# Metaphlan4 --mpa3 --add\_viruses failed **URL:** \ **Category:** MetaPhlAn\ **Created:** [December 5, 2022, 11:34pm UTC](https://forum.biobakery.org/t/metaphlan4-mpa3-add-viruses-failed/4489 "2022-12-05T23:34:19Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![Nirvana](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nirvana/32/1819_2.png) [@Nirvana](https://forum.biobakery.org/u/Nirvana)\ **Post date:** [December 5, 2022, 11:34pm UTC](https://forum.biobakery.org/t/metaphlan4-mpa3-add-viruses-failed/4489/1 "2022-12-05T23:34:19Z")
Hi all! I am trying to run MetaPhlan 4 by adding parameters: --add\_viruses and --mpa3 to allow the profiling of viral organisms, and then it returns the error: No MetaPhlAn BowTie2 database found (–index option)! But if I remove these two parameters, it runs smoothly. Here I attach my command, the error, and the bowtie2 database I used. 1. my commands: ```auto metaphlan $FQ_DIRECTORY/$SAMPLE.fastq.gz --nproc 16 --read_min_len 30 --input_type fastq --bowtie2out $SAMPLE.bowtie2.out -o $SAMPLE.metaphlan4.txt --bowtie2db /Databases/Metaphlan4 --mpa3 --add_viruses ``` 1. the error: ```auto No MetaPhlAn BowTie2 database found (--index option)! Expecting location bowtie2db Exiting... ``` 1. Those files are within the Bowtie2 database. ```auto mpa_latest mpa_vJan21_CHOCOPhlAnSGB_202103.4.bt2l mpa_vJan21_CHOCOPhlAnSGB_202103.rev.2.bt2l mpa_vJan21_CHOCOPhlAnSGB_202103.1.bt2l mpa_vJan21_CHOCOPhlAnSGB_202103.md5 mpa_vJan21_CHOCOPhlAnSGB_202103.tar mpa_vJan21_CHOCOPhlAnSGB_202103.2.bt2l mpa_vJan21_CHOCOPhlAnSGB_202103.pkl mpa_vJan21_CHOCOPhlAnSGB_202103_VINFO.csv mpa_vJan21_CHOCOPhlAnSGB_202103.3.bt2l mpa_vJan21_CHOCOPhlAnSGB_202103.rev.1.bt2l mpa_vJan21_CHOCOPhlAnSGB_202103_VSG.fna ``` Really appreciate your help and time! Thanks in advance! ---
**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:** [December 6, 2022, 8:29am UTC](https://forum.biobakery.org/t/metaphlan4-mpa3-add-viruses-failed/4489/2 "2022-12-06T08:29:28Z")
Hi @Nirvana Currently, the metaphlan4 vJan21 database do not profile viral species. For using the --add\_viruses parameter (together with the --mpa3 parameter) you should use the metaphlan 3.0 (or 3.1) database available here: [Index of /biobakery3/metaphlan\_databases](http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/) ---
**Author:** ![nickp60](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nickp60/32/1031_2.png) [@nickp60](https://forum.biobakery.org/u/nickp60)\ **Post date:** [February 26, 2023, 5:14pm UTC](https://forum.biobakery.org/t/metaphlan4-mpa3-add-viruses-failed/4489/3 "2023-02-26T17:14:21Z")
Is this still the case with Metaphlan 4.0.5? And if not, what is the timeline for adding them back to the database? The removal of virus sequences was omitted from the [changelog](https://github.com/biobakery/MetaPhlAn/blob/master/CHANGELOG.md) and the [Metaphlan4 announcement](https://forum.biobakery.org/t/metaphlan-4-published-database-update/4850). The manuscript implies that they are present but not extensively represented, rather than entirely absent: > The current methods also do not extensively incorporate viral or eukaryotic microbial sequences, due to their unique genomic architectures and quality control requirements relative to bacterial and archaeal genomes. I now need to downgrade and reprocess several hundred samples. ---
**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:** [February 27, 2023, 9:19am UTC](https://forum.biobakery.org/t/metaphlan4-mpa3-add-viruses-failed/4489/4 "2023-02-27T09:19:04Z")
Hi @nickp60 We apologise for the inconvenience. In (any) version 4, we had decided not to include the previous viral markers, that had not change since MetaPhlAn2. Part of the reason for this (apart for the reason that the database is quite old already), is that we are currently working on a new version that integrates both known and unknown viral species clusters and we hope to release later this year as the new version 4.1 ---
**Author:** ![mwylerCH](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mwylerch/32/2902_2.png) [@mwylerCH](https://forum.biobakery.org/u/mwylerCH)\ **Post date:** [June 27, 2024, 7:17am UTC](https://forum.biobakery.org/t/metaphlan4-mpa3-add-viruses-failed/4489/5 "2024-06-27T07:17:01Z")
@aitor.blancomiguez I guess also with v4.1 viruses are not available right? ---
**Author:** ![Claudia\_Mengoni](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/claudia_mengoni/32/2871_2.png) [@Claudia\_Mengoni](https://forum.biobakery.org/u/Claudia_Mengoni)\ **Post date:** [July 1, 2024, 7:46am UTC](https://forum.biobakery.org/t/metaphlan4-mpa3-add-viruses-failed/4489/6 "2024-07-01T07:46:23Z")
Hi @mwylerCH Virus detection is available in MetaPhlAn 4.1 by using the parameter --profile\_vsc. You can find a small tutorial here: [MetaPhlAn 4.1 · biobakery/biobakery Wiki · GitHub](https://github.com/biobakery/biobakery/wiki/MetaPhlAn-4.1#3-metaphlan-viral-module-tutorial) ---
**Author:** ![mwylerCH](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mwylerch/32/2902_2.png) [@mwylerCH](https://forum.biobakery.org/u/mwylerCH)\ **Post date:** [July 1, 2024, 11:27am UTC](https://forum.biobakery.org/t/metaphlan4-mpa3-add-viruses-failed/4489/7 "2024-07-01T11:27:21Z")
Grazie, it works (the subsequent merging doesn’t work, probably because I’m using `-t rel_ab_w_read_stats`, but doesn’t require technical skills) ---
**Author:** ![mwylerCH](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/mwylerch/32/2902_2.png) [@mwylerCH](https://forum.biobakery.org/u/mwylerCH)\ **Post date:** [July 2, 2024, 2:40pm UTC](https://forum.biobakery.org/t/metaphlan4-mpa3-add-viruses-failed/4489/8 "2024-07-02T14:40:00Z")
update: everything works smooth, made a small typo