test_dia runs into THERMORAWFILEPARSER error #661
Description
Description of the bug
I am running test locally on MacOS and it runs into exit code 134.
traceback
❯ nextflow run bigbio/quantms -r 1.7.0 -profile test_dia,docker
N E X T F L O W ~ version 25.10.4
Launching `https://github.com/bigbio/quantms` [elated_euclid] DSL2 - revision: e719f43a9f [1.7.0]
executor > local (4)
executor > local (4)
executor > local (5)
[9b/d2e6e6] BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (PXD026600.sdrf.tsv) [100%] 1 of 1 ✔
executor > local (6)
[9b/d2e6e6] BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (PXD026600.sdrf.tsv) [100%] 1 of 1 ✔
executor > local (6)
[9b/d2e6e6] BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (PXD026600.sdrf.tsv) [100%] 1 of 1 ✔
[3f/b89f0a] BIGBIO_QUANTMS:QUANTMS:CREATE_INPUT_CHANNEL:SDRF_PARSING (PXD026600.sdrf.tsv) [100%] 1 of 1 ✔
[- ] BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:DECOMPRESS -
[- ] BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:MZML_INDEXING -
[bd/7e0014] BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER (RD139_Narrow_UPS1_0_1fmol_inj2) [ 0%] 0 of 2, retries: 2
[- ] BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:MZML_STATISTICS -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:ID:PEPTIDE_DATABASE_SEARCH:COMET -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:ID:PSM_RESCORING:PERCOLATOR -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:ID:PSM_FDR_CONTROL:ID_FILTER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:FEATURE_MAPPER:ISOBARIC_ANALYZER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:FEATURE_MAPPER:ID_MAPPER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:FILE_MERGE -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_INFERENCE:PROTEIN_INFERENCE_GENERIC -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_INFERENCE:ID_FILTER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_QUANT:ID_CONFLICT_RESOLVER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_QUANT:PROTEIN_QUANTIFIER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_QUANT:MSSTATS_CONVERTER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:MSSTATS_TMT -
[- ] BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PEPTIDE_DATABASE_SEARCH:COMET -
[- ] BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PSM_RESCORING:PERCOLATOR -
[- ] BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PSM_FDR_CONTROL:ID_FILTER -
[- ] BIGBIO_QUANTMS:QUANTMS:LFQ:PROTEOMICSLFQ -
[- ] BIGBIO_QUANTMS:QUANTMS:LFQ:MSSTATS_LFQ -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:GENERATE_CFG -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:INSILICO_LIBRARY_GENERATION -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:PRELIMINARY_ANALYSIS -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:ASSEMBLE_EMPIRICAL_LIBRARY -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:INDIVIDUAL_ANALYSIS -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:FINAL_QUANTIFICATION -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:CONVERT_RESULTS -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:MSSTATS_LFQ -
[- ] BIGBIO_QUANTMS:QUANTMS:SUMMARY_PIPELINE -
[51/dcbb39] NOTE: Process `BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER (RD139_Narrow_UPS1_0_25fmol_inj1)` terminated with an error exit status (134) -- Execution is retried (1)
[e9/0d49ce] NOTE: Process `BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER (RD139_Narrow_UPS1_0_25fmol_inj1)` terminated with an error exit status (134) -- Execution is retried (2)
ERROR ~ Error executing process > 'BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER (RD139_Narrow_UPS1_0_25fmol_inj1)'
Caused by:
Process `BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER (RD139_Narrow_UPS1_0_25fmol_inj1)` terminated with an error exit status (134)
Command executed:
ThermoRawFileParser.sh -i='RD139_Narrow_UPS1_0_25fmol_inj1.raw' -f=2 -o=./ 2>&1 | tee 'RD139_Narrow_UPS1_0_25fmol_inj1_conversion.log'
cat <<-END_VERSIONS > versions.yml
"BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER":
ThermoRawFileParser: $(ThermoRawFileParser.sh --version)
END_VERSIONS
Command exit status:
134
Command output:
Waiting for dumping threads to resume
=================================================================
External Debugger Dump:
=================================================================
mono_gdb_render_native_backtraces not supported on this platform, unable to find gdb or lldb
=================================================================
Basic Fault Address Reporting
=================================================================
Memory around native instruction pointer (0x7fffff547e2c):0x7fffff547e1c 04 00 44 89 e2 89 de 89 c7 b8 ea 00 00 00 0f 05 ..D.............
0x7fffff547e2c 89 c5 f7 dd 3d 00 f0 ff ff b8 00 00 00 00 0f 47 ....=..........G
0x7fffff547e3c c5 e9 7a ff ff ff 66 0f 1f 44 00 00 4c 89 ef e8 ..z...f..D..L...
0x7fffff547e4c 90 b2 ff ff e9 4e ff ff ff 0f 1f 00 4c 89 ef e8 .....N......L...
=================================================================
Managed Stacktrace:
=================================================================
at <unknown> <0xffffffff>
at System.Xml.XmlTextReaderImpl:ReadData <0x00783>
at System.Xml.XmlTextReaderImpl:InitStreamInput <0x00513>
at System.Xml.XmlTextReaderImpl:InitStreamInput <0x0005f>
at System.Xml.XmlTextReaderImpl:.ctor <0x000d3>
at System.Xml.XmlTextReaderImpl:.ctor <0x00087>
at System.Xml.XmlTextReader:.ctor <0x0006f>
at ConfigXmlTextReader:.ctor <0x00047>
at System.Configuration.Configuration:Load <0x00167>
at System.Configuration.Configuration:Init <0x0020b>
at System.Configuration.Configuration:.ctor <0x0018b>
at System.Configuration.Configuration:.ctor <0x00147>
at System.Configuration.InternalConfigurationFactory:Create <0x000a7>
at System.Configuration.ConfigurationManager:OpenExeConfigurationInternal <0x003fe>
at System.Configuration.ClientConfigurationSystem:get_Configuration <0x0006b>
at System.Configuration.ClientConfigurationSystem:System.Configuration.Internal.IInternalConfigSystem.GetSection <0x0003f>
at System.Configuration.ConfigurationManager:GetSection <0x0005d>
at System.Configuration.ConfigurationManager:get_AppSettings <0x0003b>
at log4net.Util.SystemInfo:GetAppSetting <0x00037>
at log4net.Util.SystemInfo:.cctor <0x000cf>
at System.Object:runtime_invoke_void <0x0009d>
at <unknown> <0xffffffff>
at log4net.Core.LoggerManager:GetVersionInfo <0x00143>
at log4net.Core.LoggerManager:.cctor <0x00107>
at System.Object:runtime_invoke_void <0x0009d>
at <unknown> <0xffffffff>
at log4net.LogManager:GetLogger <0x00043>
at log4net.LogManager:GetLogger <0x0005b>
at ThermoRawFileParser.MainClass:.cctor <0x00047>
at System.Object:runtime_invoke_void <0x0009d>
=================================================================
/usr/local/bin/ThermoRawFileParser.sh: line 3: 46 Aborted mono $DIR/ThermoRawFileParser.exe "$@"
Command error:
Waiting for dumping threads to resume
executor > local (6)
[9b/d2e6e6] BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (PXD026600.sdrf.tsv) [100%] 1 of 1 ✔
[3f/b89f0a] BIGBIO_QUANTMS:QUANTMS:CREATE_INPUT_CHANNEL:SDRF_PARSING (PXD026600.sdrf.tsv) [100%] 1 of 1 ✔
[- ] BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:DECOMPRESS -
[- ] BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:MZML_INDEXING -
[bd/7e0014] BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER (RD139_Narrow_UPS1_0_1fmol_inj2) [ 0%] 0 of 2, retries: 2
[- ] BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:MZML_STATISTICS -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:ID:PEPTIDE_DATABASE_SEARCH:COMET -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:ID:PSM_RESCORING:PERCOLATOR -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:ID:PSM_FDR_CONTROL:ID_FILTER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:FEATURE_MAPPER:ISOBARIC_ANALYZER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:FEATURE_MAPPER:ID_MAPPER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:FILE_MERGE -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_INFERENCE:PROTEIN_INFERENCE_GENERIC -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_INFERENCE:ID_FILTER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_QUANT:ID_CONFLICT_RESOLVER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_QUANT:PROTEIN_QUANTIFIER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:PROTEIN_QUANT:MSSTATS_CONVERTER -
[- ] BIGBIO_QUANTMS:QUANTMS:TMT:MSSTATS_TMT -
[- ] BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PEPTIDE_DATABASE_SEARCH:COMET -
[- ] BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PSM_RESCORING:PERCOLATOR -
[- ] BIGBIO_QUANTMS:QUANTMS:LFQ:ID:PSM_FDR_CONTROL:ID_FILTER -
[- ] BIGBIO_QUANTMS:QUANTMS:LFQ:PROTEOMICSLFQ -
[- ] BIGBIO_QUANTMS:QUANTMS:LFQ:MSSTATS_LFQ -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:GENERATE_CFG -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:INSILICO_LIBRARY_GENERATION -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:PRELIMINARY_ANALYSIS -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:ASSEMBLE_EMPIRICAL_LIBRARY -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:INDIVIDUAL_ANALYSIS -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:FINAL_QUANTIFICATION -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:CONVERT_RESULTS -
[- ] BIGBIO_QUANTMS:QUANTMS:DIA:MSSTATS_LFQ -
[- ] BIGBIO_QUANTMS:QUANTMS:SUMMARY_PIPELINE -
-[bigbio/quantms] Pipeline completed with errors-
[51/dcbb39] NOTE: Process `BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER (RD139_Narrow_UPS1_0_25fmol_inj1)` terminated with an error exit status (134) -- Execution is retried (1)
[e9/0d49ce] NOTE: Process `BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER (RD139_Narrow_UPS1_0_25fmol_inj1)` terminated with an error exit status (134) -- Execution is retried (2)
WARN: Killing running tasks (1)
ERROR ~ Error executing process > 'BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER (RD139_Narrow_UPS1_0_25fmol_inj1)'
Caused by:
Process `BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER (RD139_Narrow_UPS1_0_25fmol_inj1)` terminated with an error exit status (134)
Command executed:
ThermoRawFileParser.sh -i='RD139_Narrow_UPS1_0_25fmol_inj1.raw' -f=2 -o=./ 2>&1 | tee 'RD139_Narrow_UPS1_0_25fmol_inj1_conversion.log'
cat <<-END_VERSIONS > versions.yml
"BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER":
ThermoRawFileParser: $(ThermoRawFileParser.sh --version)
END_VERSIONS
Command exit status:
134
Command output:
Waiting for dumping threads to resume
=================================================================
External Debugger Dump:
=================================================================
mono_gdb_render_native_backtraces not supported on this platform, unable to find gdb or lldb
=================================================================
Basic Fault Address Reporting
=================================================================
Memory around native instruction pointer (0x7fffff547e2c):0x7fffff547e1c 04 00 44 89 e2 89 de 89 c7 b8 ea 00 00 00 0f 05 ..D.............
0x7fffff547e2c 89 c5 f7 dd 3d 00 f0 ff ff b8 00 00 00 00 0f 47 ....=..........G
0x7fffff547e3c c5 e9 7a ff ff ff 66 0f 1f 44 00 00 4c 89 ef e8 ..z...f..D..L...
0x7fffff547e4c 90 b2 ff ff e9 4e ff ff ff 0f 1f 00 4c 89 ef e8 .....N......L...
=================================================================
Managed Stacktrace:
=================================================================
at <unknown> <0xffffffff>
at System.Xml.XmlTextReaderImpl:ReadData <0x00783>
at System.Xml.XmlTextReaderImpl:InitStreamInput <0x00513>
at System.Xml.XmlTextReaderImpl:InitStreamInput <0x0005f>
at System.Xml.XmlTextReaderImpl:.ctor <0x000d3>
at System.Xml.XmlTextReaderImpl:.ctor <0x00087>
at System.Xml.XmlTextReader:.ctor <0x0006f>
at ConfigXmlTextReader:.ctor <0x00047>
at System.Configuration.Configuration:Load <0x00167>
at System.Configuration.Configuration:Init <0x0020b>
at System.Configuration.Configuration:.ctor <0x0018b>
at System.Configuration.Configuration:.ctor <0x00147>
at System.Configuration.InternalConfigurationFactory:Create <0x000a7>
at System.Configuration.ConfigurationManager:OpenExeConfigurationInternal <0x003fe>
at System.Configuration.ClientConfigurationSystem:get_Configuration <0x0006b>
at System.Configuration.ClientConfigurationSystem:System.Configuration.Internal.IInternalConfigSystem.GetSection <0x0003f>
at System.Configuration.ConfigurationManager:GetSection <0x0005d>
at System.Configuration.ConfigurationManager:get_AppSettings <0x0003b>
at log4net.Util.SystemInfo:GetAppSetting <0x00037>
at log4net.Util.SystemInfo:.cctor <0x000cf>
at System.Object:runtime_invoke_void <0x0009d>
at <unknown> <0xffffffff>
at log4net.Core.LoggerManager:GetVersionInfo <0x00143>
at log4net.Core.LoggerManager:.cctor <0x00107>
at System.Object:runtime_invoke_void <0x0009d>
at <unknown> <0xffffffff>
at log4net.LogManager:GetLogger <0x00043>
at log4net.LogManager:GetLogger <0x0005b>
at ThermoRawFileParser.MainClass:.cctor <0x00047>
at System.Object:runtime_invoke_void <0x0009d>
=================================================================
/usr/local/bin/ThermoRawFileParser.sh: line 3: 46 Aborted mono $DIR/ThermoRawFileParser.exe "$@"
Command error:
Waiting for dumping threads to resume
=================================================================
External Debugger Dump:
=================================================================
mono_gdb_render_native_backtraces not supported on this platform, unable to find gdb or lldb
=================================================================
Basic Fault Address Reporting
=================================================================
Memory around native instruction pointer (0x7fffff547e2c):0x7fffff547e1c 04 00 44 89 e2 89 de 89 c7 b8 ea 00 00 00 0f 05 ..D.............
0x7fffff547e2c 89 c5 f7 dd 3d 00 f0 ff ff b8 00 00 00 00 0f 47 ....=..........G
0x7fffff547e3c c5 e9 7a ff ff ff 66 0f 1f 44 00 00 4c 89 ef e8 ..z...f..D..L...
0x7fffff547e4c 90 b2 ff ff e9 4e ff ff ff 0f 1f 00 4c 89 ef e8 .....N......L...
=================================================================
Managed Stacktrace:
=================================================================
at <unknown> <0xffffffff>
at System.Xml.XmlTextReaderImpl:ReadData <0x00783>
at System.Xml.XmlTextReaderImpl:InitStreamInput <0x00513>
at System.Xml.XmlTextReaderImpl:InitStreamInput <0x0005f>
at System.Xml.XmlTextReaderImpl:.ctor <0x000d3>
at System.Xml.XmlTextReaderImpl:.ctor <0x00087>
at System.Xml.XmlTextReader:.ctor <0x0006f>
at ConfigXmlTextReader:.ctor <0x00047>
at System.Configuration.Configuration:Load <0x00167>
at System.Configuration.Configuration:Init <0x0020b>
at System.Configuration.Configuration:.ctor <0x0018b>
at System.Configuration.Configuration:.ctor <0x00147>
at System.Configuration.InternalConfigurationFactory:Create <0x000a7>
at System.Configuration.ConfigurationManager:OpenExeConfigurationInternal <0x003fe>
at System.Configuration.ClientConfigurationSystem:get_Configuration <0x0006b>
at System.Configuration.ClientConfigurationSystem:System.Configuration.Internal.IInternalConfigSystem.GetSection <0x0003f>
at System.Configuration.ConfigurationManager:GetSection <0x0005d>
at System.Configuration.ConfigurationManager:get_AppSettings <0x0003b>
at log4net.Util.SystemInfo:GetAppSetting <0x00037>
at log4net.Util.SystemInfo:.cctor <0x000cf>
at System.Object:runtime_invoke_void <0x0009d>
at <unknown> <0xffffffff>
at log4net.Core.LoggerManager:GetVersionInfo <0x00143>
at log4net.Core.LoggerManager:.cctor <0x00107>
at System.Object:runtime_invoke_void <0x0009d>
at <unknown> <0xffffffff>
at log4net.LogManager:GetLogger <0x00043>
at log4net.LogManager:GetLogger <0x0005b>
at ThermoRawFileParser.MainClass:.cctor <0x00047>
at System.Object:runtime_invoke_void <0x0009d>
=================================================================
/usr/local/bin/ThermoRawFileParser.sh: line 3: 46 Aborted mono $DIR/ThermoRawFileParser.exe "$@"
Work dir:
/Users/jnimoca/Jose_BI/2_Infrastructure/PY19_quantms_test/work/75/bfbd54af971afb43616e286316fae9
Container:
quay.io/biocontainers/thermorawfileparser:1.4.5--h05cac1d_1
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
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '.nextflow.log' file for details
WARN: Failed to render execution report -- see the log file for details
WARN: Failed to render execution timeline -- see the log file for details
Command used and terminal output
nextflow run bigbio/quantms -r 1.7.0 -profile test_dia,dockerRelevant files
System information
MacOs 15.7.3
Nextflow 25.10.4
Macbook Pro M3 Max
Executor local
Container Docker
quantms 1.7.0