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When running metabolic-c, I get the following error: #197

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hyShen-hzau opened this issue Oct 14, 2024 · 1 comment
Open

When running metabolic-c, I get the following error: #197

hyShen-hzau opened this issue Oct 14, 2024 · 1 comment

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@hyShen-hzau
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Describe the bug
When I run ‘perl METABOLIC-C.pl -in-gn /data_SSD/home/newshy/Metabolic/Sharp/test -r /data_SSD/home/newshy/Metabolic/test2.txt -o result3 -t 15’, a bug occurs. My input file is a fasta file. However, the error in the log is ‘Error: reads file does not look like a FASTQ file’.

To Reproduce
Steps to reproduce the behavior:

  1. Go to 'METABOLIC_log.log'
  2. Click on '....'
  3. Scroll down to
  4. [2024-10-13 22:57:20] Drawing element cycling diagrams...
    Renaming result4/All_gene_collections.gene.scaffold.3.bt2.tmp to result4/All_gene_collections.gene.scaffold.3.bt2
    Renaming result4/All_gene_collections.gene.scaffold.4.bt2.tmp to result4/All_gene_collections.gene.scaffold.4.bt2
    Renaming result4/All_gene_collections.gene.scaffold.1.bt2.tmp to result4/All_gene_collections.gene.scaffold.1.bt2
    Renaming result4/All_gene_collections.gene.scaffold.2.bt2.tmp to result4/All_gene_collections.gene.scaffold.2.bt2
    Renaming result4/All_gene_collections.gene.scaffold.rev.1.bt2.tmp to result4/All_gene_collections.gene.scaffold.rev.1.bt2
    Renaming result4/All_gene_collections.gene.scaffold.rev.2.bt2.tmp to result4/All_gene_collections.gene.scaffold.rev.2.bt2
    Renaming result4/All_gene_collections.gene.scaffold.3.bt2.tmp to result4/All_gene_collections.gene.scaffold.3.bt2
    Renaming result4/All_gene_collections.gene.scaffold.4.bt2.tmp to result4/All_gene_collections.gene.scaffold.4.bt2
    Renaming result4/All_gene_collections.gene.scaffold.1.bt2.tmp to result4/All_gene_collections.gene.scaffold.1.bt2
    Renaming result4/All_gene_collections.gene.scaffold.2.bt2.tmp to result4/All_gene_collections.gene.scaffold.2.bt2
    Renaming result4/All_gene_collections.gene.scaffold.rev.1.bt2.tmp to result4/All_gene_collections.gene.scaffold.rev.1.bt2
    Renaming result4/All_gene_collections.gene.scaffold.rev.2.bt2.tmp to result4/All_gene_collections.gene.scaffold.rev.2.bt2
    Error: reads file does not look like a FASTQ file
    Error: reads file does not look like a FASTQ file
    terminate called after throwing an instance of 'int'
    terminate called after throwing an instance of 'int'
    (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
    (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
    Illegal division by zero at METABOLIC-C.pl line 2097.
    Illegal division by zero at METABOLIC-C.pl line 2097.

Expected behavior
A clear and concise description of what you expected to happen.

Screenshots
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Additional context
METABOLIC.log

@LvbBo
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LvbBo commented Nov 25, 2024

Hi, ----------"My input file is a fasta file. However, the error in the log is ‘Error: reads file does not look like a FASTQ file’."
Input file should be a FASTQ file, not a fasta file, two different type files.

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