quantms with Mac - Githubissues

Tried out the same pipeline in VScode and got a similar error:

(R-cb2110) emiljohansson@emiljmbp lab1 % sudo nextflow run bigbio/quantms -r master --input 'sdrf.tsv' --outdir 'results' --database 'uniprotkb_Human_AND_reviewed_true_2024_08_15.fasta' -profile docker --root_folder ~/emiljohansson/R/CB2110/lab1 --local_input_type raw --add_decoys true --max_memory 8GB --max_cpus 4 --platform linux/amd64 Password:

N E X T F L O W ~ version 24.07.0-edge

Launching https://github.com/bigbio/quantms [crazy_tesla] DSL2 - revision: 3586089523 [master]

WARN: The following invalid input values have been detected:

--platform: linux/amd64

                                    ,--./,-.
    ___     __   __   __   ___     /,-._.--~'

|\ | | / `/ \ |) | } { | \| | \, \/ | \ |___ \`-.,-`-,` .,._,' nf-core/quantms v1.2.0-g3586089

Core Nextflow options revision : master runName : crazy_tesla containerEngine : docker launchDir : /Users/emiljohansson/R/CB2110/lab1 workDir : /Users/emiljohansson/R/CB2110/lab1/work projectDir : /Users/emiljohansson/.nextflow/assets/bigbio/quantms userName : root profile : docker configFiles :

Input/output options input : sdrf.tsv outdir : results root_folder : /Users/emiljohansson/emiljohansson/R/CB2110/lab1 local_input_type : raw acquisition_method : null

Protein database database : uniprotkb_Human_AND_reviewed_true_2024_08_15.fasta add_decoys : true

Database search instrument : null

Modification localization luciphor_debug : 0

PSM re-scoring (general) run_fdr_cutoff : 0.10

PSM re-scoring (Percolator) description_correct_features : 0

Consensus ID consensusid_considered_top_hits: 0 min_consensus_support : 0

Isobaric analyzer select_activation : HCD

Protein Quantification (LFQ) feature_with_id_min_score : 0.10 feature_without_id_min_score : 0.75 lfq_intensity_threshold : 1000

DIA-NN scan_window : 8

Statistical post-processing contrasts : pairwise

Quality control enable_pmultiqc : true pmultiqc_idxml_skip : true

Max job request options max_cpus : 4 max_memory : 8GB max_time : 10d

!! Only displaying parameters that differ from the pipeline defaults !!

If you use nf-core/quantms for your analysis please cite:

The nf-core framework https://doi.org/10.1038/s41587-020-0439-x
Software dependencies https://github.com/nf-core/quantms/blob/master/CITATIONS.md

executor > local (1) [87/a4b657] NFC…QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (sdrf.tsv) | 0 of 1 [- ] NFC…QUANTMS:QUANTMS:CREATE_INPUT_CHANNEL:SDRFPARSING - executor > local (1) [87/a4b657] NFC…QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (sdrf.tsv) | 0 of 1 [- ] NFC…QUANTMS:QUANTMS:CREATE_INPUT_CHANNEL:SDRFPARSING - [- ] NFCORE_QUANTMS:QUANTMS:FILE_PREPARATION:DECOMPRESS - [- ] NFCORE_QUANTMS:QUANTMS:FILE_PREPARATION:MZMLINDEXING - [- ] NFC…TMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER - [- ] NFC…_QUANTMS:QUANTMS:FILE_PREPARATION:MZMLSTATISTICS - [- ] NFCORE_QUANTMS:QUANTMS:DECOYDATABASE - [- ] NFC…S:TMT:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET - [- ] NFC…S:QUANTMS:TMT:ID:PSMRESCORING:EXTRACTPSMFEATURES - Plus 29 more processes waiting for tasks… WARN: There's no process matching config selector: MULTIQC -- Did you mean: PMULTIQC? WARN: Undocumented setting docker.userEmulation is not supported any more - please remove it from your config ERROR ~ Error executing process > 'NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (sdrf.tsv)'

Caused by: Process NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (sdrf.tsv) terminated with an error exit status (1)

Command executed:

check_samplesheet.py "sdrf.tsv" true --CHECK_MS 2>&1 | tee input_check.log

cat <<-END_VERSIONS > versions.yml "NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK": sdrf-pipelines: $(parse_sdrf --version 2>&1 | awk -F ' ' '{print $2}') END_VERSIONS

Command exit status: 1

Command output: (empty)

Command error: executor > local (1) [87/a4b657] NFC…QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (sdrf.tsv) | 1 of 1, failed: 1 ✘ [- ] NFC…QUANTMS:QUANTMS:CREATE_INPUT_CHANNEL:SDRFPARSING - [- ] NFCORE_QUANTMS:QUANTMS:FILE_PREPARATION:DECOMPRESS - [- ] NFCORE_QUANTMS:QUANTMS:FILE_PREPARATION:MZMLINDEXING - [- ] NFC…TMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER - [- ] NFC…_QUANTMS:QUANTMS:FILE_PREPARATION:MZMLSTATISTICS - [- ] NFCORE_QUANTMS:QUANTMS:DECOYDATABASE - [- ] NFC…S:TMT:ID:DATABASESEARCHENGINES:SEARCHENGINECOMET - [- ] NFC…S:QUANTMS:TMT:ID:PSMRESCORING:EXTRACTPSMFEATURES - Plus 29 more processes waiting for tasks… Execution cancelled -- Finishing pending tasks before exit -[nf-core/quantms] Pipeline completed with errors- WARN: There's no process matching config selector: MULTIQC -- Did you mean: PMULTIQC? WARN: Undocumented setting docker.userEmulation is not supported any more - please remove it from your config ERROR ~ Error executing process > 'NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (sdrf.tsv)'

Caused by: Process NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (sdrf.tsv) terminated with an error exit status (1)

Command executed:

check_samplesheet.py "sdrf.tsv" true --CHECK_MS 2>&1 | tee input_check.log

cat <<-END_VERSIONS > versions.yml "NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK": sdrf-pipelines: $(parse_sdrf --version 2>&1 | awk -F ' ' '{print $2}') END_VERSIONS

Command exit status: 1

Command output: (empty)

Caused by: Process NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (sdrf.tsv) terminated with an error exit status (1)

Command executed:

check_samplesheet.py "sdrf.tsv" true --CHECK_MS 2>&1 | tee input_check.log

cat <<-END_VERSIONS > versions.yml "NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK": sdrf-pipelines: $(parse_sdrf --version 2>&1 | awk -F ' ' '{print $2}') END_VERSIONS

Command exit status: 1

Command output: (empty)

Command error: WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested touch: cannot touch '.command.trace': Permission denied

Work dir: /Users/emiljohansson/R/CB2110/lab1/work/87/a4b657405d49abcd7ab2a3d93d687c

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

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

thanadol-git / quantms_example

quantms with Mac #2

|\ | | / `/ \ |) | } { | \| | \, \/ | \ |___ \`-.,-`-,` .,._,' nf-core/quantms v1.2.0-g3586089

!! Only displaying parameters that differ from the pipeline defaults !!

thanadol-git / quantms_example

quantms with Mac #2

|\ | | / / \ |__) |__ } { | \| | \__, \__/ | \ |___ \-.,--, .,._,' nf-core/quantms v1.2.0-g3586089

!! Only displaying parameters that differ from the pipeline defaults !!

|\ | | / `/ \ |) | } { | \| | \, \/ | \ |___ \`-.,-`-,` .,._,' nf-core/quantms v1.2.0-g3586089