run-asm-pipeline.sh doesnt create .hic files

[Andrea Garavito]

Good day to all.

I'm currently trying to run the run-asm-pipeline.sh pipeline to analyze a plant genome of abour 2.4G. As I'm having problems running the pipeline on the cluster that I use, I tried to run it with the GSM1551550_HIC001_merged_nodups.txt and GSE95797_Hs1.fasta data downloaded from the ncbi.

The pipeline ran, but didn't create any .hic files. Trying to know why I stumbled upon this discussion with a similar problem:

https://www.aidenlab.org/forum.html?place=topic%2F3d-genomics%2FUB2-LVp2foY%2Fdiscussion

I did the same as suggested, that is run the  visualize/run-asm-visualizer.sh independently as follows (I'm using SGE as job manager, and a node with more memory, otherwise, I have the message : Error occurred during initialization of VM Could not reserve enough space for 50331648KB object heap)

module load system/java/jre8
module load system/parallel/20150822
qsub -q bigmem.q -b yes -V -N test -cwd -pe parallel_smp 8 "~/bin/visualize/run-asm-visualizer.sh ~/test/GSE95797_Hs1.0.cprops ~/test/GSE95797_Hs1.0.asm ~/test/GSM1551550_HIC001_merged_nodups.txt"

And that gave me:

...Remapping contact data from the original contig set to assembly
...Building track files
...Building the hic file
temp.GSE95797_Hs1.0.asm_mnd.txt does not exist or does not contain any reads.

Effectively, the file is empty.

Do you have any suggestions?

Thank you

Andrea

[Olga Dudchenko]

Hi Andrea, Most likely your fasta labels in the GSE file and in HIC001 files don't match. Make sure you use the fasta that was used during the alignment step when creating the mnd file. Best, -Olga

[Andrea Garavito]

Thanks Olga for your answer.

Effectively, it seems that I downloaded the wrong mnd file.

Best

Andrea

[thapap...@gmail.com]

Hi,

run-asm-pipeline.sh gives me .FINAL.assembly, .FINAL.fasta but no .FINAL.hic output. Is it error if not which .hic should be used with .FINAL.assembly for visualization in Juicebox.

Any help would be great.

Thanks

[Olga Dudchenko]

Hello,

This was answered on github.

Best,

Olga

[thapap...@gmail.com]

Hi Olaga,

I looked into the github these are the posts about the run-asm-pipeline.sh. 

run-asm-pipeline.sh with awk error #38
tail: write error: Broken pipe #46
Java error in run-asm-pipeline.sh #52
run-asm-pipeline-post-review.sh assembly review FINAL.fasta full of Ns #68
run-asm-pipeline-post-review.sh generate .hic file does not look the same as I have adjusted. #66
error with run-asm-pipeline.sh #100
The produced hic file by run-asm-pipeline.sh is only 400k #103

It would be great if you could let me know any posts i have missed.

All the post discuss about the errors while running run-asm-pipeline.sh (some .hic files were not created).

For me its running, i am getting .hic files (-p_utg.0.hic, -p_utg.1.hic, -p_utg.2.hic, -p_utg.polished.hic, -p_utg.rawchrom.hic, -p_utg.resolved.hic), the issue is that i am not getting the " .FINAL.hic" file but i get the .FINAL.assembly, .FINAL.fasta.

Which .hic file (-p_utg.0.hic, -p_utg.1.hic, -p_utg.2.hic, -p_utg.polished.hic, -p_utg.rawchrom.hic, -p_utg.resolved.hic) can i use with the FINAL.assembly file to view.

Thank you so much.

Best

[Olga Dudchenko]

https://github.com/aidenlab/3d-dna/issues/106