Error in compileCode when running mapDamage

[Fishball99]

This is my script: `haystac sample \ --fastq-r1 "/data1/user/zhaozh/2.PIG/1.screen/10.CSSS_230928/rawdata/X101SC23023451-Z01-J242/01.RawData/SS16/SS16_1.fq.gz" \ --fastq-r2 "/data1/user/zhaozh/2.PIG/1.screen/10.CSSS_230928/rawdata/X101SC23023451-Z01-J242/01.RawData/SS16/SS16_2.fq.gz" \ --output "Sample_SS16" \ --cores 64 \ --mem 102400 \ --collapse True

haystac analyse --mode abundances \ --database /data1/user/yuwq/haystac_db2/pathogen20240321/ \ --sample "Sample_SS16" \ --output "Output_SS16" \ --aDNA \ --cores 64 \ --mem 102400`

Error printed in snakemake log is here: [Mon Jun 10 15:49:25 2024] Error in rule run_mapdamage: jobid: 1069 output: /data1/user/yuwq/haystac_db2/Output_ZJSS026/mapdamage/Sample_ZJSS026/COLLAPSED/Trypanosoma_cruzi/GCF_000209065.1 log: /data1/user/yuwq/haystac_db2/Output_ZJSS026/mapdamage/Sample_ZJSS026/COLLAPSED/Trypanosoma_cruzi_GCF_000209065.1.log (check log file(s) for error message) conda-env: /data1/user/yuwq/haystac/cache/conda/f6339089f4a4ca604fcdb438cc255db4 shell: mapDamage -i /data1/user/yuwq/haystac_db2/Output_ZJSS026/rmdup_bam/Sample_ZJSS026/COLLAPSED/Trypanosoma_cruzi/Trypanosoma_cruzi_GCF_000209065.1_dirichlet_COLLAPSED_rmdup.bam -r /data1/user/yuwq/haystac/cache/ncbi/Trypanosoma_cruzi/GCF_000209065.1.fasta.gz -d /data1/user/yuwq/haystac_db2/Output_ZJSS026/mapdamage/Sample_ZJSS026/COLLAPSED/Trypanosoma_cruzi/GCF_000209065.1 2> /data1/user/yuwq/haystac_db2/Output_ZJSS026/mapdamage/Sample_ZJSS026/COLLAPSED/Trypanosoma_cruzi_GCF_000209065.1.log (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job run_mapdamage since they might be corrupted:

And the detailed content of log is here: Started with the command: /data1/user/yuwq/haystac/cache/conda/f6339089f4a4ca604fcdb438cc255db4/bin/mapDamage -i /data1/user/yuwq/haystac_db2/Output_ZJSS026/rmdup_bam/Sample_ZJSS026/COLLAPSED/Trypanosoma_cruzi/Trypanosoma_cruzi_GCF_000209065.1_dirichlet_COLLAPSED_rmdup.bam -r /data1/user/yuwq/haystac/cache/ncbi/Trypanosoma_cruzi/GCF_000209065.1.fasta.gz -d /data1/user/yuwq/haystac_db2/Output_ZJSS026/mapdamage/Sample_ZJSS026/COLLAPSED/Trypanosoma_cruzi/GCF_000209065.1 Performing Bayesian estimates Error in compileCode(f, code, language = language, verbose = verbose) : Compilation ERROR, function(s)/method(s) not created! Error in if (nzchar(SHLIB_LIBADD)) SHLIB_LIBADD else character() : argument is of length zero Calls: -> .shlib_internal Execution halted Calls: source ... withVisible -> eval -> eval -> cxxfunction -> compileCode In addition: Warning messages: 1: package ‘foreach’ was built under R version 4.0.5 2: package ‘RcppGSL’ was built under R version 4.0.5 3: In system(cmd, intern = !verbose) : running command '/data1/user/yuwq/haystac/cache/conda/f6339089f4a4ca604fcdb438cc255db4/lib/R/bin/R CMD SHLIB file1a5d6179c6e26.cpp 2> file1a5d6179c6e26.cpp.err.txt' had status 1 The Bayesian statistics program failed to finish Traceback (most recent call last): File "/data1/user/yuwq/haystac/cache/conda/f6339089f4a4ca604fcdb438cc255db4/bin/mapDamage", line 371, in sys.exit(main()) File "/data1/user/yuwq/haystac/cache/conda/f6339089f4a4ca604fcdb438cc255db4/bin/mapDamage", line 354, in main mapdamage.rscript.run_stats(options) File "/data1/user/yuwq/haystac/cache/conda/f6339089f4a4ca604fcdb438cc255db4/lib/python3.9/site-packages/mapdamage/rscript.py", line 142, in run_stats raise e File "/data1/user/yuwq/haystac/cache/conda/f6339089f4a4ca604fcdb438cc255db4/lib/python3.9/site-packages/mapdamage/rscript.py", line 139, in run_stats check_call(arg) File "/data1/user/yuwq/haystac/cache/conda/f6339089f4a4ca604fcdb438cc255db4/lib/python3.9/subprocess.py", line 373, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['Rscript', '/data1/user/yuwq/haystac/cache/conda/f6339089f4a4ca604fcdb438cc255db4/lib/python3.9/site-packages/mapdamage/Rscripts/stats/runGeneral.R', '--args', '30', '10000', '10', '50000', '0', '0', '1', '1', '0', '0', '1', '12', '/data1/user/yuwq/haystac_db2/Output_ZJSS026/mapdamage/Sample_ZJSS026/COLLAPSED/Trypanosoma_cruzi/GCF_000209065.1/', '/data1/user/yuwq/haystac/cache/conda/f6339089f4a4ca604fcdb438cc255db4/lib/python3.9/site-packages/mapdamage/Rscripts/stats/', '/data1/user/yuwq/haystac_db2/Output_ZJSS026/mapdamage/Sample_ZJSS026/COLLAPSED/Trypanosoma_cruzi/GCF_000209065.1/Stats_out', '0', '0', '0', '/data1/user/yuwq/haystac_db2/Output_ZJSS026/mapdamage/Sample_ZJSS026/COLLAPSED/Trypanosoma_cruzi/GCF_000209065.1/acgt_ratio.csv', '0', '0']' returned non-zero exit status 1.

Thank you for your response!

[antonisdim]

Hello,

I am really sorry for the delay ! I'll have a look this week and get back to you ASAP.

Thank you !

[Fishball99]

Thank you,

Looking forward to your response!