hi im trying to use it via singularity. i did the firs stepof Quantify IR
i think something is not working well but i can not put the finger on the reason i would like for you're help please:
this is the command i ran, the data is a very reliable data. the bam files was created well.
i ran this command
singularity run --bind /sci/labs/maayan.salton/adi8897:/data /sci/labs/maayan.salton/adi8897/master_project/IRFinder.sif BAM -r /data/IR_finder_venv/IRFinder-2.0-beta/REF/Human-GRCh38-release110 -d /data/master_project/SART3/irfinder/SRR21796788 /data/master_project/SART3/row_data/bam_files/sorted_files/SRR21796788_Aligned.out_sorted.bam
the error logfile did not say anything but: please look at this file it does not look well
i would like your help to understand it
IRFinder-IR-nondir.txt
hi im trying to use it via singularity. i did the firs stepof Quantify IR i think something is not working well but i can not put the finger on the reason i would like for you're help please: this is the command i ran, the data is a very reliable data. the bam files was created well.
i ran this command singularity run --bind /sci/labs/maayan.salton/adi8897:/data /sci/labs/maayan.salton/adi8897/master_project/IRFinder.sif BAM -r /data/IR_finder_venv/IRFinder-2.0-beta/REF/Human-GRCh38-release110 -d /data/master_project/SART3/irfinder/SRR21796788 /data/master_project/SART3/row_data/bam_files/sorted_files/SRR21796788_Aligned.out_sorted.bam
the error logfile did not say anything but: please look at this file it does not look well i would like your help to understand it IRFinder-IR-nondir.txt
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Chr | Start | End | Name | Null | Strand | ExcludedBases | Coverage | IntronDepth | IntronDepth50Percentile | IntronDepth75Percentile | ExonToIntronReadsLeft | ExonToIntronReadsRight | IntronDepthFirst50bp | IntronDepthLast50bp | SpliceLeft | SpliceRight | SpliceExact | IRratio | Warnings | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- 1 | 924948 | 925921 | SAMD11/ENSG00000187634/clean | 0 | + | 140 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 3 | 3 | 0 | LowCover | 1 | 925189 | 925921 | SAMD11/ENSG00000187634/clean | 0 | + | 90 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0 | LowCover | 1 | 925800 | 925921 | SAMD11/ENSG00000187634/clean | 0 | + | 10 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0 | LowCover | 1 | 926013 | 930154 | SAMD11/ENSG00000187634/clean | 0 | + | 70 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | LowCover | 1 | 930336 | 931038 | SAMD11/ENSG00000187634/clean | 0 | + | 10 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | LowCover | 1 | 930336 | 935771 | SAMD11/ENSG00000187634/clean | 0 | + | 771 | 0.00193 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | LowCover | 1 | 931089 | 935771 | SAMD11/ENSG00000187634/clean | 0 | + | 710 | 0.002266 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | LowCover | 1 | 935896 | 939039 | SAMD11/ENSG00000187634/clean | 0 | + | 10 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 1 | 0 | LowCover | 1 | 939129 | 939274 | SAMD11/ENSG00000187634/anti-near | 0 | + | 13 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 1 | 0 | LowCover | 1 | 939129 | 939271 | SAMD11/ENSG00000187634/anti-near | 0 | + | 10 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | LowCover | 1 | 939129 | 941143 | SAMD11/ENSG00000187634/anti-near | 0 | + | 336 | 0.066746 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 2 | 0 | 0 | LowCover | 1 | 939412 | 941143 | SAMD11/ENSG00000187634/anti-near | 0 | + | 185 | 0.072445 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | LowCover | 1 | 939460 | 941143 | SAMD11/ENSG00000187634/anti-near | 0 | + | 137 | 0.072445 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | LowCover | 1 | 939412 | 942409 | SAMD11/ENSG00000187634/anti-near | 0 | + | 484 | 0.133705 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 0 | 0 | LowCover |