hicDetectLoops dataset error

[TheCatalyticMicroChip]

I get data set error when I try to compute loops, even if I change -pit and the p-values.

Command line:
ln -s '/data/dnb02/galaxy_db/files/014/320/dataset_14320954.dat' 'matrix.h5' && hicDetectLoops --matrix 'matrix.h5' --peakWidth 6 --windowSize 10 --pValuePreselection 0.01 --peakInteractionsThreshold 5 --maximumInteractionPercentageThreshold 0.1 --pValue 0.01 --maxLoopDistance 2000000 --chromosomes 'chr1' --statisticalTest wilcoxon-rank-sum --outFileName output_loop.bedgraph --threads ${GALAXY_SLOTS:-4} -tpc ${GALAXY_SLOTS:-4}

Error:
An error occurred with this dataset: INFO:hicexplorer.hicDetectLoops:peak interactions threshold set to 5.0

[joachimwolff]

You need to share your history with me, this error here can mean all and everything.

//edit:

I successfully re-run the loop detection as it is described in the tutorial on GTN, I think you used maybe a wrong input data set. Please check if you really operate on GM12878 cell data set and not on the previously used dm3 matrix.

[TheCatalyticMicroChip]

I have shared my history with you. Thanks

[joachimwolff]

Your command seems alright for and the error is a bit meaningless. As I wrote, for me it was running successful, maybe it helps to download the data from the ftp server directly to your histroy (via Paste/Fetch data option) instead of importing it from the Shared Data. It could be that this file is also effected by our data loss.

[bgruening]

galaxy@sn04:~$ ll /data/dnb02/galaxy_db/files/014/320/dataset_14320954.dat
-rw-r--r--. 1 galaxy galaxy 1581838731 Mar 22 02:24 /data/dnb02/galaxy_db/files/014/320/dataset_14320954.dat

The dataset seems to contain data.

[joachimwolff]

As far as I remember this was clarified via e-mail. Please reopen if this is not correct and the issue is unsolved.