SamStudio8
commented
10 months ago Hi @c3305637, I'm afraid I can't advise about mapping our containers to a Samba share specifically as this is beyond the scope of our support. I would advise that if possible, you instead mount the SMB share on the host that you run the workflow on and then refer to the paths as local paths to run the workflow from your box.
Hi, I'm trying to basecall from pod5 files and keep running into the error below. I'm running Epi2me on a Linux machine. Would the pod5 folder being located on a mapped network drive be contributing to this at all? Log below.
This is epi2me-labs/wf-basecalling v1.1.1.
[24/c4a324] Submitted process > cram_cache [2c/d90b4b] Submitted process > getParams [16/819179] Submitted process > wf_dorado:make_mmi [0d/d88198] Submitted process > getVersions [54/8a55bb] Submitted process > wf_dorado:dorado (1) ERROR ~ Error executing process > 'wf_dorado:dorado (1)' Caused by: Process
wf_dorado:dorado (1)terminated with an error exit status (125) Command executed: set +e source /opt/nvidia/entrypoint.d/*-gpu-driver-check.sh # runtime driver check msg set -eCW-2569: convert the pod5s contextually
if [[ "false" == "true" && "pod5" == "fast5" ]]; then pod5 convert fast5 ./*.fast5 --output . --threads 8 --one-to-one ./ fi
Run dorado on the new pod5s
dorado basecaller ${DRD_MODELS_PATH}/dna_r10.4.1_e8.2_400bps_hac@v4.2.0 . --modified-bases-models ${DRD_MODELS_PATH}/dna_r10.4.1_e8.2_400bps_hac@v4.2.0_5mCG_5hmCG@v2 --device cuda:all | samtools view --no-PG -b -o 0.ubam -
CW-2569: delete the pod5s, if emit not required.
if [[ "false" == "true" && "pod5" == "fast5" ]]; then rm -r converted/ fi Command exit status: 125 Command output: (empty) Command error: docker: invalid spec: /run/user/1000/gvfs/smb-share:server=resprsvm03.newcastle.edu.au,share=canepi/Sequencing_Data_Raw/1_RAW/230918_BH_Nanopore_AS/20230918_LEE12621A2_AS_SUPbasecalling/LEE12621A2_AS/20230918_1243_X3_FAV02769_33366469/pod5_pass:/run/user/1000/gvfs/smb-share:server=resprsvm03.newcastle.edu.au,share=canepi/Sequencing_Data_Raw/1_RAW/230918_BH_Nanopore_AS/20230918_LEE12621A2_AS_SUPbasecalling/LEE12621A2_AS/20230918_1243_X3_FAV02769_33366469/pod5_pass: too many colons. See 'docker run --help'. Work dir: /media/ptwo/DataDisk/epi2melabs/instances/wf-basecalling_01HGVSVABBK5Y7QXYZDCR6M4WN/work/54/8a55bb9b58bd5389327245018d39c0 Tip: view the complete command output by changing to the process work dir and entering the command
cat .command.out-- Check '/media/ptwo/DataDisk/epi2melabs/instances/wf-basecalling_01HGVSVABBK5Y7QXYZDCR6M4WN/nextflow.log' file for details