2i6yqj 100%
73054219 nt in 160286 seqs, min 302, max 596, avg 456
Getting sizes 100%
Median abundance: 1
Writing output 100%
In addition to that I am reporting, with the following command, measures of CPU and memory usage:
while ps -p 31835 --no-headers --format “etime pid %cpu %mem rss”; do sleep 10; done > test.txt
31835 refers to the process I want to monitor.
I saw that the command basically starts with one process, namely qiime (if seen with a top command)
and that is the process I mention before,
afterwards it goes into vsearc, with another process. That process terminates, however I still see the abovementioned one which is still going and staying at what reported by the verbose option it is still going.
Thanks a lot if you could tell me what is making the program staying that way.
Thanks a lot again