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pinellolab / CRISPResso2

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
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How to solve Error 0? #416

Closed ShawnYuXX closed 5 months ago

ShawnYuXX commented 5 months ago

(crispresso2_env) YudeMacBook-Pro:NGS shwan$ CRISPRessoPooled -r1 PE-reporter-seq-LGC16574_L2_1.fq.gz -r2 PE-reporter-seq-LGC16574_L2_2.fq.gz -f AMPLICONS_FILE_PE_reporter.txt --name ONLY_AMPLICONS_240409 > NGS_XXYu240409.log INFO @ Tue, 09 Apr 2024 21:05:35: Creating Folder CRISPRessoPooled_on_ONLY_AMPLICONS_240409

INFO @ Tue, 09 Apr 2024 21:05:35: Done!

INFO @ Tue, 09 Apr 2024 21:05:35: Checking dependencies...

INFO @ Tue, 09 Apr 2024 21:05:35: All the required dependencies are present!

INFO @ Tue, 09 Apr 2024 21:05:35: Only the Amplicon description file was provided. The analysis will be perfomed using only the provided amplicons sequences.

INFO @ Tue, 09 Apr 2024 21:05:35: Processing input

INFO @ Tue, 09 Apr 2024 21:05:35: Merging paired sequences with Flash...

INFO @ Tue, 09 Apr 2024 21:06:16: Done!

CRITICAL @ Tue, 09 Apr 2024 21:06:24:

ERROR: 0

Colelyman commented 5 months ago

Would you mind rerunning with the --debug flag and posting the output? If you could also provide the contents of CRISPResso_RUNNING_LOG.txt, we can see the output of Flash and see if something went wrong there.

ShawnYuXX commented 5 months ago

The running. log like this:

                         ~~~CRISPRessoPooled~~~                             
  -Analysis of CRISPR/Cas9 outcomes from POOLED deep sequencing data-       

          _                                                   _             
         '  )                                                '  )           
         .-'            _______________________              .-'            
        (____          | __  __  __     __ __  |            (____           
     C)|     \         ||__)/  \/  \|  |_ |  \ |         C)|     \          
       \     /         ||   \__/\__/|__|__|__/ |           \     /          
        \___/          |_______________________|            \___/           

                      [CRISPResso version 2.2.14]

[Note that starting in version 2.3.0 FLASh and Trimmomatic will be replaced by fastp for read merging and trimming. Accordingly, the --flash_command and --trimmomatic_command parameters will be replaced with --fastp_command. Also, --trimmomatic_options_string will be replaced with --fastp_options_string.

Also in version 2.3.0, when running CRISPRessoPooled in mixed-mode (amplicon file and genome are provided) the default behavior will be as if the --demultiplex_only_at_amplicons parameter is provided. This change means that reads and amplicons do not need to align to the exact locations.] [For support contact k.clement@utah.edu or support@edilytics.com]

ShawnYuXX commented 5 months ago

User CRISPResso version 2.2.14 [Command used]: /Users/shwan/opt/anaconda3/envs/crispresso2_env/bin/CRISPRessoPooled -r1 PE_reporter_seq_LGC16574_L2_1.fq.gz -r2 PE_reporter_seq_LGC16574_L2_2.fq.gz -f AMPLICONS_FILE_PE.txt --name ONLY_AMPLICONS_240409

[Execution log]: Processing input Merging paired sequences with Flash... [FLASH] Starting FLASH v1.2.11 [FLASH] Fast Length Adjustment of SHort reads [FLASH]
[FLASH] Input files: [FLASH] PE_reporter_seq_LGC16574_L2_1.fq.gz [FLASH] PE_reporter_seq_LGC16574_L2_2.fq.gz [FLASH]
[FLASH] Output files: [FLASH] CRISPRessoPooled_on_ONLY_AMPLICONS_240409/out.extendedFrags.fastq.gz [FLASH] CRISPRessoPooled_on_ONLY_AMPLICONS_240409/out.notCombined_1.fastq.gz [FLASH] CRISPRessoPooled_on_ONLY_AMPLICONS_240409/out.notCombined_2.fastq.gz [FLASH] CRISPRessoPooled_on_ONLY_AMPLICONS_240409/out.hist [FLASH] CRISPRessoPooled_on_ONLY_AMPLICONS_240409/out.histogram [FLASH]
[FLASH] Parameters: [FLASH] Min overlap: 10 [FLASH] Max overlap: 100 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: true [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 12 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH]
[FLASH] Starting reader and writer threads [FLASH] Starting 12 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 150000 read pairs [FLASH] Processed 175000 read pairs [FLASH] Processed 200000 read pairs [FLASH] Processed 225000 read pairs [FLASH] Processed 250000 read pairs [FLASH] Processed 7475000 read pairs [FLASH] Processed 7486029 read pairs [FLASH]
[FLASH] Read combination statistics: [FLASH] Total pairs: 7486029 [FLASH] Combined pairs: 7441581 [FLASH] Innie pairs: 7424973 (99.78% of combined) [FLASH] Outie pairs: 16608 (0.22% of combined) [FLASH] Uncombined pairs: 44448 [FLASH] Percent combined: 99.41% [FLASH]
[FLASH] Writing histogram files. [FLASH]
[FLASH] FLASH v1.2.11 complete! [FLASH] 40.830 seconds elapsed Done!

ERROR: 0

ShawnYuXX commented 5 months ago

Thank you for your answer ! I found this problem was a formatting error in my document