envcheck error

[suvi93]

Hi Peng,

I am trying to run the pipeline with the following command -

CUDA_VISIBLE_DEVICES=0 nextflow run /crex/proj/snic2021-6-151/nobackup/Suvi/tools/ccsmethphase \ --dsname vv19 \ --genome /crex/proj/snic2021-6-151/private/Suvi/ref/Vv19/ccs/vv19.fa \ --input /crex/proj/snic2021-6-151/private/Suvi/samples/Viatica19_stuff/ccsmeth/input_sheet.tsv \ --chrSet scaffold_1, scaffold_2, scaffold_3, scaffold_4, scaffold_5, scaffold_6, scaffold_7, scaffold_8, scaffold_9, scaffold_10 \ --max_cpus 15 \ --max_memory "20.GB" \ --max_time "48.h" \ -profile singularity

i keep getting this error -

ERROR ~ Error executing process > 'CheckAGModel (CheckAGModel)'

Caused by: Process CheckAGModel (CheckAGModel) terminated with an error exit status (255)

Command executed:

date; hostname; pwd

ccsmeth aggregate model if [[ true == true && true == true ]]; then if [ "aggregate" != "aggregate" ]; then echo "### INFO: params.cf_mode != aggregate" elif [ null3 == null3 ] ; then echo "### INFO: gonna use the default ccsmeth_ag_model=tools/ccsmeth/models/model_ccsmeth_5mCpG_aggregate_attbigru_b11.v2p.ckpt" elif [[ null3 != .ckpt && null3 != .checkpoint ]]; then echo "### ERROR: not recognized ccsmeth_ag_model=null3" exit -1 fi cp -a null3 ccsmeth_aggregate_model.ckpt ls -lh ccsmeth_aggregate_model.ckpt fi

echo "### Check ag_model DONE"

Command exit status: 255

Command output: (empty)

Command error: INFO: Converting SIF file to temporary sandbox... FATAL: while extracting /Viatica19_stuff/ccsmeth/local_singularity_cache/nipengcsu-ccsmethphase-latest.img: root filesystem extraction failed: extract command failed: ERROR : Failed to create user namespace: user namespace disabled : exit status 1

Work dir: Viatica19_stuff/ccsmeth/work/35/43c8a171fa7797ff93679faa5cf006

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line -- Check '.nextflow.log' file for details WARN: Killing running tasks (1)

executor > local (2) [- ] process > CheckGenome [ 0%] 0 of 1 [- ] process > CheckCMModel (CheckCMModel) - [35/43c8a1] process > CheckAGModel (CheckAGModel) [100%] 1 of 1, failed: 1 ✘ [- ] process > CCSMETH_pbccs_call_hifi - [- ] process > SAMTOOLS_index_bam [ 0%] 0 of 1 [- ] process > CCSMETH_call_mods_denovo - [- ] process > CCSMETH_align_hifi - [- ] process > SAMTOOLS_merge_sortedbams - [- ] process > CLAIR3_hifi - [- ] process > WHATSHAP_snv_phase_haplotag - [- ] process > CCSMETH_call_freq_bam - [- ] process > DSS_callDMR - ERROR ~ Error executing process > 'CheckAGModel (CheckAGModel)'

Caused by: Process CheckAGModel (CheckAGModel) terminated with an error exit status (255)

Command executed:

date; hostname; pwd

ccsmeth aggregate model

if [[ true == true && true == true ]]; then if [ "aggregate" != "aggregate" ]; then echo "### INFO: params.cf_mode != aggregate" elif [ null3 == null3 ] ; then echo "### INFO: gonna use the default ccsmeth_ag_model=tools/ccsmeth/models/model_ccsmeth_5mCpG_aggregate_attbigru_b11.v2p.ckpt" elif [[ null3 != .ckpt && null3 != .checkpoint ]]; then echo "### ERROR: not recognized ccsmeth_ag_model=null3" exit -1 fi cp -a null3 ccsmeth_aggregate_model.ckpt ls -lh ccsmeth_aggregate_model.ckpt fi

echo "### Check ag_model DONE"

Command exit status: 255

Command output: (empty)

Command error: INFO: Converting SIF file to temporary sandbox... FATAL: while extracting Viatica19_stuff/ccsmeth/local_singularity_cache/nipengcsu-ccsmethphase-latest.img: root filesystem extraction failed: extract command failed: ERROR : Failed to create user namespace: user namespace disabled : exit status 1

Work dir: Viatica19_stuff/ccsmeth/work/35/43c8a171fa7797ff93679faa5cf006

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

-- Check '.nextflow.log' file for details

i did change the DEFAULT_CCSMETH_CM_MODEL and DEFAULT_CCSMETH_AG_MODEL variable in the nextflow.config file with the absolute path to the model files in the ccsmeth directory. apart from this, no other changes have been made.

i still keep getting CheckAGMiodel or CheckCMModel error and don't get why. could you please help me out?

Thanks, Suvi

[PengNi]

Hi @suvi93 , sorry for the delay. It seemes this issue is related to "Unprivileged Singularity containers". You may ask your admins to check if Singularity was installed properly. Ref: https://singularity-admindoc.readthedocs.io/en/latest/security.html, https://stackoverflow.com/questions/73618551/error-failed-to-create-user-namespace-user-namespace-disabled-even-after-dis

Best, Peng

[suvi93]

Hi Peng,

i managed to fix that issue but now i have another issue -

Feb-21 08:05:35.657 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'WHATSHAP_snv_phase_haplotag (G1.m64077_220928_112919)'

Caused by: Process WHATSHAP_snv_phase_haplotag (G1.m64077_220928_112919) terminated with an error exit status (1)

Command executed:

date; hostname; pwd

vcf_prefix=G1.m64077_220928_112919.hifi.ccsmeth.modbam.pbmm2.merged_size1.clair3_merge.vcf.gz if [[ G1.m64077_220928_112919.hifi.ccsmeth.modbam.pbmm2.merged_size1.clair3_merge.vcf.gz == .vcf.gz ]]; then vcf_prefix=${vcf_prefix%.vcf.gz} elif [[ G1.m64077_220928_112919.hifi.ccsmeth.modbam.pbmm2.merged_size1.clair3_merge.vcf.gz == .vcf ]]; then vcf_prefix=${vcf_prefix%.vcf} fi

echo ${vcf_prefix}

gunzip -c G1.m64077_220928_112919.hifi.ccsmeth.modbam.pbmm2.merged_size1.clair3_merge.vcf.gz | awk '/^#/ || ($4 != "." && $5 != "." && length($4) == 1 && length($5) == 1 && $7 =="PASS")' - > ${vcf_prefix}.SNV_PASS.vcf whatshap phase --ignore-read-groups --reference genome_ref_dir/test.genome_ref.fasta -o ${vcf_prefix}.SNV_PASS_whatshap.vcf ${vcf_prefix}.SNV_PASS.vcf G1.m64077_220928_112919.hifi.ccsmeth.modbam.pbmm2.merged_size1.bam > ${vcf_prefix}.SNV_PASS_whatshap.whatshap_phased.log 2>&1 rm ${vcf_prefix}.SNV_PASS.vcf bgzip -@ 10 ${vcf_prefix}.SNV_PASS_whatshap.vcf && tabix -C -p vcf ${vcf_prefix}.SNV_PASS_whatshap.vcf.gz whatshap haplotag --ignore-read-groups --output-haplotag-list G1.m64077_220928_112919.hifi.ccsmeth.modbam.pbmm2.merged_size1.SNV_PASS_whatshap.bam.readlist -o G1.m64077_220928_112919.hifi.ccsmeth.modbam.pbmm2.merged_size1.SNV_PASS_whatshap.bam --reference genome_ref_dir/test.genome_ref.fasta ${vcf_prefix}.SNV_PASS_whatshap.vcf.gz G1.m64077_220928_112919.hifi.ccsmeth.modbam.pbmm2.merged_size1.bam > G1.m64077_220928_112919.hifi.ccsmeth.modbam.pbmm2.merged_size1.SNV_PASS_whatshap.whatshap_haplotag.log 2>&1 samtools index -c -@ 10 G1.m64077_220928_112919.hifi.ccsmeth.modbam.pbmm2.merged_size1.SNV_PASS_whatshap.bam

Command exit status: 1 Command output: Wed Feb 21 08:05:35 CET 2024 s193.uppmax.uu.se /crex/proj/snic2021-6-151/private/Suvi/samples/Viatica19_stuff/ccsmeth/work/fa/980ae96e4da7324282336725e1943f

Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred INFO: Environment variable SINGULARITYENV_CUDA_VISIBLE_DEVICES is set, but APPTAINERENV_CUDA_VISIBLE_DEVICES is preferred Wed Feb 21 08:05:35 CET 2024 s193.uppmax.uu.se /crex/proj/snic2021-6-151/private/Suvi/samples/Viatica19_stuff/ccsmeth/work/fa/980ae96e4da7324282336725e1943f

gzip: G1.m64077_220928_112919.hifi.ccsmeth.modbam.pbmm2.merged_size1.clair3_merge.vcf.gz: unexpected end of file

when i check the work directory and the results directory, it looks like clair3 did not run as it outputs an empty file. i'm not sure where its going wrong as none of the out or err files say exactly what the problem is.

Thanks & regards, Suvi