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Dowell-Lab / FStitch

Fast Stitch Reader (FStitch) -- fast-processing tool written in C for the annotation of regions of active transcription.
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Ignacio FStitch error -- "provided vector X is empty" #8

Open magruca opened 5 years ago

magruca commented 5 years ago

In GitLab by @magr0763 on Sep 28, 2018, 10:09

Ignacio emailed me this issue earlier in the week.

$ /scratch/Shares/dowell/FStitch/fstitch-revisions_092118/FastReadStitcher/src/FStitch train -r /scratch/Shares/dowell/processed_groseq/bedtools/SRR1105737.trim.pos.bedGraph -t /Users/igtr4848/dowell_lab/ATAC-TF-detector/Fstitch_training/SRR1105737_fstitch_training.bed -o /scratch/Shares/dowell/processed_groseq/fstitch/SRR1105737.bedGraph.hmminfo

Strand specified: 4 NOTE: segmented strand not specified. Attempting to determine strand from reads histogram file... Input bedgraph file determined to be positive based on file contents. ERROR: provided vector X is empty. As such, there are no initial weights to report on. Regression failed. !!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!!!!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!!!!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!!!!parameter and x vectors are not same dimension!!!!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!!

!!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!!

!!parameter and x vectors are not same dimension!!

!!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!!!!parameter and x vectors are not same dimension!!

!!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!!

!!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!!!!parameter and x vectors are not same dimension!!

!!parameter and x vectors are not same dimension!! !!parameter and x vectors are not same dimension!! Deleted a 390 contigs totaling 34320 bytes.

He was trying to run train on a deepTools bedGraph output. However, as stated in the LLR issue I submitted, I was able to train on a deepTools bedGraph. That said, when he ran this line:

grep -v " 0" /scratch/Shares/dowell/processed_groseq/bedtools/SRR1105737.trim.pos.bedGraph

/scratch/Shares/dowell/processed_groseq/bedtools/SRR1105737.trim.pos.nozeros.bedGraph

to remove 0 values, the training ran correctly and he got a .hmminfo output. We need to isolate where this is breaking and resolve the error output.