Error in rule hisat2_to_Genome

[ptnaimelmm]

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]

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!)