CRITICAL ERROR: Can not call software version for bowtie2 even add the bowtie2 path to run

[wend...@gmail.com]

Dear All,

When I try to use the demo with the command line:

humann2 --input demo.fastq --bowtie2 ~/.local/bin/bowtie2 --output demo_fastq

it shows the error"CRITICAL ERROR: Can not call software version for bowtie2".

However, when I use "which bowtie2", it shows "~/.local/bin/bowtie2".

Could anyone tell me how to slove it? I have read all the talks in this group about the same error, but I can't slove it.

Thank you very much for your help and time. 

Sincerely,

Wendi

[任文頔]

Dear Peng,

Thank you very much. I will try it now.

Yes, I can run "bowtie2", and the output is:

...

 Other:

  --qc-filter        filter out reads that are bad according to QSEQ filter

  --seed <int>       seed for random number generator (0)

  --non-deterministic seed rand. gen. arbitrarily instead of using read attributes

  --version          print version information and quit

  -h/--help          print this usage message

(ERR): bowtie2-align exited with value 1

Thanks a lot.

Sincerely,

Wendi

2018-04-26 14:33 GMT+08:00 王鹏 <liuwan...@gmail.com>:

Hello:

Here are two ways may help you:

1. You could try to  choose absolute path, like  "/Users/tongxueer/bowtie2.5”;

      2. Add the bowtie2 path to your environment variable，like write the  "export PATH=/Users/tongxueer/bowtie2.5:$PATH” into your .bashrc file, or just run "export PATH=/Users/tongxueer/bowtie2.5:$PATH” on the command line, then run the human2 without “--bowtie2” parameter ;

Hope this may help you~

Best,

Wangpeng

Can you run bowtie2 software  with “bowtie2” on your command line?

If not,

[wend...@gmail.com]

在 2018年4月26日星期四 UTC+8下午2:01:39，wend...@gmail.com写道：

[Lauren McIver]

Hi Wendi - The bowtie2 option expects the folder with the bowtie2 executable. Can you try modifying your command to the following?

humann2 --input demo.fastq --bowtie2 ~/.local/bin/ --output demo_fastq

I think this should resolve the error you are seeing. Please let me know if you continue to see the error.

Thanks!

Lauren

[任文頔]

Dear Mclver,

Thank you very much. I will try it soon.

Sincerely,

Wendi

[任文頔]

Dear Mclver,

I am sorry that I still see the same error even if I use 

humann2 --input demo.fastq --bowtie2 ~/.local/bin/ --output demo_fastq.

I am sorry that I am away for a vacation so I just try it.

Thank you again!

Sincerely,

Wendi

[Lauren McIver]

Hi Wendi - Can you check your bowtie2 version by running "$ ~/.local/bin/bowtie2 --version" and also get a listing of your local bin folder with "$ ls ~/.local/bin/" ? I am not quite sure why you are seeing this error and this additional information will help me debug it. Please feel free to email me directly if you prefer with this information for your environment.

Thanks,

Lauren

[hiren...@gmail.com]

[hiren...@gmail.com]

Hi,

I also having same error.Can anyone suggest any solution?

On Thursday, April 26, 2018 at 8:01:39 AM UTC+2, wend...@gmail.com wrote:

[Lauren McIver]

Hi - Can you try running "$ bowtie2 --version" and check that the output is as expected? The first line should include the version number. If you see an error from bowtie2, can you try reinstalling bowtie2 and then try running humann2 again.

Thanks!

Lauren

[Hiren Ghosh]

 

Hi, I am having a problem while running humann2. Can anybody help me out.

Error:

$humann2 -i V37filtration_Dnase_I_II_III_kneaddata_merged.fastq -o out_V37_humann2 --protein-database /home/project/Database/chocophlan2/uniref/ --nucleotide-database /home/project/Database/chocophlan2/chocophlan/ --metaphlan-options /home/anaconda3/envs/metaphlan2/bin/metaphlan_databases/

Output files will be written to: /mnt/work/home/hig18/project/DSMZ/lung_microbiome/V37/merged_cleand_V37/out_V37_humann2

The database file for MetaPhlAn does not exist at /home/hig18/anaconda3/envs/metaphlan2/bin/db_v20/mpa_v20_m200.pkl . Please provide the location with --metaphlan-options 

--

Hiren Ghosh, Doctoral Research Scholar
Biomedizinisches Forschungszentrum Seltersberg
Institut für Medizinische Mikrobiologie
Justus-Liebig-Universität
Schubertstr. 81
35392 Gießen , Germany

Mobile No: 017672157634

Email:hiren...@med.uni-giessen.de

[Lauren McIver]

Hi - It looks like you have the latest version of MetaPhlAn2 installed. The databases for MetaPhlAn2 have moved with the new version. HUMAnN2 is not yet compatible with the latest version of MetaPhlAn2 but will be in the next release. To resolve the error install a prior version of MetaPhlAn2 or use the HUMAnN2 option "--metaphlan-options" to provide the location of the databases. For example add something like --metaphlan-options='--mpa_pkl databases/mpa_v20_m200.pkl --bowtie2db databases/mpa_v20_m200' providing the full paths.

Thanks!

Lauren