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dfguan / pins

scaffolding based on Hi-C, 10X linked reads, linkage disequilibrium information.
MIT License
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Hi-c scaffolding using hic_it #2

Open Karimi-81 opened 3 years ago

Karimi-81 commented 3 years ago

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

carolhsb commented 3 years ago

Hi,

I had the same problem. Then I've started running the pipeline step by step. It's running so far...