# Metaphlan marker level analysis

**URL:** <https://forum.biobakery.org/t/metaphlan-marker-level-analysis/744>\
**Category:** MetaPhlAn\
**Created:** [July 21, 2020, 12:31pm UTC](https://forum.biobakery.org/t/metaphlan-marker-level-analysis/744 "2020-07-21T12:31:26Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![nousiaso](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nousiaso/32/411_2.png) [@nousiaso](https://forum.biobakery.org/u/nousiaso)\
**Post date:** [July 21, 2020, 12:31pm UTC](https://forum.biobakery.org/t/metaphlan-marker-level-analysis/744/1 "2020-07-21T12:31:26Z")

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Greetings to your nice forum.

I have finished running my analysis of metaphlan 3.0 on my datasets and trying to run all the marker analyses on the bowtie output. i used the code below

metaphlan -t marker\_ab\_table --bowtie2out metagenome\_dataset1\_.bowtie2.bz2 --nreads 9533350 --nproc 12 --input\_type bowtie2out -o marker\_abundance\_table\_dataset1.txt

but I don’t get any results… (the metagenomic profile has given a lot of taxonomies so I know I have a lot o f things as i have seen the txt output of metaphlan)

thanks

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**Author:** ![nousiaso](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nousiaso/32/411_2.png) [@nousiaso](https://forum.biobakery.org/u/nousiaso)\
**Post date:** [July 21, 2020, 2:04pm UTC](https://forum.biobakery.org/t/metaphlan-marker-level-analysis/744/2 "2020-07-21T14:04:27Z")

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mm the number of reads was not correct that i provided. it is also stated at the end of the bowtie output

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**Author:** ![nousiaso](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nousiaso/32/411_2.png) [@nousiaso](https://forum.biobakery.org/u/nousiaso)\
**Post date:** [July 21, 2020, 2:13pm UTC](https://forum.biobakery.org/t/metaphlan-marker-level-analysis/744/3 "2020-07-21T14:13:08Z")

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but this was not the issue… still doesnt give results

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**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\
**Post date:** [July 22, 2020, 8:09am UTC](https://forum.biobakery.org/t/metaphlan-marker-level-analysis/744/4 "2020-07-22T08:09:06Z")

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> metaphlan -t marker\_ab\_table --bowtie2out metagenome\_dataset1\_.bowtie2.bz2 --nreads 9533350 --nproc 12 --input\_type bowtie2out -o marker\_abundance\_table\_dataset1.txt

There’s no need to provide `nreads` for `marker_ab_table`.

You forgot to provide the input file in the command line you posted here, this is the correct command:

`metaphlan -t marker_ab_table --input_type bowtie2out -o marker_abundance_table_dataset1.txt metagenome_dataset1_.bowtie2.bz2 `

`--bowtie2out` refers to the output file in which the marker-to-reads BowTie2 mapping file is stored, you have to use this file as input file.

The command you run before may have overwritten the previous MetaPhlAn profile

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**Author:** ![nousiaso](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nousiaso/32/411_2.png) [@nousiaso](https://forum.biobakery.org/u/nousiaso)\
**Post date:** [July 22, 2020, 9:40am UTC](https://forum.biobakery.org/t/metaphlan-marker-level-analysis/744/5 "2020-07-22T09:40:56Z")

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thank you for your reply. Fortunately it didnt overwrite the original bowtie output. I would like to ask something else also. I got the relative abundances table but the ids of the rel abundance reads to the mapped ones are not giving me the organism name (just the ncbi id). How is it possible to get the actual names of the organisms so as to run in hclust2 ?  
or the names are manually written afterwards by the user?

thanks again for the reply

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**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\
**Post date:** [July 22, 2020, 2:42pm UTC](https://forum.biobakery.org/t/metaphlan-marker-level-analysis/744/6 "2020-07-22T14:42:43Z")

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You can add them manually by looking-up the species name using this mapping file attached below [mpa\_v30\_CHOCOPhlAn\_201901\_markers\_per\_species.txt](https://forum.biobakery.org/uploads/short-url/uqdJxTfmweQ5ZRUDi73BEFoeO4u.txt) (1.9 MB)

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**Author:** ![nousiaso](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nousiaso/32/411_2.png) [@nousiaso](https://forum.biobakery.org/u/nousiaso)\
**Post date:** [July 22, 2020, 2:44pm UTC](https://forum.biobakery.org/t/metaphlan-marker-level-analysis/744/7 "2020-07-22T14:44:33Z")

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thank you for the reply