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

[1580542426]

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]

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]

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

[1580542426]

[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]

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

[1580542426]

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]

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]

@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!