Run quality checks failed

[AhlemBoudell]

Hi,

Sorry for disturbing again but when i ran the second step in the cluster it terminated with the errors in the following files, any idea what caused that?

slurm-9815462_2.log slurm-9815462_1.log config-hicproNew.txt

[nservant]

Hi Could you check if you have another log file with a clear error ? in the log folder ? In addition, note that LIGATION_SITE = ^GATC is not correct. Here, HiC-Pro is expecting the LIGATION motif, not the RESTRICTION one. So, in case of DpnII enzyme, it should be GATCGATC Best

[AhlemBoudell]

Thanks for the note! Will correct that now, but should i re-run the first step then?

hicproNew.log

[nservant]

yes it would be better ... sorry for that. Could you check in the Rout files (in the logs) if you see any error ?

[AhlemBoudell]

Among the log files, those are the ones that show an issue i think one is warnings about the restriction fragments u mentioned . i will re-run it now .. thanks alot! but i also faced the issue with the previous run when i didnt provide any ligation site

mapped_2hic_fragments.log plot_hic_contacts.log

[nservant]

There are no errors in your logs file ? Indeed you have quite a lot of "reads not assigned to restriction fragments", but this is not related to the LIGATION_SITE parameter. This is more a matter of restriction fragment BED file. For instance a common mistake is to use different chromosomes names between the bowtie2 indexes and the Bed files ...

[AhlemBoudell]

those are all the log files for one of my 2 samples.

and i double checked the bed file with the fasta file that i digested and both had the same chromosomes names.

bowtie_CEC_4_H7KG7CCX2_L1_2P_global_ce11.log

bowtie_CEC_4_H7KG7CCX2_L1_2P_ce11.bwt2glob.unmap_local.log bowtie_CEC_4_H7KG7CCX2_L1_1P_ce11.bwt2glob.unmap_local.log bowtie_CEC_4_H7KG7CCX2_L1_1P_global_ce11.log

[AhlemBoudell]

mapped_2hic_fragments.log mergeSAM.log merge_stat.log merge_stats.log

[AhlemBoudell]

merge_valid_interactions.log readsTrimming.log

[AhlemBoudell]

Hi,

In the new run I found this error in one of the log files:

/sw/csi/R/3.5.0/el7_intel2018/lib64/R/bin/exec/R: error while loading shared libraries: libiomp5.so: cannot open shared object file: No such file or directory

after it exited with this error: Fri Mar 27 03:09:39 +03 2020 Run quality checks for all samples ... /sw/csi/hicpro/2.10.0/el7_gnu6.4.0/HiC-Pro_2.10.0/scripts/make_plots.sh -c /ibex/scratch/projects/c2055/config-hicproNew.txt -p "all" >> hicproNew.log make: *** [hic_qc] Error 127

Any idea?

[nservant]

Hi It looks like your R installation has some issue ... N

[AhlemBoudell]

Thanks alot for all the help!