Empty file generated at R3_test
leocaserta opened this issue · comments
Hello
I tried LORCAN for the first time and after around 30 minutes i recceived an error message. My command and the error message are described below. Besides the "Empty file generated at R3_test" there was also "sh: parallel: command not found".
Do you have any idea for the reason and solution of this error?
Thank you!
LORCAN -V -i /home/lcc88/Desktop/PRRSV/PRRSV_serum_03_18_20/basecalled_40min -o /home/lcc88/Desktop/PRRSV/PRRSV_serum_03_18_20 -L log_main.txt -I /home/lcc88/Desktop/PRRSV/PRRSV_serum_03_18_20/Sample_id_PRRSV_serum_ISU_03_18_20_ampliseq.txt -n 24 -m 10 -M 5000 -P 10 -D 5 -d PRRSV_dp_LORCAN
OK: all arguments are present
current working directory: /home/lcc88/LORCAN/LORCAN/1.8/lib
(i) readDIR: /home/lcc88/Desktop/PRRSV/PRRSV_serum_03_18_20/basecalled_40min
(I) sampleID: /home/lcc88/Desktop/PRRSV/PRRSV_serum_03_18_20/Sample_id_PRRSV_serum_ISU_03_18_20_ampliseq.txt
(o) Cdir: /home/lcc88/Desktop/PRRSV/PRRSV_serum_03_18_20
(L) Main log name: log_main.txt
(n) NberThreads: 24
(m) Min nber reads per BC: 10
(M) Consensus MaxRead: 5000
(P) Consensus MinRead: 10
(D) delta: 5
(d) DBchoice: PRRSV_dp_LORCAN
=> (R0_Checking script dependencies) already completed
=> running R1_Seqkit...
sh: parallel: command not found
=> running R2_porechop...
=> running R3_Seqkit_after_porechop...
sh: parallel: command not found
!!! Empty file generated at R3_test:
/home/lcc88/Desktop/PRRSV/PRRSV_serum_03_18_20/0_logs/2_stats_fastq_postporechop.txt (exit!)
Hi,
It seems that your system is missing one of the parallelization module called by LORCAN.pl.
On which system are you running?
What does this command line return?
man parallel
If you obtain a help page, it means that Gnu parallel is installed. Otherwise, please install Gnu parallel on your system.
Hi
Thank you for your response. I am running on Linux (HPC cloud). The cloud has GNU parallel installed in it.
In this case, should i replace the path to perl parallel by the path to GNU parallel?:
Actual path:
our $PERL ="/home/lcc88/miniconda3/envs/LORCAN-env/bin/perl";
Path to GNU parallel:
our $PERL ="/programs/parallel/bin/parallel";
?
Thank you again
Hello,
$PERL should be pointing to your Perl binary, not to Gnu Parallel.
So
our $PERL ="/home/lcc88/miniconda3/envs/LORCAN-env/bin/perl";
is probably correct.
If GNU parallel is installed (and man parallel returns something meaningful; see previous message),
then you are set and you can run the LORCAN pipeline.
GNU parallel is needed at line 128 of:
https://github.com/aramette/LORCAN/blob/master/1.8/lib/LORCAN_subs.pm
to parallelize the calculation of the seqkit stats call.