Closed diekhans closed 1 year ago
FLAIR collapse creates isoform ids without the underscore separating the isoform id and the gene id, causing bed_to_gtf to fail. For example
d3380a06-a1bc-4689-87de-6299d205d24b/a34b3c2cdc097afcadab320f573a6cc04fefcddcGL000221.1:4000
Copy and paste the exact command you tried to run
${HOME}/bin/flair/flair.py collapse --query flair_all_corrected.bed -g $genome -f $annotation --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
How did you install Flair? (We'd prefer it if you used one of the top two because they are the least likely to have package compatibility problems.)
conda create -n flair -c conda-forge -c bioconda flair
What happened?
See attached error log
e.flair_module23FAST_91272191.log
What else do we need to know? This run created 93 invalid ids
bad.ids.txt
An example showing files containing one of the invalid ids
hits.txt
FLAIR collapse creates isoform ids without the underscore separating the isoform id and the gene id, causing bed_to_gtf to fail. For example
Copy and paste the exact command you tried to run
How did you install Flair? (We'd prefer it if you used one of the top two because they are the least likely to have package compatibility problems.)
conda create -n flair -c conda-forge -c bioconda flair)What happened?
See attached error log
e.flair_module23FAST_91272191.log
What else do we need to know? This run created 93 invalid ids
bad.ids.txt
An example showing files containing one of the invalid ids
hits.txt