rm: cannot remove file, no such file or directory--is this an error?

[peanut-buddy]

Hello!

I am new to using Rcorrector. I noticed in the output of some files, the job seems to have completed successfully (reads were processed and corrected) but I noticed the rm error and was wondering if that's typical, or did the program did not complete?

Thank you!

From the output file: Processed 22401462 reads Corrected 4048538 bases. rm: cannot remove 'tmp_34047852011a711e1950ffddb6b6ccd2.bc': No such file or directory rm: cannot remove 'tmp_34047852011a711e1950ffddb6b6ccd2.mer_counts': No such file or directory rm: cannot remove 'tmp_34047852011a711e1950ffddb6b6ccd2.jf_dump': No such file or directory

[mourisl]

What was your running command and other output on the screen? Thanks.

[peanut-buddy]

I ran the command like this: run_rcorrector.pl -1 ${i}_1.fastq -2 ${i}_2.fastq -od ${i}_rcor (in the main directory where the fastq files are stored) To specify: I noticed this issue occurring multiple times.

Here is output on the screen from an output with the rm error:

Put the kmers into bloom filter jellyfish bc -m 23 -s 100000000 -C -t 1 -o tmp_5f496c2d20c7b4420ddb8aabd4d939aa.bc Photuris.frontalis_SRR2104391_Head_M_1.fastq Photuris.frontalis_SRR2104391_Head_M_2.fastq Count the kmers in the bloom filter jellyfish count -m 23 -s 100000 -C -t 1 --bc tmp_5f496c2d20c7b4420ddb8aabd4d939aa.bc -o tmp_5f496c2d20c7b4420ddb8aabd4d939aa.mer_counts Photuris.frontalis_SRR2104391_Head_M_1.fastq Photuris.frontalis_SRR2104391_Head_M_2.fastq Dump the kmers jellyfish dump -L 2 tmp_5f496c2d20c7b4420ddb8aabd4d939aa.mer_counts > tmp_5f496c2d20c7b4420ddb8aabd4d939aa.jf_dump Error correction /usr/local/apps/eb/Rcorrector/1.0.2-foss-2016b/bin/rcorrector -od Photuris.frontalis_SRR2104391_Head_M_rcor -p Photuris.frontalis_SRR2104391_Head_M_1.fastq Photuris.frontalis_SRR2104391_Head_M_2.fastq -c tmp_5f496c2d20c7b4420ddb8aabd4d939aa.jf_dump Stored 54053926 kmers Weak kmer threshold rate: 0.003575 (estimated from 0.950/1 of the chosen kmers) Bad quality threshold is 9 Processed 22746012 reads Corrected 6963497 bases. rm: cannot remove 'tmp_5f496c2d20c7b4420ddb8aabd4d939aa.bc': No such file or directory rm: cannot remove 'tmp_5f496c2d20c7b4420ddb8aabd4d939aa.mer_counts': No such file or directory rm: cannot remove 'tmp_5f496c2d20c7b4420ddb8aabd4d939aa.jf_dump': No such file or directory

Here's the output of a run that seemed fine:

Put the kmers into bloom filter jellyfish bc -m 23 -s 100000000 -C -t 1 -o tmp_5f496c2d20c7b4420ddb8aabd4d939aa.bc Photuris.frontalis_SRR2104391_Head_M_1.fastq Photuris.frontalis_SRR2104391_Head_M_2.fastq Count the kmers in the bloom filter jellyfish count -m 23 -s 100000 -C -t 1 --bc tmp_5f496c2d20c7b4420ddb8aabd4d939aa.bc -o tmp_5f496c2d20c7b4420ddb8aabd4d939aa.mer_counts Photuris.frontalis_SRR2104391_Head_M_1.fastq Photuris.frontalis_SRR2104391_Head_M_2.fastq Dump the kmers jellyfish dump -L 2 tmp_5f496c2d20c7b4420ddb8aabd4d939aa.mer_counts > tmp_5f496c2d20c7b4420ddb8aabd4d939aa.jf_dump Error correction /usr/local/apps/eb/Rcorrector/1.0.2-foss-2016b/bin/rcorrector -od Photuris.frontalis_SRR2104391_Head_M_rcor -p Photuris.frontalis_SRR2104391_Head_M_1.fastq Photuris.frontalis_SRR2104391_Head_M_2.fastq -c tmp_5f496c2d20c7b4420ddb8aabd4d939aa.jf_dump Stored 54053926 kmers Weak kmer threshold rate: 0.003575 (estimated from 0.950/1 of the chosen kmers) Bad quality threshold is 9 Processed 22746012 reads Corrected 6963497 bases.

Could have it have deleted the intermediate files before the other R2 had finished, if so, would this affect the output? Thank you!

[mourisl]

Did you run rcorrector on the same files at the same time? So the intermediate files got removed by other runs. Since the output of “Corrected XXX bases” showed the same value I don't think the results were affected though.

[peanut-buddy]

I did run the all the files at the same time. Thank you for helping me figure this out!!