search

BrooksLabUCSC / flair

Full-Length Alternative Isoform analysis of RNA
Other
208 stars 71 forks source link

alarming "errors" when running multiple modules #268

Open diekhans opened 1 year ago

diekhans commented 1 year ago

Copy and paste the exact command you tried to run

flair 123 -g $genome -f $annotation --shortread $shortread_bed --threads ${NSLOTS} -r /nfs/users/project/gencode_006070/jlagarde/nanopore/sequencing_runs/runs/20210715/20210713_HS_BLaER1_PCRcDNA110_H0C2/20210713_HS_BLaER1_PCRcDNA110_H0C2/20210713_1407_MN24456_FAP82103_6d0f8d57/20210713_HS_BLaER1_PCRcDNA110_H0C2.guppy.v6.0.1-gpu.fastq.gz /nfs/users/project/gencode_006070/jlagarde/nanopore/sequencing_runs/runs/20210701/20210628_HS_BLaER1_PCRcDNA110_H0N2/20210628_HS_BLaER1_PCRcDNA110_H0N2/20210628_1623_MN24456_FAP84999_e7c35d5c/20210628_HS_BLaER1_PCRcDNA110_H0N2.guppy.v6.0.1-gpu.fastq.gz /nfs/users/project/gencode_006070/jlagarde/nanopore/sequencing_runs/runs/20210223/reads/20210222_HS_BLaER1_PCRcDNA110_H0T3/20210222_HS_BLaER1_PCRcDNA110_H0T3/20210222_HS_BLaER1_PCRcDNA110_H0T3/20210222_1723_MN26202_FAP51075_d4666859/20210222_HS_BLaER1_PCRcDNA110_H0T3.guppy.v6.0.1-gpu.fastq.gz /nfs/users/project/gencode_006070/jlagarde/nanopore/sequencing_runs/runs/20210319/reads/20210316_HS_BLaER1_PCRcDNA110_H03C/20210316_HS_BLaER1_PCRcDNA110_H03C/20210316_HS_BLaER1_PCRcDNA110_H03C/20210316_1818_MN24456_FAP06181_4f7727ad/20210316_HS_BLaER1_PCRcDNA110_H03C.guppy.v6.0.1-gpu.fastq.gz /nfs/users/project/gencode_006070/jlagarde/nanopore/sequencing_runs/runs/20210322/reads/20210319_HS_BLaER1_PCRcDNA110_H03C_BIS/20210319_HS_BLaER1_PCRcDNA110_H03C_BIS/20210319_HS_BLaER1_PCRcDNA110_H03C_BIS/20210319_1412_MN24456_FAP06181_48d651f9/20210319_HS_BLaER1_PCRcDNA110_H03C_BIS.guppy.v6.0.1-gpu.fastq.gz /nfs/users/project/gencode_006070/jlagarde/nanopore/sequencing_runs/runs/20210319/reads/20210316_HS_BLaER1_PCRcDNA110_H03N/20210316_HS_BLaER1_PCRcDNA110_H03N/20210316_HS_BLaER1_PCRcDNA110_H03N/20210316_1819_MN26202_FAP50933_42375c2c/20210316_HS_BLaER1_PCRcDNA110_H03N.guppy.v6.0.1-gpu.fastq.gz /nfs/users/project/gencode_006070/jlagarde/nanopore/sequencing_runs/runs/20210322/reads/20210319_HS_BLaER1_PCRcDNA110_H03N_BIS2/20210319_HS_BLaER1_PCRcDNA110_H03N_BIS2/20210319_HS_BLaER1_PCRcDNA110_H03N_BIS2/20210319_1509_MN26202_FAP50933_8689e433/20210319_HS_BLaER1_PCRcDNA110_H03N_BIS2.guppy.v6.0.1-gpu.fastq.gz /nfs/users/project/gencode_006070/jlagarde/nanopore/sequencing_runs/runs/20210628/20210622_HS_BLaER1_PCRcDNA110_H0T2/20210622_HS_BLaER1_PCRcDNA110_H0T2/20210622_1202_MN26202_FAP46789_a0c99f09/20210622_HS_BLaER1_PCRcDNA110_H0T2.guppy.v6.0.1-gpu.fastq.gz -m $minimap_path

How did you install Flair?

bioconda

What happened?

Output had alarming messages about unrecognized arguments, but it did not stop. This caused us to spend time investigating this, as we worried it was the cause of problems. This may be normal behavior, but it wastes time. This also caused concern that in might not detect invalid arguents.

Align unrecognized arguments: -f /nfs/users/rg/projects/references/Annotation/H.sapiens/gencode43/gencode.v43.primary_assembly.annotation.gtf --shortread /nfs/users/project/gencode_006070_no_backup/scarbonell/TFM/long_reads/FLAIR/all/data/junctions_from_sam_junctions.bed
Correct unrecognized arguments: -r /nfs/users/project/gencode_006070/jlagarde/nanopore/sequencing_runs/runs/20210715/20210713_HS_BLaER1_PCRcDNA110_H0C2/20210713_HS_BLaER1_PCRcDNA110_H0C2/20210713_1407_MN24456_FAP82103_6d0f8d57/20210713_HS_BLaER1_PCRcDNA110_H0C2.guppy.v6.0.1-gpu.fastq.gz /nfs/users/project/gencode_006070/jlagarde/nanopore/sequencing_runs/runs/20210701/20210628_HS_BLaER1_PCRcDNA110_H0N2/20210628_HS_BLaER1_PCRcDNA110_H0N2/20210628_1623_MN24456_FAP84999_e7c35d5c/20210628_HS_BLaER1_PCRcDNA110_H0N2.guppy.v6.0.1-gpu.fastq.gz /nfs/users/project/gencode_006070/jlagarde/nanopore/sequencing_runs/runs/20210223/reads/20210222_HS_BLaER1_PCRcDNA110_H0T3/20210222_HS_BLaER1_PCRcDNA110_H0T3/20210222_HS_BLaER1_PCRcDNA110_H0T3/20210222_1723_MN26202_FAP51075_d4666859/20210222_HS_BLaER1_PCRcDNA110_H0T3.guppy.v6.0.1-gpu.fastq.gz /nfs/users/project/gencode_006070/jlagarde/nanopore/sequencing_runs/runs/20210319/reads/20210316_HS_BLaER1_PCRcDNA110_H03C/20210316_HS_BLaER1_PCRcDNA110_H03C/20210316_HS_BLaER1_PCRcDNA110_H03C/20210316_1818_MN24456_FAP06181_4f7727ad/20210316_HS_BLaER1_PCRcDNA110_H03C.guppy.v6.0.1-gpu.fastq.gz /nfs/users/project/gencode_006070/jlagarde/nanopore/sequencing_runs/runs/20210322/reads/20210319_HS_BLaER1_PCRcDNA110_H03C_BIS/20210319_HS_BLaER1_PCRcDNA110_H03C_BIS/20210319_HS_BLaER1_PCRcDNA110_H03C_BIS/20210319_1412_MN24456_FAP06181_48d651f9/20210319_HS_BLaER1_PCRcDNA110_H03C_BIS.guppy.v6.0.1-gpu.fastq.gz /nfs/users/project/gencode_006070/jlagarde/nanopore/sequencing_runs/runs/20210319/reads/20210316_HS_BLaER1_PCRcDNA110_H03N/20210316_HS_BLaER1_PCRcDNA110_H03N/20210316_HS_BLaER1_PCRcDNA110_H03N/20210316_1819_MN26202_FAP50933_42375c2c/20210316_HS_BLaER1_PCRcDNA110_H03N.guppy.v6.0.1-gpu.fastq.gz /nfs/users/project/gencode_006070/jlagarde/nanopore/sequencing_runs/runs/20210322/reads/20210319_HS_BLaER1_PCRcDNA110_H03N_BIS2/20210319_HS_BLaER1_PCRcDNA110_H03N_BIS2/20210319_HS_BLaER1_PCRcDNA110_H03N_BIS2/20210319_1509_MN26202_FAP50933_8689e433/20210319_HS_BLaER1_PCRcDNA110_H03N_BIS2.guppy.v6.0.1-gpu.fastq.gz /nfs/users/project/gencode_006070/jlagarde/nanopore/sequencing_runs/runs/20210628/20210622_HS_BLaER1_PCRcDNA110_H0T2/20210622_HS_BLaER1_PCRcDNA110_H0T2/20210622_1202_MN26202_FAP46789_a0c99f09/20210622_HS_BLaER1_PCRcDNA110_H0T2.guppy.v6.0.1-gpu.fastq.gz -m /users/rg/scarbonell/bin/minimap2/
Collapse unrecognized arguments: --shortread /nfs/users/project/gencode_006070_no_backup/scarbonell/TFM/long_reads/FLAIR/all/data/junctions_from_sam_junctions.bed

We know it's ugly but we promise it helps us solve problems faster.

What else do we need to know?