# HUMAnN3 Diamond Cannot Find tmp file

**URL:** <https://forum.biobakery.org/t/humann3-diamond-cannot-find-tmp-file/2709>\
**Category:** HUMAnN\
**Created:** [October 22, 2021, 6:40pm UTC](https://forum.biobakery.org/t/humann3-diamond-cannot-find-tmp-file/2709 "2021-10-22T18:40:17Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![y3zhu](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/y3zhu/32/1080_2.png) [@y3zhu](https://forum.biobakery.org/u/y3zhu)\
**Post date:** [October 22, 2021, 6:40pm UTC](https://forum.biobakery.org/t/humann3-diamond-cannot-find-tmp-file/2709/1 "2021-10-22T18:40:17Z")

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Hi, I am trying to run my fastq files with humann3. But I’m getting a critical error message when humann3 is attempting to run diamond. I have diamond 0.9.36 installed. I’m not sure why this is happening, could you help me? Thank you!

The error message:

> Running diamond …
> 
> Aligning to reference database: uniref90\_201901b\_ec\_filtered.dmnd
> 
> CRITICAL ERROR: Can not find file /oasis/tscc/scratch/yiz023/A033\_10\_fastq/A033\_10\_T0\_merged\_humann\_temp/tmp2g66y6/diamond\_m8\_5Lv3R4

The command I’m using:

> humann --input A033\_10\_T0\_merged.fastq --output A033\_10\_fastq

The databases I downloaded:

> humann\_databases --download chocophlan full humann\_dbs  
> Download URL: [http://huttenhower.sph.harvard.edu/humann\_data/chocophlan/full\_chocophlan.v296\_201901b.tar.gz](http://huttenhower.sph.harvard.edu/humann_data/chocophlan/full_chocophlan.v296_201901b.tar.gz)  
> Downloading file of size: 16.01 GB
> 
> humann\_databases --download uniref uniref90\_ec\_filtered\_diamond humann\_dbs  
> Download URL: [http://huttenhower.sph.harvard.edu/humann\_data/uniprot/uniref\_ec\_filtered/uniref90\_ec\_filtered\_201901b\_subset.tar.gz](http://huttenhower.sph.harvard.edu/humann_data/uniprot/uniref_ec_filtered/uniref90_ec_filtered_201901b_subset.tar.gz)  
> Downloading file of size: 1.61 GB

UPDATE:  
I tried again by running the demo file. This time it gave me another error saying cannot find executable diamond, but I do have diamond installed.

> Decompressing gzipped file …
> 
> Running metaphlan …
> 
> Found g\_\_Bacteroides.s\_\_Bacteroides\_dorei : 57.96% of mapped reads  
> Found g\_\_Bacteroides.s\_\_Bacteroides\_vulgatus : 42.04% of mapped reads
> 
> Total species selected from prescreen: 2
> 
> Selected species explain 100.00% of predicted community composition
> 
> Creating custom ChocoPhlAn database …
> 
> Running bowtie2-build …
> 
> Running bowtie2 …
> 
> Total bugs from nucleotide alignment: 2  
> g\_\_Bacteroides.s\_\_Bacteroides\_vulgatus: 1195 hits  
> g\_\_Bacteroides.s\_\_Bacteroides\_dorei: 1260 hits
> 
> Total gene families from nucleotide alignment: 545
> 
> Unaligned reads after nucleotide alignment: 88.3095238095 %
> 
> Running diamond …
> 
> Aligning to reference database: uniref90\_demo\_prots\_v201901b.dmnd
> 
> CRITICAL ERROR: Can not find executable diamond

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<div class="post-metadata">

**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\
**Post date:** [November 5, 2021, 3:15pm UTC](https://forum.biobakery.org/t/humann3-diamond-cannot-find-tmp-file/2709/2 "2021-11-05T15:15:01Z")

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I think there are a couple of different issues at play here. In the first case it looks like the HUMAnN task is having trouble creating one of the temp files it created during the translated search step. Were you about to confirm that this file exists after the task terminated? Seeing the `scratch` in the file path, I wonder if it might’ve been auto-cleaned before the task completed?

In the second example, it looks like you’re running in a different environment (or perhaps didn’t have all the modules loaded that you were using in the first environment?). You should be able to check if DIAMOND is available by running `diamond --version`.