barcode tool usage about celescope

[zhouyiqi91]

You probably ran the barcode.py program directly from source. For example:
python celescope/tools/barcode.py -h
This is not the correct way to run the program.
After you have installed celescope, you can run the barcode program like this:
celescope rna barcode -h

Please take a look at
https://github.com/singleron-RD/CeleScope/blob/master/docs/quick_start.md

[zhouyiqi91]

Sorry for the late reply. Running the barcode step requires running the sample step first.

celescope rna sample \
 --outdir ./ \
 --sample test \
 --chemistry auto \
 --fq1 ../../../data/rawDATA_TargetedAmplification/TA-1C_AHW75CBGXL_R1_PE150.fastq.gz

[singlecoated]

That was exactly the case, I will try running the program within celescope itself. Many thanks for your fast help !

[singlecoated]

Good morning,

thanks to your previous help I could successfully run the barcode tool calling it from the celescope binary, much appreciated.

Unfortunately, I now have a new error message. Here I paste the output with the calling command and messages. I can identify a previous warning related to the sample_summary.metrics and an 'assay not found', I'm not sure if it has something to do with that.

Just to clarify, I am running the barcode tool on a pair of fq files independently, don't have any full run of celescope (in case some kind of initial sampleinfo or config files have to be provided as is the case in other pipelines).

Also, barcode whitelist file and linkers are the ones dowloaded from this same github for the v3.0 chemistry.

Many thanks in advance.

--- CELESCOPE OUTPUT START ---

2023-04-12 12:03:50,137 - celescope.tools.barcode.barcode - INFO - start...
Args: Namespace(subparser_assay='rna', chemistry='auto', pattern=None, whitelist='./singleron_v3_bclist.txt', linker='./singleron_v3_linkers.txt', lowQual=0, lowNum=2, nopolyT=False, noLinker=False, filterNoPolyT=False, allowNoLinker=False, gzip=True, output_R1=False, fq1='../../../data/rawDATA_TargetedAmplification/TA-1C_AHW75CBGXL_R1_PE150.fastq.gz', fq2='../../../data/rawDATA_TargetedAmplification/TA-1C_AHW75CBGXL_R2_PE150.fastq.gz', match_dir=None, outdir='./', sample='test', thread='12', debug=True, func=<function barcode at 0x7f26b6653550>)
2023-04-12 12:03:50,137 - celescope.tools.barcode.parse_pattern - INFO - start...
2023-04-12 12:03:50,137 - celescope.tools.barcode.parse_pattern - INFO - done. time used: 0:00:00.000118
2023-04-12 12:03:50,157 - celescope.tools.barcode.get_mismatch_dict - INFO - start...
2023-04-12 12:03:50,162 - celescope.tools.barcode.get_mismatch_dict - INFO - done. time used: 0:00:00.005109
2023-04-12 12:03:50,167 - celescope.tools.barcode.get_mismatch_dict - INFO - start...
2023-04-12 12:03:50,177 - celescope.tools.barcode.get_mismatch_dict - INFO - done. time used: 0:00:00.010517
2023-04-12 12:03:50,177 - celescope.tools.barcode.parse_pattern - INFO - start...
2023-04-12 12:03:50,177 - celescope.tools.barcode.parse_pattern - INFO - done. time used: 0:00:00.000016
2023-04-12 12:03:50,192 - celescope.tools.barcode.get_mismatch_dict - INFO - start...
2023-04-12 12:03:50,196 - celescope.tools.barcode.get_mismatch_dict - INFO - done. time used: 0:00:00.004317
2023-04-12 12:03:50,197 - celescope.tools.barcode.get_mismatch_dict - INFO - start...
2023-04-12 12:03:50,284 - celescope.tools.barcode.get_mismatch_dict - INFO - done. time used: 0:00:00.086985
2023-04-12 12:03:50,285 - celescope.tools.barcode.parse_pattern - INFO - start...
2023-04-12 12:03:50,285 - celescope.tools.barcode.parse_pattern - INFO - done. time used: 0:00:00.000041
2023-04-12 12:03:50,287 - celescope.tools.barcode.get_mismatch_dict - INFO - start...
2023-04-12 12:03:50,332 - celescope.tools.barcode.get_mismatch_dict - INFO - done. time used: 0:00:00.045505
2023-04-12 12:03:50,334 - celescope.tools.barcode.get_mismatch_dict - INFO - start...
2023-04-12 12:03:50,461 - celescope.tools.barcode.get_mismatch_dict - INFO - done. time used: 0:00:00.127026
2023-04-12 12:03:50,461 - celescope.tools.barcode.parse_pattern - INFO - start...
2023-04-12 12:03:50,461 - celescope.tools.barcode.parse_pattern - INFO - done. time used: 0:00:00.000044
2023-04-12 12:03:50,463 - celescope.tools.barcode.get_mismatch_dict - INFO - start...
2023-04-12 12:03:50,465 - celescope.tools.barcode.get_mismatch_dict - INFO - done. time used: 0:00:00.001743
2023-04-12 12:03:50,497 - celescope.tools.barcode.get_mismatch_dict - INFO - start...
2023-04-12 12:03:50,590 - celescope.tools.barcode.get_mismatch_dict - INFO - done. time used: 0:00:00.093359
2023-04-12 12:03:50,591 - celescope.tools.barcode.parse_pattern - INFO - start...
2023-04-12 12:03:50,591 - celescope.tools.barcode.parse_pattern - INFO - done. time used: 0:00:00.000046
2023-04-12 12:03:50,624 - celescope.tools.barcode.get_mismatch_dict - INFO - start...
2023-04-12 12:03:50,625 - celescope.tools.barcode.get_mismatch_dict - INFO - done. time used: 0:00:00.001766
2023-04-12 12:03:50,626 - celescope.tools.barcode.get_mismatch_dict - INFO - start...
2023-04-12 12:03:50,802 - celescope.tools.barcode.get_mismatch_dict - INFO - done. time used: 0:00:00.175075
2023-04-12 12:03:50,802 - celescope.tools.barcode.check_chemistry - INFO - start...
../../../data/rawDATA_TargetedAmplification/TA-1C_AHW75CBGXL_R1_PE150.fastq.gz
2023-04-12 12:03:50,802 - celescope.tools.barcode.get_chemistry - INFO - start...
2023-04-12 12:03:51,052 - celescope.tools.barcode.get_chemistry - INFO - [('scopeV3.0.1', 9490), ('scopeV2.2.1', 1), ('scopeV2.1.1', 0)]
2023-04-12 12:03:51,053 - celescope.tools.barcode.get_chemistry - INFO - chemistry: scopeV3.0.1
2023-04-12 12:03:51,053 - celescope.tools.barcode.get_chemistry - INFO - done. time used: 0:00:00.250556
2023-04-12 12:03:51,053 - celescope.tools.barcode.check_chemistry - INFO - done. time used: 0:00:00.250662
2023-04-12 12:03:51,053 - celescope.tools.step.get_slot_key - INFO - start...
2023-04-12 12:03:51,053 - celescope.tools.step.get_slot_key - WARNING - Assay not found in sample_summary.metrics
Traceback (most recent call last):
File "/home/oreina/miniconda3/envs/celescope/bin/celescope", line 8, in
sys.exit(main())
File "/home/oreina/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/celescope.py", line 45, in main
args.func(args)
File "/home/oreina/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 46, in wrapper
result = func(*args, **kwargs)
File "/home/oreina/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/barcode.py", line 728, in barcode
with Barcode(args, display_title='Demultiplexing') as runner:
File "/home/oreina/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/barcode.py", line 200, in init
self._assay = self.get_slot_key(
File "/home/oreina/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/utils.py", line 46, in wrapper
result = func(*args, **kwargs)
File "/home/oreina/miniconda3/envs/celescope/lib/python3.9/site-packages/celescope/tools/step.py", line 205, in get_slot_key
return self.__content_dict[slot][step_name + '_summary'][key]
KeyError: 'sample_summary'

--- CELESCOPE OUTPUT END ---

[singlecoated]

No worries, and MANY thanks for your help, I could run everything without problems now.

Warm regards.