search

aidenlab / juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
http://aidenlab.org
MIT License
413 stars 181 forks source link

aligned/merged1.txt does not exist or does not contain any reads. #294

Closed 1580542426 closed 1 year ago

1580542426 commented 1 year ago

When I use HiC to help assemble genome, I run the following code: /ME4012_Vol0002/Ahome_Dir/hechuanmeng/SY_genome/SY_genome/sanya_genome/raw_data/3d-DNA/juicer/scripts/juicer.sh -t 30 -g RT -z reference/SanyaOcu.p_ctg.fa -y restriction_sites/SanyaOcu.p_ctg_DpnII.txt -p restriction_sites/SanyaOcu.p_ctg.chrom.sizes -D /ME4012_Vol0002/Ahome_Dir/hechuanmeng/SY_genome/SY_genome/sanya_genome/raw_data/3d-DNA/juicer/ -s DpnII The following errors are reported: Picked up _JAVA_OPTIONS: -Xmx1024m -Xms1024m Exception in thread "main" java.lang.RuntimeException: Unknown command: statistics at juicebox.tools.HiCTools.main(HiCTools.java:98) Picked up _JAVA_OPTIONS: -Xmx1024m -Xms1024m Exception in thread "main" java.lang.RuntimeException: Unknown command: statistics at juicebox.tools.HiCTools.main(HiCTools.java:98) Picked up _JAVA_OPTIONS: -Xmx150000m -Xms150000m /ME4012_Vol0002/Ahome_Dir/hechuanmeng/SY_genome/SY_genome/sanya_genome/raw_data/3d-DNA/aligned/merged1.txt does not exist or does not contain any reads. Could you tell me how to solve this problem?Thanks!

moshe-olshansky commented 1 year ago

Hi there, Could you ask this question via the 3D Genomics newsgroup? When you do so, please list the structure of your /ME4012_Vol0002/Ahome_Dir/hechuanmeng/SY_genome/SY_genome/sanya_genome/raw_data/3d-DNA/juicer and /ME4012_Vol0002/Ahome_Dir/hechuanmeng/SY_genome/SY_genome/sanya_genome/raw_data/3d-DNA/juicer/scripts folders.

1580542426 commented 1 year ago

Thank you. The problem has been solved, but there are new problems

1580542426 commented 1 year ago

[fsync] Input/output error ***! Alignment of /ME4012_Vol0002/Ahome_Dir/hechuanmeng/SY_genome/SY_genome/sanya_genome/raw_data/3d-DNA/splits/SY_R1.fastq.gz /ME4012_Vol0002/Ahome_Dir/hechuanmeng/SY_genome/SY_genome/sanya_genome/raw_data/3d-DNA/splits/SY_R2.fastq.gz failed.

moshe-olshansky commented 1 year ago

I think that before that statement the aligner (bwa) should have issued its own statements. What did it say?

1580542426 commented 1 year ago

I think that before that statement the aligner (bwa) should have issued its own statements. What did it say?

It doesn't say anything.I would like to ask whether the reference genome file required for HIC auxiliary assembly is the contigs file assembled by HIFI or the reference genome file attached to chromosomes by others.Thanks!

sa501428 commented 1 year ago

If you're working with genome assembly, you should post this question to the forum: https://groups.google.com/g/3d-genomics Also see: https://www.dnazoo.org/methods

sa501428 commented 1 year ago

@1580542426 please stop copy-pasting your question to other unrelated Github issues - these are intended for tracking bugs. Questions about how to run Juicer or 3D-DNA should be asked on the forum (https://groups.google.com/g/3d-genomics) and will get answered there. Thanks!