# q2-shotgun bracken error
**URL:** https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171
**Category:** Technical Support
**Tags:** kraken
**Created:** [February 7, 2024, 2:15am UTC](https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171 "2024-02-07T02:15:36Z")
**Posts on this page:** 20
**Page:** 1
### Author:  [@MiriamGorostidi](https://forum.qiime2.org/u/MiriamGorostidi)
#### Post date: [February 7, 2024, 2:15am UTC](https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171/1 "2024-02-07T02:15:36Z")
Heyy you all!
I'm trying the recent q2-shotgun library for trying to find Fungal sequences in ur Shallow Shotgun Sequencing data.
Following @Micro_Biologist tutorial ([Importing Kraken2 and bracken databases into qiime2!](https://forum.qiime2.org/t/importing-kraken2-and-bracken-databases-into-qiime2/28384)), I downloaded the PlusPF database (since this one includes fungi information) and import it to qiime2-shotgun distribution.
Then I runned kraken2 (following the github tutorial [https://github.com/caporaso-lab/q2-books/blob/main/q2-shotgun/q2-shotgun/00-tutorial.md](https://github.com/caporaso-lab/q2-books/blob/main/q2-shotgun/q2-shotgun/00-tutorial.md) ), apparently being this execution successful. However, when I try to run the bracken step, the following error appears:
```auto
Plugin error from moshpit:
An error was encountered while running Bracken, (return code 1), please inspect stdout and stderr to learn more.
Debug info has been saved to /tmp/qiime2-q2cli-err-cs94efi4.log
```
Taking a look at the .log file, I see that there's something wrong with the Kraken2 step, since no reads were found:
cat /tmp/qiime2-q2cli-err-cs94efi4.log
> Running external command line application(s). This may print messages to stdout and/or stderr.
> The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.
> Command: bracken -d /tmp/qiime2/mgorostidi/data/ab5f1fa9-9c39-4a7d-b7b4-81fd3f428998/data -i /tmp/qiime2/mgorostidi/data/24e0eb23-b553-4272-b706-d2e8d265b722/data/11326-Q-76401-0059-2019-03-08-290.report.txt -o /tmp/tmpiwgpufzu/11326-Q-76401-0059-2019-03-08-290.bracken.output.txt -w /tmp/q2-Kraken2ReportDirectoryFormat-le\_95\_e2/11326-Q-76401-0059-2019-03-08-290.report.txt -t 0 -r 100 -l S
> Checking for Valid Options...
> Running Bracken
> python src/est\_abundance.py -i /tmp/qiime2/mgorostidi/data/24e0eb23-b553-4272-b706-d2e8d265b722/data/11326-Q-76401-0059-2019-03-08-290.report.txt -o /tmp/tmpiwgpufzu/11326-Q-76401-0059-2019-03-08-290.bracken.output.txt -k /tmp/qiime2/mgorostidi/data/ab5f1fa9-9c39-4a7d-b7b4-81fd3f428998/data/database100mers.kmer\_distrib -l S -t 0
> Checking report file: /tmp/qiime2/mgorostidi/data/24e0eb23-b553-4272-b706-d2e8d265b722/data/11326-Q-76401-0059-2019-03-08-290.report.txt
> **Error: no reads found. Please check your Kraken report**
> .......
Could someone help me with this? Since I've checked the github issues and also the qiime2-forum but haven't found anything regarding this.
And more questions..
1. This part is not included in the tutorial, but should we remove adapters from the files? (I guess yes..)
2. What's the depth required for this kind of analysis?
3. Having the following reads count per sample would be enough for fungal kingdom analysis?
4. What's the difference between using the whole PlusPF db or the 16GB one?
Sample information:
- Shallow Shotgun Sequencing
- Sequences' quality graphs show good qualities
- Paired-end sequencing (each 150 length)
- demux. qzv:
# Demultiplexed sequence counts summary
| | forward reads | reverse reads |
| --- | --- | --- |
| Minimum | 36 | 36 |
| Median | 379.0 | 379.0 |
| Mean | 467.6875 | 467.6875 |
| Maximum | 2403 | 2403 |
| Total | 29932 | 29932 |
THANK YOU SO MUCH IN ADVANCED π
---
### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [February 7, 2024, 6:12am UTC](https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171/2 "2024-02-07T06:12:07Z")
Hi @MiriamGorostidi ,
Thanks for giving q2-moshpit a try!
Have you inspected the kraken2 report as indicated in the error message? Either it really is empty for some reason, or it does not have any species-level hits. Please export the kraken2 report and inspect it and let us know what you see.
bracken requires a `level` specification, which is set to species level by default. If there are no species-level hits in your kraken2 report, then bracken2 is failing because there are no species-level hits for estimating abundances. So if that is the case you could add `--p-level G` (or whatever level makes sense based on your kraken2 report) to your `estimate-bracken` command to see if you can estimate results at genus-level.
> [@MiriamGorostidi](#):
>
> This part is not included in the tutorial, but should we remove adapters from the files? (I guess yes..)
Yes. That tutorial is an alpha release, and more detailed tutorials are forthcoming.
> [@MiriamGorostidi](#):
>
> What's the depth required for this kind of analysis?
For read-based classification with kraken2 I am not sure if there is a rule of thumb... but this would be a good paper to consult if you want to know how shallow you can go with shallow shotgun sequencing:
[https://journals.asm.org/doi/10.1128/msystems.00069-18](https://journals.asm.org/doi/10.1128/msystems.00069-18)
> [@MiriamGorostidi](#):
>
> What's the difference between using the whole PlusPF db or the 16GB one?
You can read more about the databases here:
[https://benlangmead.github.io/aws-indexes/k2](https://benlangmead.github.io/aws-indexes/k2)
> In some cases (i.e. for collections with β-8β or β-16β in the name) we used the --max-db-size option to cap the size of the database produced. This makes the index smaller at the expense of some sensitivity and accuracy. In all cases we use the defaults for k-mer length, minimizer length, and minimizer spacing.
Good luck!
---
### Author:  [@MiriamGorostidi](https://forum.qiime2.org/u/MiriamGorostidi)
#### Post date: [February 7, 2024, 7:50pm UTC](https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171/3 "2024-02-07T19:50:27Z")
Hi @Nicholas_Bokulich !
Thank you much for you rapid response π
How could I export the kraken2 report? I mean, you mean to convert the .qza to .qzv right? But which one would be the command? (I'm sorry, first time working with kraken2 too)
I will give a deep read to those two references you mention!
Thank you so much for everything!
---
### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [February 7, 2024, 9:25pm UTC](https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171/4 "2024-02-07T21:25:06Z")
Hi @MiriamGorostidi ,
Use the `qiime tools export` command to export to a text file.
Good luck!
---
### Author:  [@MiriamGorostidi](https://forum.qiime2.org/u/MiriamGorostidi)
#### Post date: [February 7, 2024, 10:34pm UTC](https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171/5 "2024-02-07T22:34:36Z")
Thank you @Nicholas_Bokulich !
Already checked and you were right! All the kraken reports have the following:
100.00 667 667 0 0 U 0 unclassified
What you suggest me to do?
I mean, taking into account that the PlusFP db includes protozoa and fungi kingdoms, this could mean that there is not any fungi or protozoa in my samples? Or should I try other approaches?
Thank you!
---
### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [February 8, 2024, 6:54am UTC](https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171/6 "2024-02-08T06:54:06Z")
> [@MiriamGorostidi](#):
>
> this could mean that there is not any fungi or protozoa in my samples?
Yes it looks that way. You could try a different database to see if you get any other hits to other organisms.
Or for a quick check you could take some of the raw reads (before inputting to QIIME 2 or doing any QC) and just try BLASTing a few to see what's there.
Let me know what you find. Good luck!
---
### Author:  [@MiriamGorostidi](https://forum.qiime2.org/u/MiriamGorostidi)
#### Post date: [February 8, 2024, 11:52pm UTC](https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171/7 "2024-02-08T23:52:34Z")
Hi @Nicholas_Bokulich !
I've Blast a couple of them and found bacterias at least, so I will try the pipeline again with another database.
Actually, I already tried it and got the following error: (I mean, everything went correct the first time and now...) Do you know what that problems about space refers to?
> Traceback (most recent call last):
> File "/pool0/home/mgorostidi/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/setuptools/\_distutils/file\_util.py", line 58, in \_copy\_file\_contents
> fdst.write(buf)
> OSError: [Errno 28] No space left on device
> During handling of the above exception, another exception occurred:
> Traceback (most recent call last):
> File "/pool0/home/mgorostidi/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 409, in from\_data
> Format.write(rec, type, format, data\_initializer,
> File "/pool0/home/mgorostidi/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/qiime2/core/archive/format/v5.py", line 20, in write
> super().write(archive\_record, type, format, data\_initializer,
> File "/pool0/home/mgorostidi/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/qiime2/core/archive/format/v1.py", line 18, in write
> super().write(archive\_record, type, format, data\_initializer,
> File "/pool0/home/mgorostidi/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/qiime2/core/archive/format/v0.py", line 62, in write
> data\_initializer(data\_dir)
> File "/pool0/home/mgorostidi/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/qiime2/core/path.py", line 45, in \_move\_or\_copy
> return self.\_copy\_dir\_or\_file(other)
> File "/pool0/home/mgorostidi/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/qiime2/core/path.py", line 33, in \_copy\_dir\_or\_file
> return distutils.dir\_util.copy\_tree(str(self), str(other))
> File "/pool0/home/mgorostidi/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/setuptools/\_distutils/dir\_util.py", line 185, in copy\_tree
> copy\_file(
> File "/pool0/home/mgorostidi/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/setuptools/\_distutils/file\_util.py", line 163, in copy\_file
> \_copy\_file\_contents(src, dst)
> File "/pool0/home/mgorostidi/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/setuptools/\_distutils/file\_util.py", line 60, in \_copy\_file\_contents
> raise DistutilsFileError(
> distutils.errors.DistutilsFileError: could not write to '/tmp/qiime2/mgorostidi/processes/1889-1707433229.17@mgorostidi/4ad844a0-0145-4f04-b916-281545965f1c.7349497406739894442/4ad844a0-0145-4f04-b916-281545965f1c/data/hash.k2d': No space left on device
> During handling of the above exception, another exception occurred:
> OSError: [Errno 28] No space left on device
> During handling of the above exception, another exception occurred:
> Traceback (most recent call last):
> File "/pool0/home/mgorostidi/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/q2cli/builtin/tools.py", line 267, in import\_data
> artifact = qiime2.sdk.Artifact.import\_data(type, input\_path,
> File "/pool0/home/mgorostidi/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/qiime2/sdk/result.py", line 329, in import\_data
> return cls._from\_view(type_, view, view\_type, provenance\_capture,
> File "/pool0/home/mgorostidi/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/qiime2/sdk/result.py", line 364, in \_from\_view
> artifact.\_archiver = archive.Archiver.from\_data(
> File "/pool0/home/mgorostidi/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 421, in from\_data
> cls.\_destroy\_temp\_path(uuid)
> File "/pool0/home/mgorostidi/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 301, in \_destroy\_temp\_path
> cache.process\_pool.remove(str(process\_alias))
> File "/pool0/home/mgorostidi/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/qiime2/core/cache.py", line 1637, in remove
> with self.cache.lock:
> File "/pool0/home/mgorostidi/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/qiime2/core/cache.py", line 292, in **enter**
> self.flufl\_lock.lock()
> File "/pool0/home/mgorostidi/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/flufl/lock/\_lockfile.py", line 328, in lock
> self.\_write()
> File "/pool0/home/mgorostidi/miniconda3/envs/qiime2-shotgun-2023.9/lib/python3.8/site-packages/flufl/lock/\_lockfile.py", line 493, in \_write
> fp.write(self.\_claimfile)
> OSError: [Errno 28] No space left on device
> An unexpected error has occurred:
> [Errno 28] No space left on device
> See above for debug info.
---
### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [February 9, 2024, 5:05am UTC](https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171/8 "2024-02-09T05:05:40Z")
Hi @MiriamGorostidi ,
This means that you ran out of disk space on your computer (or wherever this is running). You will need to delete some files to make space, or find another computer with more disk space.
Good luck!
---
### Author:  [@MiriamGorostidi](https://forum.qiime2.org/u/MiriamGorostidi)
#### Post date: [February 16, 2024, 10:18pm UTC](https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171/9 "2024-02-16T22:18:44Z")
Hii @Nicholas_Bokulich !
I know what was happening.
First, the guy that sent me the fastq files sent the incorrect ones, so of course, there was not any classification made in those ones.
Second, the server where I am running the analysis had a temp folder with no enough space, so this is why the error regarding disk space appeared. Once the tech support redirect the analysis to a temp folder with more space I have never had that error again.
Thank ou so much for your help π
---
### Author:  [@MiriamGorostidi](https://forum.qiime2.org/u/MiriamGorostidi)
#### Post date: [February 28, 2024, 1:13am UTC](https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171/10 "2024-02-28T01:13:58Z")
Hi again @Nicholas_Bokulich !
I'm back since I have tried to analyze my samples using pluspf and standard reference databases from [Index zone by BenLangmead](https://benlangmead.github.io/aws-indexes/k2)
However, the results were not what we were expecting. Since I know, this exact samples were already analyzed some years ago, using SHOGUN and, at least, the bacterial information was more than I am obtaining. Should I give SHOGUN a try? My goal is to try to find fungal information in shallow shotgun..
Thank you!
---
### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [February 28, 2024, 5:49am UTC](https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171/11 "2024-02-28T05:49:10Z")
Hi @MiriamGorostidi ,
You have what's known as "Segal's Law":
> **[Segal's law](https://en.wikipedia.org/wiki/Segal%27s_law)**
>
> Segal's law is an adage that states:
> .mw-parser-output .templatequote{overflow:hidden;margin:1em 0;padding:0 32px}.mw-parser-output .templatequotecite{line-height:1.5em;text-align:left;margin-top:0}@media(min-width:500px){.mw-parser-output .templatequotecite{padding-left:1.6em}} A man with a watch knows what time it is. A man with two watches is never sure. At surface level, the adage emphasizes the consistency that arises when information comes from a single source and points out the potential p...
You are comparing two different methods and see a difference, but you do not actually know the true composition as you are analyzing a sample with unknown composition (I assume, based on your descriptions). The only way to tell which is giving a more accurate answer would be to test these using samples of known composition, e.g., a simulated or mock community.
Good luck!
---
### Author:  [@MiriamGorostidi](https://forum.qiime2.org/u/MiriamGorostidi)
#### Post date: [February 29, 2024, 11:57pm UTC](https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171/12 "2024-02-29T23:57:34Z")
Hi @Nicholas_Bokulich !
No sorry, I didn't explain myself correctly.
I have some metagenomics files, where I want to see if there is any fungi read. Since it is my first time doing this kind of analysis, I gave q2-shotgun a try. I directly used PlusPF database, but every taxonomy classification was 100% unclassified. At this point I had two options: 1) assume that my samples don't have any fungi and 2) try the same pipeline using the Standard database, to confirm that the pipeline I wrote was ok and it found Bacterial reads.
However, the results for this Standard db were not so good, I mean, there was almost no bacterial reads and the % of unclassified was really high, almost 100% too.
What I didn't know is that these exact samples were already analyzed, years ago, using SHOGUN, and they did find many more bacterial results.
So at this point, I don't know if I am doing something wrong and not using the q2-shotgun plugin correctly, if it is due to Kraken2 profiler and I should try another profiler, if I should use SHOGUN and replicate at least the bacterial analysis and then try with the fungal one (but I am finding it quite hard to set up... There are almost not examples of how to use it... And do you know if SHOGUN could be use for fungal analysis?)
If you have any other idea I'm glad to hear from you π
Thank you so much again!
Best,
Miriam
---
### Author:  [@misialq](https://forum.qiime2.org/u/misialq)
#### Post date: [March 1, 2024, 3:17pm UTC](https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171/14 "2024-03-01T15:17:59Z")
Hi @MiriamGorostidi,
just to be sure we are on the same page, could you please share the exact command you ran for both, Kraken2 classification and Bracken estimation? Thanks!
Cheers,
Michal
---
### Author:  [@MiriamGorostidi](https://forum.qiime2.org/u/MiriamGorostidi)
#### Post date: [March 1, 2024, 6:16pm UTC](https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171/15 "2024-03-01T18:16:10Z")
Hi @misialq
Yes, of course, here is the code:
```auto
CONFIDENCE_PERCENTAGE=0.60
MINIMUM_BASE_QUALITY=20
THREADS=10
echo "Running Kraken2 classification..."
qiime moshpit classify-kraken2 \
--i-seqs demux.qza \
--i-kraken2-db "$SHOTGUN_FOLDER/kraken2-databases/$REF_DATABASE_NAME/krakendb_$REF_DATABASE_NAME.qza" \
--p-threads $THREADS \
--p-confidence $CONFIDENCE_PERCENTAGE \
--p-minimum-base-quality $MINIMUM_BASE_QUALITY \
--output-dir $SHOTGUN_FOLDER/results/$ANALYSIS_NAME \
--p-report-minimizer-data
READ_LENGTH=150
echo "Running Bracken estimation..."
qiime moshpit estimate-bracken \
--i-bracken-db "$SHOTGUN_FOLDER/kraken2-databases/$REF_DATABASE_NAME/brackendb_$REF_DATABASE_NAME.qza" \
--p-read-len $READ_LENGTH \
--i-kraken-reports $SHOTGUN_FOLDER/results/$ANALYSIS_NAME/reports.qza \
--o-reports $SHOTGUN_FOLDER/results/$ANALYSIS_NAME/bracken-reports.qza \
--o-taxonomy $SHOTGUN_FOLDER/results/$ANALYSIS_NAME/taxonomy-bracken.qza \
--o-table $SHOTGUN_FOLDER/results/$ANALYSIS_NAME/table-bracken.qza
```
However, Brakcen has always given errors, since almost all the results from Kraken2 were 100% unclassified.
(Taking advantage of this comment I would like to ask something: Imagine that I have 10 samples and 8 of them have actually results, but 2 don't (these two could have 100% unclassified results). Would Bracken run correctly? Or is it necessary to remove those that don't have results?)
\*\* I downloaded and created the kraken databases following the steps from the tutorial I mentioned above:
> [@Importing Kraken2 and bracken databases into qiime2!](https://forum.qiime2.org/t/importing-kraken2-and-bracken-databases-into-qiime2/28384):
>
> Hello all, With the release of Qiime2-shotgun and [shotgun metagenomics tutorial](https://forum.qiime2.org/t/draft-tutorial-for-shotgun-metagenomics-with-qiime-2/28040). I'm just giving a quick writeup/tutorial on how to import precompiled [kraken2 and bracken databases](https://benlangmead.github.io/aws-indexes/k2). The first step is to download the appropriate database. My metagenomes are from environmental biofilms and have representatives from across the tree of life, however (and I have tried!) the full nucleotide database was too large for my computer. For this tutorial I'll use the 'PlusPFP with DB capped at 16 GB' Databβ¦
Thank youuu in advance for your help!
---
### Author:  [@misialq](https://forum.qiime2.org/u/misialq)
#### Post date: [March 6, 2024, 6:47am UTC](https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171/16 "2024-03-06T06:47:06Z")
Hi @MiriamGorostidi,
Thanks for sharing those! Your commands seem to be ok - I'm not sure what's going on. I see you did not run the `classify-kraken2` command in the verbose mode - could you by any chance re-run it with the `--verbose` flag and share the log? I'm curious to see what Kraken is saying while it's running... Once you've done that, do you think you could also share the reports qza file (if it's not too large)?
Thanks!
Michal
---
### Author:  [@MiriamGorostidi](https://forum.qiime2.org/u/MiriamGorostidi)
#### Post date: [March 6, 2024, 8:27pm UTC](https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171/17 "2024-03-06T20:27:23Z")
Hi @misialq !
Yes of course, I am already running it with --verbose. However, where is the .log file saved? How can I read it?
Thank you again!
---
### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [March 7, 2024, 6:10am UTC](https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171/18 "2024-03-07T06:10:29Z")
Hi @MiriamGorostidi ,
> [@MiriamGorostidi](#):
>
> I am already running it with --verbose. However, where is the .log file saved? How can I read it?
When running in `--verbose` mode messages will just be written directly into the terminal and are not saved anywhere, but you can read them directly there.
---
### Author:  [@MiriamGorostidi](https://forum.qiime2.org/u/MiriamGorostidi)
#### Post date: [March 7, 2024, 9:47pm UTC](https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171/19 "2024-03-07T21:47:13Z")
Hii!!
Here's part of the output that appears in the terminal: (It is almost the same for all the samples.. 0 sequences classify):
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.
Command: kraken2 --threads 10 --confidence 0.6 --minimum-base-quality 20 --minimum-hit-groups 2 --report-minimizer-data --db /pool0/home/mgorostidi/tmpdirs/qiime2/mgorostidi/data/b2987de0-d162-427d-b2f0-a59b08fc60c0/data --paired --report /pool0/home/mgorostidi/tmpdirs/q2-Kraken2ReportDirectoryFormat-p0sye63s/11326-Q-76401-0036-2018-02-10.report.txt --output /pool0/home/mgorostidi/tmpdirs/q2-Kraken2OutputDirectoryFormat-zm788ojt/11326-Q-76401-0036-2018-02-10.output.txt /pool0/home/mgorostidi/tmpdirs/qiime2/mgorostidi/data/48ac24f2-5421-4327-8efe-3f4bf47cefeb/data/11326-Q-76401-0036-2018-02-10\_38\_L001\_R1\_001.fastq.gz /pool0/home/mgorostidi/tmpdirs/qiime2/mgorostidi/data/48ac24f2-5421-4327-8efe-3f4bf47cefeb/data/11326-Q-76401-0036-2018-02-10\_157\_L001\_R2\_001.fastq.gz
Loading database information... done.
188636 sequences (55.78 Mbp) processed in 1.188s (9525.0 Kseq/m, 2816.73 Mbp/m).
0 sequences classified (0.00%)
188636 sequences unclassified (100.00%)
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.
Command: kraken2 --threads 10 --confidence 0.6 --minimum-base-quality 20 --minimum-hit-groups 2 --report-minimizer-data --db /pool0/home/mgorostidi/tmpdirs/qiime2/mgorostidi/data/b2987de0-d162-427d-b2f0-a59b08fc60c0/data --paired --report /pool0/home/mgorostidi/tmpdirs/q2-Kraken2ReportDirectoryFormat-p0sye63s/11326-Q-76401-0036-2018-02-12.report.txt --output /pool0/home/mgorostidi/tmpdirs/q2-Kraken2OutputDirectoryFormat-zm788ojt/11326-Q-76401-0036-2018-02-12.output.txt /pool0/home/mgorostidi/tmpdirs/qiime2/mgorostidi/data/48ac24f2-5421-4327-8efe-3f4bf47cefeb/data/11326-Q-76401-0036-2018-02-12\_39\_L001\_R1\_001.fastq.gz /pool0/home/mgorostidi/tmpdirs/qiime2/mgorostidi/data/48ac24f2-5421-4327-8efe-3f4bf47cefeb/data/11326-Q-76401-0036-2018-02-12\_158\_L001\_R2\_001.fastq.gz
Loading database information... done.
415307 sequences (123.18 Mbp) processed in 2.423s (10284.0 Kseq/m, 3050.29 Mbp/m).
0 sequences classified (0.00%)
415307 sequences unclassified (100.00%)
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.
Command: kraken2 --threads 10 --confidence 0.6 --minimum-base-quality 20 --minimum-hit-groups 2 --report-minimizer-data --db /pool0/home/mgorostidi/tmpdirs/qiime2/mgorostidi/data/b2987de0-d162-427d-b2f0-a59b08fc60c0/data --paired --report /pool0/home/mgorostidi/tmpdirs/q2-Kraken2ReportDirectoryFormat-p0sye63s/11326-Q-76401-0037-2018-03-12.report.txt --output /pool0/home/mgorostidi/tmpdirs/q2-Kraken2OutputDirectoryFormat-zm788ojt/11326-Q-76401-0037-2018-03-12.output.txt /pool0/home/mgorostidi/tmpdirs/qiime2/mgorostidi/data/48ac24f2-5421-4327-8efe-3f4bf47cefeb/data/11326-Q-76401-0037-2018-03-12\_40\_L001\_R1\_001.fastq.gz /pool0/home/mgorostidi/tmpdirs/qiime2/mgorostidi/data/48ac24f2-5421-4327-8efe-3f4bf47cefeb/data/11326-Q-76401-0037-2018-03-12\_159\_L001\_R2\_001.fastq.gz
Loading database information... done.
482549 sequences (140.00 Mbp) processed in 2.685s (10784.3 Kseq/m, 3128.71 Mbp/m).
2 sequences classified (0.00%)
482547 sequences unclassified (100.00%)
---
### Author:  [@gregcaporaso](https://forum.qiime2.org/u/gregcaporaso)
#### Post date: [March 12, 2024, 11:27pm UTC](https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171/20 "2024-03-12T23:27:18Z")
---
### Author:  [@cherman2](https://forum.qiime2.org/u/cherman2)
#### Post date: [March 28, 2024, 3:22pm UTC](https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171/21 "2024-03-28T15:22:08Z")
Hi @MiriamGorostidi,
Sorry for the delay!
Our developers are currently hosting a workshop but they will respond as soon as possible!
Thank you for your patience.
[Next page](https://forum.qiime2.org/t/q2-shotgun-bracken-error/29171.md?page=2)