an integer is required (got type _io.BufferedWriter)

[Divyoj-Singh]

Hi I am trying to use pfd for converting sra file to fastq files in a pipeline. I have a cluster with 100 cores.following is my code: variable word1 has the SRR id.

time $path_to_parallel_fastq_dump --threads 100 --sra-id $word1 --tmpdir $path_to_sra_folder --outdir $path_to_fastq_folder$word1.fastq |& tee $path_to_stats_folder/srafastq/fout1$word1.txt

But, I am getting following error: File "/home/csb/tools/parallel-fastq-dump-master/parallel-fastq-dump", line 123, in main() File "/home/csb/tools/parallel-fastq-dump-master/parallel-fastq-dump", line 116, in main pfd(args, si, extra_args) File "/home/csb/tools/parallel-fastq-dump-master/parallel-fastq-dump", line 50, in pfd os.close(fd) TypeError: an integer is required (got type _io.BufferedWriter)

Can you please help ?

[rvalieris]

hello, sorry, looks like https://github.com/rvalieris/parallel-fastq-dump/pull/33 introduced a bug, to fix, replace the line: os.close(fd) to fd.close()

I will commit a fix soon.

also, --outdir $path_to_fastq_folder$word1.fastq --outdir should be a path to a directory, you don't have to add $word1.fastq in the end

[Divyoj-Singh]

Thanks!! Will check it out!

On Sat, Mar 13, 2021 at 5:45 PM Renan Valieris @.***> wrote:

hello, sorry, looks like #33 https://github.com/rvalieris/parallel-fastq-dump/pull/33 introduced a bug, to fix, replace the line: os.close(fd) to fd.close()

I will commit a fix soon.

also, --outdir $path_to_fastq_folder$word1.fastq --outdir should be a path to a directory, you don't have to add $word1.fastq in the end

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