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aidenlab / 3d-dna

3D de novo assembly (3D DNA) pipeline
MIT License
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Not including fragment map and not geneated the final fasta file use the run-asm-pipeline-post-review #178

Open Jiangjiangzhang6 opened 9 months ago

Jiangjiangzhang6 commented 9 months ago

the genome was ultra large scale about 23G, after I motif the assembly via the juicerbox, and conduct the next step with the command "bash ~/software/3d-dna-master/run-asm-pipeline-post-review.sh -r ../fusion_second2.0.review.assembly ../fusion_second2.fasta ../aligned/merged_nodups.txt"

but there was not any fasta file generated . I check the log file image image

how could I headle with this bug, thank you

Djangodu commented 7 months ago

the genome was ultra large scale about 23G, after I motif the assembly via the juicerbox, and conduct the next step with the command "bash ~/software/3d-dna-master/run-asm-pipeline-post-review.sh -r ../fusion_second2.0.review.assembly ../fusion_second2.fasta ../aligned/merged_nodups.txt"

but there was not any fasta file generated . I check the log file image image

how could I headle with this bug, thank you

hello, friend I miss the same issue, all the same~ if you have the solution, please show it and generous share the method.

Snipaste_2024-03-22_10-26-11
Jiangjiangzhang6 commented 7 months ago

the genome was ultra large scale about 23G, after I motif the assembly via the juicerbox, and conduct the next step with the command "bash ~/software/3d-dna-master/run-asm-pipeline-post-review.sh -r ../fusion_second2.0.review.assembly ../fusion_second2.fasta ../aligned/merged_nodups.txt" but there was not any fasta file generated . I check the log file image image how could I headle with this bug, thank you

hello, friend I miss the same issue, all the same~ if you have the solution, please show it and generous share the method. Snipaste_2024-03-22_10-26-11

hello, you should check your input fasta, maybe you can use the seqkit or seqtik the reason maybe the fasta contain the other information that not ATGC ,like X , space ,or others

Djangodu commented 7 months ago

the genome was ultra large scale about 23G, after I motif the assembly via the juicerbox, and conduct the next step with the command "bash ~/software/3d-dna-master/run-asm-pipeline-post-review.sh -r ../fusion_second2.0.review.assembly ../fusion_second2.fasta ../aligned/merged_nodups.txt" but there was not any fasta file generated . I check the log file image image how could I headle with this bug, thank you

hello, friend I miss the same issue, all the same~ if you have the solution, please show it and generous share the method. Snipaste_2024-03-22_10-26-11

hello, you should check your input fasta, maybe you can use the seqkit or seqtik the reason maybe the fasta contain the other information that not ATGC ,like X , space ,or others

So, did your fasta file with this problem? and after your check and modification, re-run this pipeline successful?