outfile is abnormal

[shiyi-pan]

hi, I installed the PSMC and tried to run it using the following script:

#!/bin/bash

#$ -cwd #$ -j y #$ -S /bin/bash

#$ -l mem_free=4G

PSMC=/ds3512/home/panyp/PSMC/psmc FASTQ=/ds3512/home/panyp/panshaung/SRR5285353.fastq $PSMC/utils/fq2psmcfa -q20 $FASTQ > diploid.psmcfa $PSMC/psmc -N25 -t15 -r5 -p "4+25*2+4+6" -o diploid.psmc diploid.psmcfa

but the outfile is empty.

-rw-rw-r-- 1 panyp panyp 74618 Jul 30 21:09 diploid.psmc -rw-rw-r-- 1 panyp panyp 0 Jul 30 21:09 diploid.psmcfa -rw-rw-r-- 1 panyp panyp 4293737928 Apr 20 2018 /ds3512/home/panyp/panshaung/SRR5285353.fastq

my fastq file is about 4 Gb. this is obviously abnormal , but i don't got an error message. I don't why.can you give me some help.thank you .

[haolong]

I can’t help but you may want to run the program step by step to debug. Replace those variables with real path or name.

Sent from my iPhone

On Jul 30, 2020, at 9:27 AM, shiyi-pan [email protected] wrote:

 hi, I installed the PSMC and tried to run it using the following script:

#!/bin/bash

#$ -cwd #$ -j y #$ -S /bin/bash

#$ -l mem_free=4G

PSMC=/ds3512/home/panyp/PSMC/psmc FASTQ=/ds3512/home/panyp/panshaung/SRR5285353.fastq $PSMC/utils/fq2psmcfa -q20 $FASTQ > diploid.psmcfa $PSMC/psmc -N25 -t15 -r5 -p "4+25*2+4+6" -o diploid.psmc diploid.psmcfa

but the outfile is empty.

-rw-rw-r-- 1 panyp panyp 74618 Jul 30 21:09 diploid.psmc -rw-rw-r-- 1 panyp panyp 0 Jul 30 21:09 diploid.psmcfa -rw-rw-r-- 1 panyp panyp 4293737928 Apr 20 2018 /ds3512/home/panyp/panshaung/SRR5285353.fastq

my fastq file is about 4 Gb. this is obviously abnormal , but i don't got an error message. I don't why.can you give me some help.thank you .

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[shiyi-pan]

thank you very much . i think maybe my fastq file is wrong . it not a consensus sequence . I will try to generate a real consensus sequence and try again.