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zy-optimistic / GAEP

A genome assembly assessment pipeline.
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GAEP hangs in the middle of something after showing some error code #12

Open lingvv opened 1 year ago

lingvv commented 1 year ago

Hello! I'm encountering an issue when attempting to execute the pipe commands. An error code is displayed, causing GAEP to become unresponsive.

Error code:

Error occurred while processing the filter "%QUAL<10 || DP <= 3" (1:1)
Thread 2 terminated abnormally: [var_calling] Can't run "/usr/local/bin/bcftools filter  -e '%QUAL<10 || DP <= 3' ./gaep_output_69540/variants_calling//gaep_pm1_t2_.2.vcf -o ./gaep_output_69540/variants_calling//gaep_pm1_t2_.2.flt.vcf".
/usr/local/bin/bcftools filter  -e '%QUAL<10 || DP <= 3' ./gaep_output_69540/variants_calling//gaep_pm1_t2_.1.vcf -o ./gaep_output_69540/variants_calling//gaep_pm1_t2_.1.flt.vcf
Error occurred while processing the filter "%QUAL<10 || DP <= 3" (1:1)
Thread 1 terminated abnormally: [var_calling] Can't run "/usr/local/bin/bcftools filter  -e '%QUAL<10 || DP <= 3' ./gaep_output_69540/variants_calling//gaep_pm1_t2_.1.vcf -o ./gaep_output_69540/variants_calling//gaep_pm1_t2_.1.flt.vcf".

Here are the commands I used: ./gaep pipe -r <assembled_genome.fasta> --lr <long_read.fastq.gz> --sr1 <forward_short_read.fq.gz> --sr2 <reverse_short_read.fq.gz > -o <output_prefix>

I've included the entire log in the attached text file for your reference. Your guidance in resolving this issue would be greatly appreciated. Thank you!

image gaep_logfile.txt

lingvv commented 1 year ago

Hello! I faced similar error when running macc as well. The log file is copied from the terminal and attached in this thread. Thank you so much for your attention!

Commands: (base) rndvivien@SG-LP-7469:~/GAEP$ ./gaep macc -r <assembled_genome.fast> -i <forward_illumin [macc_logfile.txt](https://github.com/zy-optimistic/GAEP/files/13162208/macc_logfile.txt) a.fq.gz> -I <reverse_illumina.fq.gz> -d <output_directory>

zy-optimistic commented 1 year ago

Please try executing the relevant 'vcftools' command directly and check for any errors. If no errors occur, please run GAEP again.

KANGYUlab commented 5 months ago

Please try executing the relevant 'vcftools' command directly and check for any errors. If no errors occur, please run GAEP again.

Hi, I also had the same problem: /path/soft/bcftools-1.19/bcftools filter -e '%QUAL<10 || DP <= 3' ./gaep_output_1200/variants_calling//gaep_output.chr21_hap1.vcf -o ./gaep_output_1200/variants_calling//gaep_output.chr21_hap1.flt.vcf Error occurred while processing the filter "%QUAL<10 || DP <= 3" (1:1) Thread 13 terminated abnormally: [var_calling] Can't run "/path/soft/bcftools-1.19/bcftools filter -e '%QUAL<10 || DP <= 3' ./gaep_output_1200/variants_calling//gaep_output.chr21_hap1.vcf -o ./gaep_output_1200/variants_calling//gaep_output.chr21_hap1.flt.vcf".

I'm sure that vcftool can run properly on its own. How to fix it? Thanks a lot.