dfguan / pins Goto Github PK

Another point, in the following command:
10x_trim -c -p $prefix $r1 $r2 # generate trimmed read files $prefix_{1,2}.fq.gz
where is 10x_trim, it seems that there is no 10x_trim available.

Hi There,
The following command was suggested for hic scaffolding, but the help of program says that -c is the candidate number. Can you please clarify what is the $ref. I would be appreciated if you clarify what are the functions of -x, -c and -r parameters.

./bin/pin_hic_it -i $N -c $asm.fai -x $ref -O $outdir $bam1 $bam2 $bam3 ...

I encountered with this issue, which likely is related to memory:
[M::proc_bam] finish processing 380278349 read pairs 13073362 (0.03) passed
/var/spool/slurmd/job47058396/slurm_script: line 20: 25428 Segmentation fault (core dumped) /home/karimi81/pins/bin/pin_hic_it -i 3 -c hifiasm_ccs.p_ctg.fa.fai -x hifiasm_ccs.p_ctg.fa

Is there any option to control number of CPU or parallel computing.
Thank you