# Baqlava failing at depletion step due to misnamed file?

**URL:** <https://forum.biobakery.org/t/baqlava-failing-at-depletion-step-due-to-misnamed-file/8745>\
**Category:** BAQLaVa\
**Created:** [January 28, 2026, 9:37pm UTC](https://forum.biobakery.org/t/baqlava-failing-at-depletion-step-due-to-misnamed-file/8745 "2026-01-28T21:37:00Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![scottdaniel\_at\_chop](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/scottdaniel_at_chop/32/3505_2.png) [@scottdaniel\_at\_chop](https://forum.biobakery.org/u/scottdaniel_at_chop)\
**Post date:** [January 28, 2026, 9:37pm UTC](https://forum.biobakery.org/t/baqlava-failing-at-depletion-step-due-to-misnamed-file/8745/1 "2026-01-28T21:37:00Z")

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Hi again,

Hopefully this boils down to a simple user error but I’m running Baqlava again on some metagenomic samples and I’m getting a repeating error where it’s not finding the `bowtie2_unaligned.fa` file. The exact error is:

```auto
(Jan 28 15:37:20) [1/10 - 10.00%] **Failed** Task 0: Running HUMAnN to depete bacterial reads from file
Run Finished
Task 0 failed
  Name: Running HUMAnN to depete bacterial reads from file
  Original error: 
  Failed to produce target `/scr1/users/danielsg/CHOPMC-551_Thomas_shotgun/baqlava_out/Fib.1_1/Fib_temp/Fib_humann_temp/Fib_bowtie2_unaligned.fa'. Original exception: Traceback (most recent call last):
    File "/home/danielsg/miniconda3/envs/baqlava/lib/python3.10/site-packages/anadama2/runners.py", line 219, in _get_task_result
      targ_compares.append(list(target.compare()))
    File "/home/danielsg/miniconda3/envs/baqlava/lib/python3.10/site-packages/anadama2/tracked.py", line 379, in compare
      stat = os.stat(self.name)
  FileNotFoundError: [Errno 2] No such file or directory: '/scr1/users/danielsg/CHOPMC-551_Thomas_shotgun/baqlava_out/Fib.1_1/Fib_temp/Fib_humann_temp/Fib_bowtie2_unaligned.fa'

```

The strange bit is that I can see a file there about called:

`Fib.1_1_bowtie2_unaligned.fa` which is about 4.6GB in size. So I’m assuming that there are some viruses in there and it’s strange I’m getting this error.

Any help would be appreciated.

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<div class="post-metadata">

**Author:** ![scottdaniel\_at\_chop](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/scottdaniel_at_chop/32/3505_2.png) [@scottdaniel\_at\_chop](https://forum.biobakery.org/u/scottdaniel_at_chop)\
**Post date:** [January 30, 2026, 6:45pm UTC](https://forum.biobakery.org/t/baqlava-failing-at-depletion-step-due-to-misnamed-file/8745/2 "2026-01-30T18:45:01Z")

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I found a little clue. I tried running it with `--bypass-bacterial-depletion` which allowed some of the samples to successfully produce Baqlava profiles (albeit not knowing whether those are actually bacterial reads aligning to viral markers – since I know these samples are highly enriched with bacteria). But something weird is happening, samples are getting renamed in the final output files:

 ![image](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/b/b9878a7362daa922f47fa1772deb2cc45b1940f4.png)

I’m guessing Baqlava (or one of the compenent softwares) is stripping everything after the first dot.

I guess the workaround for now is to replace all instances of dots with underscores.

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<div class="post-metadata">

**Author:** ![scottdaniel\_at\_chop](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/scottdaniel_at_chop/32/3505_2.png) [@scottdaniel\_at\_chop](https://forum.biobakery.org/u/scottdaniel_at_chop)\
**Post date:** [January 30, 2026, 9:34pm UTC](https://forum.biobakery.org/t/baqlava-failing-at-depletion-step-due-to-misnamed-file/8745/3 "2026-01-30T21:34:01Z")

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Yep, that was it. When I renamed all my files with the pattern “Fib.1\_1” \> “Fib\_1\_1” the error did not occur. This should be fixed or, at least, there should be something in the Readme saying “don’t use dots in your sample names”. Thanks.

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**Author:** ![jjensen44](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/jjensen44/32/3298_2.png) [@jjensen44](https://forum.biobakery.org/u/jjensen44)\
**Post date:** [February 5, 2026, 3:36pm UTC](https://forum.biobakery.org/t/baqlava-failing-at-depletion-step-due-to-misnamed-file/8745/4 "2026-02-05T15:36:02Z")

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Hey @scottdaniel_at_chop! You are correct that the behavior is due to how BAQLaVa handles filenames. This information is present in the readme under ‘Running BAQLaVa’ but as it is a single line, it may be easy to miss.

> **[GitHub - biobakery/baqlava: Bioinformatic Application for Quantification and...](https://github.com/biobakery/baqlava?tab=readme-ov-file#running-baqlava)**
>
> Bioinformatic Application for Quantification and LAbeling of VirAl taxonomy