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bichangwei / PMAT

An efficient assembly tool for plant mitochondrial genome
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What is the nextdenovo.cfg file #10

Open SCQUchenyang opened 7 months ago

SCQUchenyang commented 7 months ago

Thank you for developing such a useful tool as PMAT. I encountered a problem while using it. I am trying to assemble the mitochondrial genome of Adiantum capillus-veneris. I downloaded one of the PacBio datasets (SRR13170459) from NCBI. Then I converted it to fastq. image

I used the following command to assemble it.

/data/Zhaijx/cheny/software/PMAT-1.5.2/bin/PMAT autoMito -i SRR13170459.lite.1.fastq -o ./test_clr -st clr -g 4800m -cs nextDenovo -np nextDenovo -cpu 8 -cfg nextdenovo.cfg -m

But an error was reported

Traceback (most recent call last):
  File "modules/PMAT.py", line 687, in <module>
    args.func(args)
  File "modules/PMAT.py", line 119, in autoMito
    high_quality_seq = correct_sequences.ReadsPreprocess(CANU_PATH, args.cpu, readstype, Output, args.correctcfg).NextDenovo_correct(NEXTDENOVO_PATH)
  File "/data/Zhaijx/cheny/software/PMAT-1.5.2/bin/../modules/correct_sequences.py", line 62, in NextDenovo_correct
    if self.config_info()[1] == 'correct':
  File "/data/Zhaijx/cheny/software/PMAT-1.5.2/bin/../modules/correct_sequences.py", line 137, in config_info
    with open(self.cfg, 'r') as fin:
FileNotFoundError: [Errno 2] No such file or directory: 'nextdenovo.cfg'
[68776] Failed to execute script 'PMAT' due to unhandled exception!

Hope to get your help

bichangwei commented 7 months ago

Thank you for using PMAT. You can correct the CLR data using Canu or Nextdenovo before using PMAT, then input the corrected data as HiFi data.

Best,

Changwei NJFU

---- Replied Message ---- | From | @.> | | Date | 02/28/2024 16:54 | | To | bichangwei/PMAT @.> | | Cc | Subscribed @.***> | | Subject | [bichangwei/PMAT] What is the nextdenovo.cfg file (Issue #10) |

Thank you for developing such a useful tool as PMAT. I encountered a problem while using it. I am trying to assemble the mitochondrial genome of Adiantum capillus-veneris. I downloaded one of the PacBio datasets (SRR13170459) from NCBI. Then I converted it to fastq. image.png (view on web)

I used the following command to assemble it.

/data/Zhaijx/cheny/software/PMAT-1.5.2/bin/PMAT autoMito -i SRR13170459.lite.1.fastq -o ./test_clr -st clr -g 4800m -cs nextDenovo -np nextDenovo -cpu 8 -cfg nextdenovo.cfg -m

But an error was reported

Traceback (most recent call last): File "modules/PMAT.py", line 687, in args.func(args) File "modules/PMAT.py", line 119, in autoMito high_quality_seq = correct_sequences.ReadsPreprocess(CANU_PATH, args.cpu, readstype, Output, args.correctcfg).NextDenovo_correct(NEXTDENOVO_PATH) File "/data/Zhaijx/cheny/software/PMAT-1.5.2/bin/../modules/correct_sequences.py", line 62, in NextDenovo_correct if self.config_info()[1] == 'correct': File "/data/Zhaijx/cheny/software/PMAT-1.5.2/bin/../modules/correct_sequences.py", line 137, in config_info with open(self.cfg, 'r') as fin: FileNotFoundError: [Errno 2] No such file or directory: 'nextdenovo.cfg' [68776] Failed to execute script 'PMAT' due to unhandled exception!

Hope to get your help

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