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Exception in thread "main" java.lang.RuntimeException: Unknown parameter cutlure_32_14585_R1.s1.out.fastq
at jgi.BBDuk.(BBDuk.java:528)
at jgi.BBDuk.main(BBDuk.java:78)
Is there an adjustment or flag for NextSeq data?
The text was updated successfully, but these errors were encountered:
When you specify a TSV file, e.g. hecatomb run --reads samples.tsv, Hecatomb expects a 3-column tab separated file with the first column specifying the sample name, and the other columns the relative or full paths to the forward and reverse read files. e.g.
Hi Mike,
I am trying to run some Illumina NextSeq samples, but I am failing immediately during primer removal with this error:
Error executing rule remove_5prime_primer on cluster (jobid: 254, external: Submitted batch job 37022315, jobscript: /scratch/sahlab/N812_TruSeqNano/.snakemake/tm
p.78wklvoy/snakejob.remove_5prime_primer.254.sh).
java -ea -Xmx15200m -Xms15200m -cp /opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb_v5/snakemake/workflow/conda/75d063ee1aa3bf1dbaf0307c4aa3f5ec/opt/bbmap-38.90-3/current/ jgi.BBDuk in=/scratch/sahlab/N812_TruSeqNano/fastq/WangD_I10209_cell_cutlure_32_14585_E09_UDI0069_GCCACAGGAT_ATGGCATG_S10_R1_001.fastq.gz in2=/scratch/sahlab/N812_TruSeqNano/fastq/WangD_I10209_cell_cutlure_32_14585_E09_UDI0069_GCCACAGGAT_ATGGCATG_S10_R2_001.fastq.gz ref=/opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb_v5/snakemake/workflow/../../databases/contaminants/primerB.fa out=hecatomb_out/PROCESSING/TMP/p01/I10209_cell cutlure_32_14585_R1.s1.out.fastq out2=hecatomb_out/PROCESSING/TMP/p01/I10209_cell cutlure_32_14585_R2.s1.out.fastq stats=hecatomb_out/PROCESSING/STATS/p01/I10209_cell cutlure_32_14585.s1.stats.tsv k=16 hdist=1 mink=11 ktrim=l restrictleft=20 removeifeitherbad=f trimpolya=10 ordered=t rcomp=f ow=t threads=8 -Xmx15200m cutlure_32_14585.log
Executing jgi.BBDuk [in=/scratch/sahlab/N812_TruSeqNano/fastq/WangD_I10209_cell_cutlure_32_14585_E09_UDI0069_GCCACAGGAT_ATGGCATG_S10_R1_001.fastq.gz, in2=/scratch/sahlab/N812_TruSeqNano/fastq/WangD_I10209_cell_cutlure_32_14585_E09_UDI0069_GCCACAGGAT_ATGGCATG_S10_R2_001.fastq.gz, ref=/opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb_v5/snakemake/workflow/../../databases/contaminants/primerB.fa, out=hecatomb_out/PROCESSING/TMP/p01/I10209_cell, cutlure_32_14585_R1.s1.out.fastq, out2=hecatomb_out/PROCESSING/TMP/p01/I10209_cell, cutlure_32_14585_R2.s1.out.fastq, stats=hecatomb_out/PROCESSING/STATS/p01/I10209_cell, cutlure_32_14585.s1.stats.tsv, k=16, hdist=1, mink=11, ktrim=l, restrictleft=20, removeifeitherbad=f, trimpolya=10, ordered=t, rcomp=f, ow=t, threads=8, -Xmx15200m, cutlure_32_14585.log]
Version 38.90
Exception in thread "main" java.lang.RuntimeException: Unknown parameter cutlure_32_14585_R1.s1.out.fastq
at jgi.BBDuk.(BBDuk.java:528)
at jgi.BBDuk.main(BBDuk.java:78)
Is there an adjustment or flag for NextSeq data?
The text was updated successfully, but these errors were encountered: