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hemberg-lab / MicroExonator

Snakemake pipeline for microexon discovery and quantification
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Error in rule hisat2_to_Genome #41

Open ptnaimelmm opened 2 years ago

ptnaimelmm commented 2 years ago

Hi there,

I tried to use MicroExonator to analyze my dataset. The program finished successfully with -np. However, Errors as shown below occurred when I used it for my data analysis with "snakemake -s MicroExonator.smk --use-conda -k -c1". Could you help me to figure out what is the problem. Thanks in advance. Error log: [Tue Oct 12 18:54:15 2021] rule hisat2_to_Genome: input: Round1/SRR10316370_1_val_1.sam.row_ME.fastq, data/Genome.1.ht2 output: Round1/SRR10316370_1_val_1.sam.row_ME.Genome.Aligned.out.sam jobid: 23 wildcards: sample=SRR10316370_1_val_1 resources: tmpdir=/tmp

Activating conda environment: /scratch/users/mliu63@jhu.edu/MicroExonator/MicroExonator/.snakemake/conda/b2cf3cb0bb8978aae83afeb8d09ff3fa [Tue Oct 12 18:54:20 2021] Error in rule hisat2_to_Genome: jobid: 23 output: Round1/SRR10316370_1_val_1.sam.row_ME.Genome.Aligned.out.sam conda-env: /scratch/users/mliu63@jhu.edu/MicroExonator/MicroExonator/.snakemake/conda/b2cf3cb0bb8978aae83afeb8d09ff3fa shell: hisat2 -x data/Genome -U Round1/SRR10316370_1_val_1.sam.row_ME.fastq > Round1/SRR10316370_1_val_1.sam.row_ME.Genome.Aligned.out.sam (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job hisat2_to_Genome since they might be corrupted: Round1/SRR10316370_1_val_1.sam.row_ME.Genome.Aligned.out.sam Job failed, going on with independent jobs. Select jobs to execute...

Best regards,

Mingming Errors.txt

ptnaimelmm commented 2 years ago

Before this error, there are a lot of indications as follows. Possible unintended interpolation of @jhu in string at /scratch/users/mliu63@jhu.edu/MicroExonator/MicroExonator/.snakemake/conda/b2cf3cb0bb8978aae83afeb8d09ff3fa/lib/perl5/5.32/core_perl/Config_heavy.pl line 241. Possible unintended interpolation of @jhu in string at /scratch/users/mliu63@jhu.edu/MicroExonator/MicroExonator/.snakemake/conda/b2cf3cb0bb8978aae83afeb8d09ff3fa/lib/perl5/5.32/core_perl/Config_heavy.pl line 242. Possible unintended interpolation of @jhu in string at /scratch/users/mliu63@jhu.edu/MicroExonator/MicroExonator/.snakemake/conda/b2cf3cb0bb8978aae83afeb8d09ff3fa/lib/perl5/5.32/core_perl/Config_heavy.pl line 269. Possible unintended interpolation of @jhu in string at /scratch/users/mliu63@jhu.edu/MicroExonator/MicroExonator/.snakemake/conda/b2cf3cb0bb8978aae83afeb8d09ff3fa/lib/perl5/5.32/core_perl/Config_heavy.pl line 270. ...... Compilation failed in require at /scratch/users/mliu63@jhu.edu/MicroExonator/MicroExonator/.snakemake/conda/b2cf3cb0bb8978aae83afeb8d09ff3fa/lib/perl5/5.32/core_perl/Config.pm line 105. [Wed Oct 13 15:27:08 2021] Error in rule hisat2_to_Genome: jobid: 23 output: Round1/93_2.sam.row_ME.Genome.Aligned.out.sam conda-env: /scratch/users/mliu63@jhu.edu/MicroExonator/MicroExonator/.snakemake/conda/b2cf3cb0bb8978aae83afeb8d09ff3fa shell: hisat2 -x data/Genome -U Round1/93_2.sam.row_ME.fastq > Round1/93_2.sam.row_ME.Genome.Aligned.out.sam (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)