Question on qiime import tools - semantic type sampleData

[Sammi (Jiyoung Kim)]

Hi Qiime2!

I was able to solve other problems previously uploaded since I had to change platform to actually run my data set. During this procedure, I ran into some problems.

So I am running Qiime on our institutes cluster which provides tremendous giga and ram to run it. The problem is that when I try to run my Qiime just importing my FASTQ files along with manifest files. it gives out the error regarding SampleData[sequencewithquality].

I am uploading the script that I ran:

#!/bin/bash

#SBATCH --partition=batch

#SBATCH --job-name=manifest

#SBATCH --ntasks=1

#SBATCH --time=24:00:00

#SBATCH --mem=10G

#SBATCH --mail-type=END,FAIL

#SBATCH [email protected]

cd $SLURM_SUBMIT_DIR

module load QIIME2/2020.6

export LC_ALL=en_US.utf-8

export LANG=en_US.utf-8

qiime tools import \

--type 'SampleData[SequenceWithQuality]' \

--input-path 16smanifest_forward4.txt \

--output-path manifest.qza \

--input-format SingleEndFastqManifestPhred33

And for the error msg is:

Traceback (most recent call last):

  File "/apps/eb/QIIME2/2020.6/lib/python3.6/site-packages/q2cli/builtin/tools.$

    view_type=input_format)

  File "/apps/eb/QIIME2/2020.6/lib/python3.6/site-packages/qiime2/sdk/result.py$

    validate_level='max')

  File "/apps/eb/QIIME2/2020.6/lib/python3.6/site-packages/qiime2/sdk/result.py$

    output_dir_fmt = pm.get_directory_format(type)

  File "/apps/eb/QIIME2/2020.6/lib/python3.6/site-packages/qiime2/sdk/plugin_ma$

    % semantic_type)

TypeError: Semantic type SampleData[SequenceWithQuality] does not have a compat$

An unexpected error has occurred:

  Semantic type SampleData[SequenceWithQuality] does not have a compatible directory format. 

See above for debug info.

I am also attaching one of my FASTQ file.
I think there is only one other option if this sample data format is wrong despite my FASTQ file being single-ended.16smanifest_forward4.txt (7.9 KB)

FASTQ file is in this:

Qiime2-Slurm

Things I tried:

1. I tried to change the --type sampledata[pairedend]
2. change the path in manifest files ( like $PWD/workDir/1.fastq or $PWD/1.fastq )

Is there anyone who can tell me what is wrong..?

[jwdebelius (Justine Debelius)]

Hi @Sammi,

I’ve moved to user support. I think the semantic type should be SampleData[SequencesWithQuality], but I often check the tutorial or use the --show-importable-types flag to check my spelling.

Best,
Justine

[Sammi (Jiyoung Kim)]

Hi @jwdebelius!

Thanks for the suggestion, I also began the script with Sampledata[SequencesWithQuality] which it never worked. I really cant find a reason why though or even other alternatives…?

[jwdebelius (Justine Debelius)]

Hi @Sammi,

If it’s a new or different error message when you run the command, it might be good to post it as a new thread.

qiime tools import \
--type 'SampleData[SequenceWithQuality]' \
--input-path 16smanifest_forward4.txt \
--output-path manifest.qza \
--input-format SingleEndFastqManifestPhred33

(As a side note, I might see if you can get an interactive session to debug with a subset of your data).

Best,
Justine

[Sammi (Jiyoung Kim)]

So I ran the script and here is what it says:

Traceback (most recent call last):
File “/apps/eb/QIIME2/2020.6/lib/python3.6/site-packages/q2cli/builtin/tools.py”, line 158, in import_data
view_type=input_format)
File “/apps/eb/QIIME2/2020.6/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 241, in import_data
validate_level=‘max’)
File “/apps/eb/QIIME2/2020.6/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 255, in _from_view
output_dir_fmt = pm.get_directory_format(type)
File “/apps/eb/QIIME2/2020.6/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py”, line 313, in get_directory_f$
% semantic_type)
TypeError: Semantic type SampleData[SequenceWithQuality] does not have a compatible directory format.

An unexpected error has occurred:

Semantic type SampleData[SequenceWithQuality] does not have a compatible directory format.

See above for debug info.

I would really appreciate if I could get to do interactive session to debug with a subset of data!

[jwdebelius (Justine Debelius)]

Hi @Sammi,

Your semantic type is still incorrect: you need to use SampleData[SequencesWithQuality] instead of SampleData[SequenceWithQuality].

You should check with your sys admin about interactive sesssion. A lot of the servers I’ve worked on have allowed that.

Best,
Justine

[Sammi (Jiyoung Kim)]

So I tried with the SampleData[SequencesWithQuality] and there was some improvement and showed an error msg for the manifest files format. I solved the issue by using csv. the format file and it has worked! I haven’t seen the manifest.qza file to verify it worked well but I think it worked with a reasonable amount of time! with almost 200 samples.

Thank you

[jwdebelius (Justine Debelius)]

Hi @Sammi,

Whooo!

I’m glad you’ve solved it.

Best,
Justine