# Metaphlan does not creating txt file only bowtie file

**URL:** <https://forum.biobakery.org/t/metaphlan-does-not-creating-txt-file-only-bowtie-file/6121>\
**Category:** MetaPhlAn\
**Created:** [October 25, 2023, 2:34pm UTC](https://forum.biobakery.org/t/metaphlan-does-not-creating-txt-file-only-bowtie-file/6121 "2023-10-25T14:34:43Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Nelly](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nelly/32/1718_2.png) [@Nelly](https://forum.biobakery.org/u/Nelly)\
**Post date:** [October 25, 2023, 2:34pm UTC](https://forum.biobakery.org/t/metaphlan-does-not-creating-txt-file-only-bowtie-file/6121/1 "2023-10-25T14:34:43Z")

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Hi, metaphlan is not creating the output txt files, only bowtie2.bz2 file without any error. I am using metaphlan 4 version and the command I am using is:

> find host -name “\*unmapped.1.fastq” | cut -d “.” -f1 | parallel -j 20 ‘metaphlan {}.unmapped.1.fastq,{}.unmapped.2.fastq --input\_type fastq --bowtie2out {}.bowtie2.bz2 --nproc 20 --bowtie2db metaphlan\_database --ignore\_eukaryotes --ignore\_archaea -o {}. output.txt’

What can be the reason?  
Help appreciated!

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**Author:** ![Nelly](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nelly/32/1718_2.png) [@Nelly](https://forum.biobakery.org/u/Nelly)\
**Post date:** [October 27, 2023, 8:36am UTC](https://forum.biobakery.org/t/metaphlan-does-not-creating-txt-file-only-bowtie-file/6121/2 "2023-10-27T08:36:36Z")

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I tried the same code for one sample without parallel processing, and it worked. My guess is that the problem lies in the comma between ‘1’ and ‘2’ fastq files. The code expects the input to be in the fastq format. I also attempted to use space separation, but it still only generates intermediate files and not the ‘output.txt’ file.

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**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\
**Post date:** [March 5, 2024, 9:27am UTC](https://forum.biobakery.org/t/metaphlan-does-not-creating-txt-file-only-bowtie-file/6121/3 "2024-03-05T09:27:00Z")

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Hi @Nelly  
I would suggest to run it as:  
find host -name “\*unmapped.1.fastq” | cut -d “.” -f1 | parallel -j 20 ‘metaphlan {}.unmapped.1.fastq,{}.unmapped.2.fastq --input\_type fastq --bowtie2out {}.bowtie2.bz2 --nproc 20 --bowtie2db metaphlan\_database --ignore\_eukaryotes --ignore\_archaea **\>** output.txt’