Qs about running time of Smufin

[zxf...@gmail.com]

Hi, there,
we are simulating 10-50x coverage paired-end NGS data and apply SMuFin on them. However, my job have been running for 60 hours and non has been done... I wonder how long am I expecting here for SMufin to complete a 10X NGS data from Chr1? thanks!

[montse]

Hello,

SMuFin default parameters have been adjusted for common sequencing scenarios (30x coverage or higher). So with a coverage fewer than that we do not know what could be exactly the behavior. I can tell you than using a whole genome sequencing of 30x SMuFin takes between 4 and 8 hours. But I need more information about your case to help you.

Can you tell me the exact command are you are running? Can you tell me the amount of resources are you are using? (number of nodes, memory available in each node, number of threads per node, etc.). And what are the main characteristics of your analysis? Is a Human whole genome sequencing? Are you running SMUFIN from BAM files or directly from FASTQ files?

[zxf...@gmail.com]

Hi,
thanks for the reply. my command: SMuFin --ref hg19.fa --normal_fastq_1 SMuFin_chr10_RD30_1_N.txt --normal_fastq_2 SMuFin_chr10_RD30_2_N.txt --tumor_f
astq_1 SMuFin_chr10_RD30_1_T.txt --tumor_fastq_2 SMuFin_chr10_RD30_2_T.txt --patient_id SMuFin_chr10_RD30 --cpus_per_node 8

I have these files listed in each txt: SMuFin_chr10_RD30_1_N.fq / SMuFin_chr10_RD30_2_N.fq / SMuFin_chr10_RD30_1_T.fq / SMuFin_chr10_RD30_2_T.fq

These fqs were simulated from the fasta provided with the paper. I gave 20gb mem for running this command.

we really want to get this work. Thank you for any suggestion!

Xuefang

[zxf...@gmail.com]

here's several possible reasons that I am thinking about could cause my problem:
1. I used _N and _T, instead of _Normal and _Tumor, would this cause SMuFin to be confused ?
2. I didn't made my fq files excutable, but they r totally readable. Should I do chmod +x X.fq?
3. I didn't use .gz file, but .fq file, could this cause the problem?

Thanks!

[SMufin]

Hi,

Did you use the MPI enviroment? If so, which one did you use?

Thank you,