help interpreting why logBaseCalling might be failing
xguse opened this issue · 10 comments
xguse commented
I am sorry to bother you all but I can't quite figure out what is going on here.
As far as I can tell WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. should not be fatal should it? Where am I going wrong here?
➜ nextflow -c /home/ubuntu/master_of_pores/nextflow.global.config run -params-file /home/ubuntu/master_of_pores/NanoPreprocess/run_configs/params.lib03_test.yaml nanopreprocess.nf -with-docker -profile local
N E X T F L O W ~ version 19.10.0
Launching `nanopreprocess.nf` [marvelous_khorana] - revision: 070dd5f042
WARN: Access to undefined parameter `demultiplexing` -- Initialise it to a default value eg. `params.demultiplexing = some_value`
WARN: Access to undefined parameter `demultiplexing_opt` -- Initialise it to a default value eg. `params.demultiplexing_opt = some_value`
WARN: Access to undefined parameter `demulti_fast5` -- Initialise it to a default value eg. `params.demulti_fast5 = some_value`
WARN: Access to undefined parameter `email` -- Initialise it to a default value eg. `params.email = some_value`
╔╦╗┌─┐┌─┐┌┬┐┌─┐┬─┐ ┌─┐┌─┐ ╔═╗╔═╗╦═╗╔═╗╔═╗
║║║├─┤└─┐ │ ├┤ ├┬┘ │ │├┤ ╠═╝║ ║╠╦╝║╣ ╚═╗
╩ ╩┴ ┴└─┘ ┴ └─┘┴└─ └─┘└ ╩ ╚═╝╩╚═╚═╝╚═╝
====================================================
BIOCORE@CRG Preprocessing of Nanopore direct RNA - N F ~ version 0.1
====================================================
kit : SQK-LSK110
flowcell : FAQ55277
fast5 : /home/ubuntu/ebs/data/seqs/input/lib03/fast5_*/*.fast5
reference : /home/ubuntu/ebs/data/seqs/references/gisaid.spike.ref.fasta
annotation : null
ref_type : transcriptome
seq_type : DNA
output : /home/ubuntu/ebs/data/seqs/output/lib03_test
qualityqc : 5
granularity : null
basecaller : guppy
basecaller_opt : null
GPU : ON
demultiplexing : null
demultiplexing_opt : null
demulti_fast5 : null
filter : null
filter_opt : null
mapper : minimap2
mapper_opt : null
map_type : unspliced
counter : YES
counter_opt : null
downsampling : null
variant_caller : NO
variant_opt : null
email : null
executor > local (3)
[ba/06efa5] process > testInput (FAQ55277_pass_d75244b2_860.fast5) [100%] 1 of 1 ✔
[82/7ab4ca] process > logBaseCalling [100%] 1 of 1, failed: 1 ✘
[87/93d147] process > baseCalling (guppy-fast5_*-0) [ 0%] 0 of 1
[- ] process > concatenateFastQFiles -
executor > local (3)
[ba/06efa5] process > testInput (FAQ55277_pass_d75244b2_860.fast5) [100%] 1 of 1 ✔
[82/7ab4ca] process > logBaseCalling [100%] 1 of 1, failed: 1 ✘
[87/93d147] process > baseCalling (guppy-fast5_*-0) [100%] 1 of 1, failed: 1
[- ] process > concatenateFastQFiles -
[- ] process > QC -
[- ] process > fastQC -
[- ] process > mapping -
[- ] process > counting -
[- ] process > joinCountQCs -
[- ] process > alnQC -
[- ] process > joinAlnQCs -
[- ] process > alnQC2 -
[- ] process > multiQC -
Sending the email to null
MultiFast5 files detected!
WARN: Killing pending tasks (1)
Error executing process > 'logBaseCalling'
Caused by:
Process `logBaseCalling` terminated with an error exit status (1)
Command executed:
echo '*********************************'
guppy_basecaller --version
guppy_basecaller --print_workflows | grep FAQ55277 | grep SQK-LSK110
echo '*********************************'
Command exit status:
1
Command output:
*********************************
: Guppy Basecalling Software, (C) Oxford Nanopore Technologies, Limited. Version 3.4.5+fb1fbfb
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Work dir:
/home/ubuntu/master_of_pores/NanoPreprocess/work/82/7ab4ca8127f24419c3fa193d19b1fd
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Failed to invoke `workflow.onComplete` event handler
-- Check script 'nanopreprocess.nf' at line: 811 or see '.nextflow.log' file for more details
lucacozzuto commented
Can you post your params.config file? You have a lot of null. And which version of guppy are you using?
xguse commented
kit: SQK-LSK110
flowcell: FAQ55277
fast5: /home/ubuntu/ebs/data/seqs/input/lib03/fast5_*/*.fast5
reference: /home/ubuntu/ebs/data/seqs/references/gisaid.spike.ref.fasta
annotation:
ref_type: transcriptome
seq_type: DNA
output: /home/ubuntu/ebs/data/seqs/output/lib03_test
qualityqc: 5
granularity:
basecaller: guppy
basecaller_opt:
GPU: "ON"
# demultiplexing:
# demultiplexing_opt: -m pAmps-final-actrun_newdata_nanopore_UResNet20v2_model.030.h5
# demulti_fast5: OFF
filter:
filter_opt:
mapper: minimap2
mapper_opt:
map_type: unspliced
counter: "YES"
counter_opt:
variant_caller: "NO"
variant_opt:
downsampling:
and I ran this to install guppy
wget https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy_3.4.5_linux64.tar.gz
tar -zvxf ont-guppy_3.4.5_linux64.tar.gz
mkdir NanoPreprocess/bin/ont-guppy_3.4.5_linux64
mv ont-guppy NanoPreprocess/bin/ont-guppy_3.4.5_linux64
cd NanoPreprocess/bin
ln -s ont-guppy_3.4.5_linux64/ont-guppy/bin/guppy_* .
cd ../../
rm -fr ont-guppy_3.4.5_linux64.tar.gzlucacozzuto commented
Well this is strange. It is failing the log. Can you go within
/home/ubuntu/master_of_pores/NanoPreprocess/work/82/7ab4ca8127f24419c3fa193d19b1fd
and check the .command.log?
PS: instead of null can you put ""?
Thanks
xguse commented
Here is whats in .command.log
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
*********************************
: Guppy Basecalling Software, (C) Oxford Nanopore Technologies, Limited. Version 3.4.5+fb1fbfb
I used this params and got the same issue:
kit: SQK-LSK110
flowcell: FAQ55277
fast5: /home/ubuntu/ebs/data/seqs/input/lib03/fast5_*/*.fast5
reference: /home/ubuntu/ebs/data/seqs/references/gisaid.spike.ref.fasta
annotation: ""
ref_type: transcriptome
seq_type: DNA
output: /home/ubuntu/ebs/data/seqs/output/lib03_test
qualityqc: 5
granularity: ""
basecaller: guppy
basecaller_opt: ""
GPU: "ON"
# demultiplexing:
# demultiplexing_opt: -m pAmps-final-actrun_newdata_nanopore_UResNet20v2_model.030.h5
# demulti_fast5: OFF
filter: ""
filter_opt: ""
mapper: minimap2
mapper_opt: ""
map_type: unspliced
counter: "YES"
counter_opt: ""
variant_caller: "NO"
variant_opt: ""
downsampling: ""
lucacozzuto commented
the command executed is
guppy_basecaller --version
guppy_basecaller --print_workflows | grep FAQ55277 | grep SQK-LSK110
you can see that the second part is not done. I'm wondering if something is wrong with that.
Have you tried our test dataset? Does it work?
xguse commented
OK so I had made some changes to the repo regarding supplying my own configs instead of using the in-directory params.config etc so I stashed all my stuff and went back to tag v1.1: cc554e9 and tried just running what y'all show in your docs nextflow run nanopreprocess.nf -with-singularity
I get the error in the same place...?
ubuntu in master_of_pores/NanoPreprocess at ip-10-77-20-191 on fl77 [$?] via 🅒 base
➜ nextflow run nanopreprocess.nf -with-singularity
N E X T F L O W ~ version 19.10.0
Launching `nanopreprocess.nf` [compassionate_leavitt] - revision: 070dd5f042
╔╦╗┌─┐┌─┐┌┬┐┌─┐┬─┐ ┌─┐┌─┐ ╔═╗╔═╗╦═╗╔═╗╔═╗
║║║├─┤└─┐ │ ├┤ ├┬┘ │ │├┤ ╠═╝║ ║╠╦╝║╣ ╚═╗
╩ ╩┴ ┴└─┘ ┴ └─┘┴└─ └─┘└ ╩ ╚═╝╩╚═╚═╝╚═╝
====================================================
BIOCORE@CRG Preprocessing of Nanopore direct RNA - N F ~ version 0.1
====================================================
kit : SQK-RNA001
flowcell : FLO-MIN106
fast5 : /home/ubuntu/master_of_pores/NanoPreprocess/../data/multifast/*.fast5
reference : /home/ubuntu/master_of_pores/NanoPreprocess/../anno/curlcake_constructs.fasta.gz
annotation :
ref_type : transcriptome
seq_type : cDNA
output : /home/ubuntu/master_of_pores/NanoPreprocess/multifast
qualityqc : 5
granularity :
basecaller : guppy
basecaller_opt :
GPU : OFF
demultiplexing :
demultiplexing_opt : -m pAmps-final-actrun_newdata_nanopore_UResNet20v2_model.030.h5
demulti_fast5 : OFF
filter :
filter_opt :
mapper : graphmap2
mapper_opt :
map_type : spliced
counter : YES
counter_opt :
downsampling :
variant_caller : NO
variant_opt :
email :
executor > local (1)
[- ] process > testInput -
[db/4d3dfa] process > logBaseCalling [ 0%] 0 of 1
[- ] process > baseCalling -
[- ] process > concatenateFastQFiles -
executor > local (1)
[- ] process > testInput -
[db/4d3dfa] process > logBaseCalling [100%] 1 of 1, failed: 1 ✘
[- ] process > baseCalling -
[- ] process > concatenateFastQFiles -
[- ] process > QC -
[- ] process > fastQC -
[- ] process > mapping -
[- ] process > counting -
[- ] process > joinCountQCs -
[- ] process > alnQC -
[- ] process > joinAlnQCs -
[- ] process > alnQC2 -
[- ] process > multiQC -
Pulling Singularity image docker://biocorecrg/mopprepr:0.7 [cache /home/ubuntu/master_of_pores/NanoPreprocess/../singularity/biocorecrg-mopprepr-0.7.img]
Skipping the email
Error executing process > 'logBaseCalling'
Caused by:
Process `logBaseCalling` terminated with an error exit status (255)
Command executed:
echo '*********************************'
guppy_basecaller --version
guppy_basecaller --print_workflows | grep FLO-MIN106 | grep SQK-RNA001
echo '*********************************'
Command exit status:
255
Command output:
(empty)
Command error:
FATAL: container creation failed: mount /proc/self/fd/6->/usr/local/var/singularity/mnt/session/rootfs error: can't mount image /proc/self/fd/6: failed to mount squashfs filesystem: invalid argument
Work dir:
/home/ubuntu/master_of_pores/NanoPreprocess/work/db/4d3dfa78fcfefdd90fdc2aabee5198
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
xguse commented
Ok so... if I use -with-docker it seems to run however.
I see that the error above is that singularity is failing.
xguse commented
OK I have a hypothesis.
Here is what I get when I have guppy_basecaller print its workflows and my combination of flowcell and kit do not exist in this output. This would cause nothing to be printed on the second line of the logBaseCalling script no?
Might this cause an error?
Also I have corrected my flowcell value. Turns out thats not flowcell ID like I figured it would mean, but TYPE, which was confusing. All errors still occur and the flowcell TYPE is now FLO-MIN111. The current config is at the bottom.
(@lucacozzuto )
Available flowcell + kit combinations are:
flowcell kit barcoding config_name
FLO-PRO001 SQK-LSK109 dna_r9.4.1_450bps_hac_prom
FLO-PRO001 SQK-LSK109-XL dna_r9.4.1_450bps_hac_prom
FLO-PRO001 SQK-DCS109 dna_r9.4.1_450bps_hac_prom
FLO-PRO001 SQK-PCS109 dna_r9.4.1_450bps_hac_prom
FLO-PRO001 SQK-PRC109 dna_r9.4.1_450bps_hac_prom
FLO-PRO001 SQK-PCB109 included dna_r9.4.1_450bps_hac_prom
FLO-PRO002 SQK-LSK109 dna_r9.4.1_450bps_hac_prom
FLO-PRO002 SQK-LSK109-XL dna_r9.4.1_450bps_hac_prom
FLO-PRO002 SQK-DCS109 dna_r9.4.1_450bps_hac_prom
FLO-PRO002 SQK-PCS109 dna_r9.4.1_450bps_hac_prom
FLO-PRO002 SQK-PRC109 dna_r9.4.1_450bps_hac_prom
FLO-PRO002 SQK-PCB109 included dna_r9.4.1_450bps_hac_prom
FLO-MIN107 SQK-DCS108 dna_r9.5_450bps
FLO-MIN107 SQK-DCS109 dna_r9.5_450bps
FLO-MIN107 SQK-LRK001 dna_r9.5_450bps
FLO-MIN107 SQK-LSK108 dna_r9.5_450bps
FLO-MIN107 SQK-LSK109 dna_r9.5_450bps
FLO-MIN107 SQK-LSK308 dna_r9.5_450bps
FLO-MIN107 SQK-LSK309 dna_r9.5_450bps
FLO-MIN107 SQK-LSK319 dna_r9.5_450bps
FLO-MIN107 SQK-LWP001 dna_r9.5_450bps
FLO-MIN107 SQK-PCS108 dna_r9.5_450bps
FLO-MIN107 SQK-PCS109 dna_r9.5_450bps
FLO-MIN107 SQK-PSK004 dna_r9.5_450bps
FLO-MIN107 SQK-RAD002 dna_r9.5_450bps
FLO-MIN107 SQK-RAD003 dna_r9.5_450bps
FLO-MIN107 SQK-RAD004 dna_r9.5_450bps
FLO-MIN107 SQK-RAS201 dna_r9.5_450bps
FLO-MIN107 SQK-RLI001 dna_r9.5_450bps
FLO-MIN107 VSK-VBK001 dna_r9.5_450bps
FLO-MIN107 VSK-VSK001 dna_r9.5_450bps
FLO-MIN107 VSK-VSK002 dna_r9.5_450bps
FLO-MIN107 SQK-LWB001 included dna_r9.5_450bps
FLO-MIN107 SQK-PBK004 included dna_r9.5_450bps
FLO-MIN107 SQK-RAB201 included dna_r9.5_450bps
FLO-MIN107 SQK-RAB204 included dna_r9.5_450bps
FLO-MIN107 SQK-RBK001 included dna_r9.5_450bps
FLO-MIN107 SQK-RBK004 included dna_r9.5_450bps
FLO-MIN107 SQK-RLB001 included dna_r9.5_450bps
FLO-MIN107 SQK-RPB004 included dna_r9.5_450bps
FLO-MIN107 VSK-VMK001 included dna_r9.5_450bps
FLO-MIN107 VSK-VMK002 included dna_r9.5_450bps
FLO-FLG001 SQK-CAS109 dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-DCS108 dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-DCS109 dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-LRK001 dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-LSK108 dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-LSK109 dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-LSK109-XL dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-LWP001 dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-PCS108 dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-PCS109 dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-PRC109 dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-PSK004 dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-RAD002 dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-RAD003 dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-RAD004 dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-RAS201 dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-RLI001 dna_r9.4.1_450bps_hac
FLO-FLG001 VSK-VBK001 dna_r9.4.1_450bps_hac
FLO-FLG001 VSK-VSK001 dna_r9.4.1_450bps_hac
FLO-FLG001 VSK-VSK002 dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-16S024 included dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-PCB109 included dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-RBK001 included dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-RBK004 included dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-RLB001 included dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-LWB001 included dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-PBK004 included dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-RAB201 included dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-RAB204 included dna_r9.4.1_450bps_hac
FLO-FLG001 SQK-RPB004 included dna_r9.4.1_450bps_hac
FLO-FLG001 VSK-VMK001 included dna_r9.4.1_450bps_hac
FLO-FLG001 VSK-VMK002 included dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-CAS109 dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-DCS108 dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-DCS109 dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-LRK001 dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-LSK108 dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-LSK109 dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-LSK109-XL dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-LWP001 dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-PCS108 dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-PCS109 dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-PRC109 dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-PSK004 dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-RAD002 dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-RAD003 dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-RAD004 dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-RAS201 dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-RLI001 dna_r9.4.1_450bps_hac
FLO-MIN106 VSK-VBK001 dna_r9.4.1_450bps_hac
FLO-MIN106 VSK-VSK001 dna_r9.4.1_450bps_hac
FLO-MIN106 VSK-VSK002 dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-16S024 included dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-PCB109 included dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-RBK001 included dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-RBK004 included dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-RLB001 included dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-LWB001 included dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-PBK004 included dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-RAB201 included dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-RAB204 included dna_r9.4.1_450bps_hac
FLO-MIN106 SQK-RPB004 included dna_r9.4.1_450bps_hac
FLO-MIN106 VSK-VMK001 included dna_r9.4.1_450bps_hac
FLO-MIN106 VSK-VMK002 included dna_r9.4.1_450bps_hac
FLO-MIN111 SQK-CAS109 dna_r10.3_450bps_hac
FLO-MIN111 SQK-DCS108 dna_r10.3_450bps_hac
FLO-MIN111 SQK-DCS109 dna_r10.3_450bps_hac
FLO-MIN111 SQK-LRK001 dna_r10.3_450bps_hac
FLO-MIN111 SQK-LSK108 dna_r10.3_450bps_hac
FLO-MIN111 SQK-LSK109 dna_r10.3_450bps_hac
FLO-MIN111 SQK-LSK109-XL dna_r10.3_450bps_hac
FLO-MIN111 SQK-LWP001 dna_r10.3_450bps_hac
FLO-MIN111 SQK-PCS108 dna_r10.3_450bps_hac
FLO-MIN111 SQK-PCS109 dna_r10.3_450bps_hac
FLO-MIN111 SQK-PRC109 dna_r10.3_450bps_hac
FLO-MIN111 SQK-PSK004 dna_r10.3_450bps_hac
FLO-MIN111 SQK-RAD002 dna_r10.3_450bps_hac
FLO-MIN111 SQK-RAD003 dna_r10.3_450bps_hac
FLO-MIN111 SQK-RAD004 dna_r10.3_450bps_hac
FLO-MIN111 SQK-RAS201 dna_r10.3_450bps_hac
FLO-MIN111 SQK-RLI001 dna_r10.3_450bps_hac
FLO-MIN111 VSK-VBK001 dna_r10.3_450bps_hac
FLO-MIN111 VSK-VSK001 dna_r10.3_450bps_hac
FLO-MIN111 VSK-VSK002 dna_r10.3_450bps_hac
FLO-MIN111 SQK-16S024 included dna_r10.3_450bps_hac
FLO-MIN111 SQK-PCB109 included dna_r10.3_450bps_hac
FLO-MIN111 SQK-RBK001 included dna_r10.3_450bps_hac
FLO-MIN111 SQK-RBK004 included dna_r10.3_450bps_hac
FLO-MIN111 SQK-RLB001 included dna_r10.3_450bps_hac
FLO-MIN111 SQK-LWB001 included dna_r10.3_450bps_hac
FLO-MIN111 SQK-PBK004 included dna_r10.3_450bps_hac
FLO-MIN111 SQK-RAB201 included dna_r10.3_450bps_hac
FLO-MIN111 SQK-RAB204 included dna_r10.3_450bps_hac
FLO-MIN111 SQK-RPB004 included dna_r10.3_450bps_hac
FLO-MIN111 VSK-VMK001 included dna_r10.3_450bps_hac
FLO-MIN111 VSK-VMK002 included dna_r10.3_450bps_hac
FLO-FLG001 SQK-RNA001 rna_r9.4.1_70bps_hac
FLO-FLG001 SQK-RNA002 rna_r9.4.1_70bps_hac
FLO-MIN106 SQK-RNA001 rna_r9.4.1_70bps_hac
FLO-MIN106 SQK-RNA002 rna_r9.4.1_70bps_hac
FLO-MIN107 SQK-RNA001 rna_r9.4.1_70bps_hac
FLO-MIN107 SQK-RNA002 rna_r9.4.1_70bps_hac
FLO-MIN110 SQK-CAS109 dna_r10_450bps_hac
FLO-MIN110 SQK-DCS108 dna_r10_450bps_hac
FLO-MIN110 SQK-DCS109 dna_r10_450bps_hac
FLO-MIN110 SQK-LRK001 dna_r10_450bps_hac
FLO-MIN110 SQK-LSK108 dna_r10_450bps_hac
FLO-MIN110 SQK-LSK109 dna_r10_450bps_hac
FLO-MIN110 SQK-LSK109-XL dna_r10_450bps_hac
FLO-MIN110 SQK-LWP001 dna_r10_450bps_hac
FLO-MIN110 SQK-PCS108 dna_r10_450bps_hac
FLO-MIN110 SQK-PCS109 dna_r10_450bps_hac
FLO-MIN110 SQK-PRC109 dna_r10_450bps_hac
FLO-MIN110 SQK-PSK004 dna_r10_450bps_hac
FLO-MIN110 SQK-RAD002 dna_r10_450bps_hac
FLO-MIN110 SQK-RAD003 dna_r10_450bps_hac
FLO-MIN110 SQK-RAD004 dna_r10_450bps_hac
FLO-MIN110 SQK-RAS201 dna_r10_450bps_hac
FLO-MIN110 SQK-RLI001 dna_r10_450bps_hac
FLO-MIN110 VSK-VBK001 dna_r10_450bps_hac
FLO-MIN110 VSK-VSK001 dna_r10_450bps_hac
FLO-MIN110 VSK-VSK002 dna_r10_450bps_hac
FLO-MIN110 SQK-16S024 included dna_r10_450bps_hac
FLO-MIN110 SQK-PCB109 included dna_r10_450bps_hac
FLO-MIN110 SQK-RBK001 included dna_r10_450bps_hac
FLO-MIN110 SQK-RBK004 included dna_r10_450bps_hac
FLO-MIN110 SQK-RLB001 included dna_r10_450bps_hac
FLO-MIN110 SQK-LWB001 included dna_r10_450bps_hac
FLO-MIN110 SQK-PBK004 included dna_r10_450bps_hac
FLO-MIN110 SQK-RAB201 included dna_r10_450bps_hac
FLO-MIN110 SQK-RAB204 included dna_r10_450bps_hac
FLO-MIN110 SQK-RPB004 included dna_r10_450bps_hac
FLO-MIN110 VSK-VMK001 included dna_r10_450bps_hac
FLO-MIN110 VSK-VMK002 included dna_r10_450bps_hac
FLO-FLG001 SQK-RNA003 rna_r9.4.1_120bps_hac
FLO-MIN106 SQK-RNA003 rna_r9.4.1_120bps_hac
FLO-MIN107 SQK-RNA003 rna_r9.4.1_120bps_hac
FLO-PRO001 SQK-RNA002 rna_r9.4.1_70bps_hac_prom
FLO-PRO002 SQK-RNA002 rna_r9.4.1_70bps_hac_prom
params {
kit = "SQK-LSK110"
flowcell = "FLO-MIN111"
fast5 = "/home/ubuntu/ebs/data/seqs/input/lib03/fast5_fail/*.fast5"
reference = "/home/ubuntu/ebs/data/seqs/references/gisaid.spike.ref.fasta"
annotation = ""
ref_type = "transcriptome"
seq_type = "cDNA"
output = "/home/ubuntu/ebs/data/seqs/output/lib03_test"
qualityqc = 5
granularity = ""
basecaller = "guppy"
basecaller_opt = ""
GPU = "ON"
demultiplexing = ""
demultiplexing_opt = ""
demulti_fast5 = "OFF"
filter = ""
filter_opt = ""
mapper = "graphmap2"
mapper_opt = ""
map_type = "spliced"
counter = "YES"
counter_opt = ""
variant_caller = "NO"
variant_opt = ""
downsampling = ""
email = ""
}
lucacozzuto commented
I see. Which version of singularity are you using?
xguse commented
I see. Which version of singularity are you using?
The problem isnt singularity. I plan on using Docker. Thats just why I thought that your demo failed at first. But when I switched to -with-docker it ran flawlessly. Thats when I started looking at what guppy_basecaller --print_workflows was presenting to the grep calls. It turns out that I am using a combination of flowcell_type and kit that the version of guppy provided in your INSTALL.sh does not contain. THATS why the logging failed. I have updated to v5.0.16 and tried again and it passed the logBaseCalling step.
The answer
logging step failed bc the step did not gracefully handle the case where the guppy version does not contain a method for dealing with a particular combination of flowcell_type and kit. The final grep returns an error when it cant satisfy the search criteria and borks the run with no helpful "reason".
I fixed the issue by updating to a newer guppy that "knows" about the newer kits.