errors after cutadapt

[Sevgi-k]

Hi, I installed aMeta after reading "Remote providers have been replaced" in the issues folder. Also, the test run worked without any errors. Right now, I am trying to run aMeta using the full nt database for one sample but I am getting errors after cutadapt trimming. Here is the log file:

Activating conda environment: /work/kaynar1/aMeta/.snakemake/conda/96dcd9900f71782aa6bfd6ab41ccd9eb Activating conda environment: /work/kaynar1/aMeta/.snakemake/conda/9bec8250133a041528200979af38c4b3 Waiting at most 5 seconds for missing files. MissingOutputException in line 1 of /work/kaynar1/aMeta/workflow/rules/krakenuniq.smk: Job Missing files after 5 seconds: results/KRAKENUNIQ/2A-12A-1-83-85_WD_4g/sequences.krakenuniq This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait. Job id: 9 completed successfully, but some output files are missing. 9 File "/home/kaynar1/.conda/envs/aMeta/lib/python3.10/site-packages/snakemake/executors/init.py", line 584, in handle_job_success File "/home/kaynar1/.conda/envs/aMeta/lib/python3.10/site-packages/snakemake/executors/init.py", line 252, in handle_job_success Removing output files of failed job KrakenUniq since they might be corrupted: results/KRAKENUNIQ/2A-12A-1-83-85_WD_4g/krakenuniq.output [Mon Aug 12 15:29:20 2024] Error in rule Bowtie2_Alignment: jobid: 5 output: results/BOWTIE2/2A-12A-1-83-85_WD_4g/AlignedToBowtie2DB.bam, results/BOWTIE2/2A-12A-1-83-85_WD_4g/AlignedToBowtie2DB.bam.bai log: logs/BOWTIE2/2A-12A-1-83-85_WD_4g.log (check log file(s) for error message) conda-env: /work/kaynar1/aMeta/.snakemake/conda/96dcd9900f71782aa6bfd6ab41ccd9eb shell: bowtie2 --large-index -x resources/library.fna --end-to-end --threads 10 --very-sensitive -U results/CUTADAPT_ADAPTER_TRIMMING/2A-12A-1-83-85_WD_4g.trimmed.fastq.gz > $(dirname results/BOWTIE2/2A-12A-1-83-85_WD_4g/AlignedToBowtie2DB.bam)/AlignedToBowtie2DB.sam 2> logs/BOWTIE2/2A-12A-1-83-85_WD_4g.log;grep @ $(dirname results/BOWTIE2/2A-12A-1-83-85_WD_4g/AlignedToBowtie2DB.bam)/AlignedToBowtie2DB.sam | awk '!seen[$2]++' > $(dirname results/BOWTIE2/2A-12A-1-83-85_WD_4g/AlignedToBowtie2DB.bam)/header_nodups.txt;grep -v '^@' $(dirname results/BOWTIE2/2A-12A-1-83-85_WD_4g/AlignedToBowtie2DB.bam)/AlignedToBowtie2DB.sam > $(dirname results/BOWTIE2/2A-12A-1-83-85_WD_4g/AlignedToBowtie2DB.bam)/AlignedToBowtie2DB.noheader.sam;cat $(dirname results/BOWTIE2/2A-12A-1-83-85_WD_4g/AlignedToBowtie2DB.bam)/header_nodups.txt $(dirname results/BOWTIE2/2A-12A-1-83-85_WD_4g/AlignedToBowtie2DB.bam)/AlignedToBowtie2DB.noheader.sam > $(dirname results/BOWTIE2/2A-12A-1-83-85_WD_4g/AlignedToBowtie2DB.bam)/AlignedToBowtie2DB.nodups.sam;samtools view -bS -q 1 -h -@ 10 $(dirname results/BOWTIE2/2A-12A-1-83-85_WD_4g/AlignedToBowtie2DB.bam)/AlignedToBowtie2DB.nodups.sam | samtools sort - -@ 10 -o results/BOWTIE2/2A-12A-1-83-85_WD_4g/AlignedToBowtie2DB.bam;samtools index results/BOWTIE2/2A-12A-1-83-85_WD_4g/AlignedToBowtie2DB.bam;rm $(dirname results/BOWTIE2/2A-12A-1-83-85_WD_4g/AlignedToBowtie2DB.bam)/header_nodups.txt;rm $(dirname results/BOWTIE2/2A-12A-1-83-85_WD_4g/AlignedToBowtie2DB.bam)/AlignedToBowtie2DB.noheader.sam;rm $(dirname results/BOWTIE2/2A-12A-1-83-85_WD_4g/AlignedToBowtie2DB.bam)/AlignedToBowtie2DB.nodups.sam;rm $(dirname results/BOWTIE2/2A-12A-1-83-85_WD_4g/AlignedToBowtie2DB.bam)/AlignedToBowtie2DB.sam; (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message

Is there any advise?