pdoris

Results 8 comments of pdoris

json produced by perl scripts not working?

Same problem here

No gbk.HiFiMapped.bam.filtered.assembled.[a/p]_ctg.gfa file(s). An error may have occurred when assembling reads with HiFiasm

same problem here apptainer exec --bind /work/06127/pdoris/Mitosif:/work/06127/pdoris/Mitosif docker://ghcr.io/marcelauliano/mitohifi:master mitohifi.py -r /work/06127/pdoris/SHRA3_HiFi_reads/cell3.fa -f /work/06127/pdoris/MitoHiFi/data/NC_001665.2.fasta -g /work/06127/pdoris/MitoHiFi/data/RNmitosequence.gbk -o 2 -t 128 INFO: Using cached SIF image 2023-06-26 11:28:22 [INFO] Welcome to MitoHifi...

No gbk.HiFiMapped.bam.filtered.assembled.[a/p]_ctg.gfa file(s). An error may have occurred when assembling reads with HiFiasm

Hifiasm is generating some output files -rw------- 1 pdoris G-820831 25061649697 Jun 26 09:18 cell3.fa -rw-r--r-- 1 pdoris G-820831 303353 Jun 26 11:29 gbk.HiFiMapped.bam.fasta -rw-r--r-- 1 pdoris G-820831 8052 Jun...

No gbk.HiFiMapped.bam.filtered.assembled.[a/p]_ctg.gfa file(s). An error may have occurred when assembling reads with HiFiasm

Hi Marcela I begin to think there are no non-nuclear mitogenome sequences in my reads. I have also run in contig mode. Mitofinder gives the reported error Traceback (most recent...

No gbk.HiFiMapped.bam.filtered.assembled.[a/p]_ctg.gfa file(s). An error may have occurred when assembling reads with HiFiasm

Being concerned that there might be no non-nuclear mitochondrial genome reads discovered in the previous run, I expanded the read files to combine data from all 4 HiFi cells that...

No gbk.HiFiMapped.bam.filtered.assembled.[a/p]_ctg.gfa file(s). An error may have occurred when assembling reads with HiFiasm

I ran the container using the provided test data: apptainer exec --bind /work/06127/pdoris/Mitosif:/work/06127/pdoris/Mitosif docker://ghcr.io/marcelauliano/mitohifi:master mitohifi.py -r /work/06127/pdoris/MitoHiFi/tests/ilDeiPorc1.reads.100.fa -f /work/06127/pdoris/MitoHiFi/data/OQ694980.1.fasta -g /work/06127/pdoris/MitoHiFi/data/OQ694980.1.gb -o 2 -t 128 INFO: Using cached SIF image...

No gbk.HiFiMapped.bam.filtered.assembled.[a/p]_ctg.gfa file(s). An error may have occurred when assembling reads with HiFiasm

Thanks, Marcela I am using apptainer I will drop t to 1 and run again I wonder if apptainer is fully compatible with the docker container https://apptainer.org/docs/user/main/docker_and_oci.html#differences-and-limitations-vs-docker Sent from my...

No gbk.HiFiMapped.bam.filtered.assembled.[a/p]_ctg.gfa file(s). An error may have occurred when assembling reads with HiFiasm

My genome is a mammal, so -o 2 is correct unless my eyes are really tricking me More info on our singularity implementation ---------------------------------------------------------------------------------------------------------------------------------------------------------------- tacc-apptainer: tacc-apptainer/1.1.8 ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Description: Application and...