picard.jar not found

[robertobarrero]

nextflow run CRG-CNAG/CalliNGS-NF --gatk /home/ubuntu/tools/GenomeAnalysisTK.jar N E X T F L O W ~ version 19.04.1 Launching CRG-CNAG/CalliNGS-NF [curious_kilby] - revision: 841638691a [master] C A L L I N G S - N F v 1.0

genome : /home/ubuntu/.nextflow/assets/CRG-CNAG/CalliNGS-NF/data/genome.fa reads : /home/ubuntu/.nextflow/assets/CRG-CNAG/CalliNGS-NF/data/reads/rep1_{1,2}.fq.gz variants : /home/ubuntu/.nextflow/assets/CRG-CNAG/CalliNGS-NF/data/known_variants.vcf.gz blacklist: /home/ubuntu/.nextflow/assets/CRG-CNAG/CalliNGS-NF/data/blacklist.bed results : results gatk : /home/ubuntu/tools/GenomeAnalysisTK.jar [warm up] executor > local executor > local (4) [b0/9254bf] process > 1D_prepare_vcf_file [100%] 1 of 1, failed: 1 [6c/73da36] process > 1B_prepare_genome_picard [100%] 1 of 1, failed: 1 ✘ [28/6cc9ac] process > 1C_prepare_star_genome_index [100%] 1 of 1, failed: 1 [7f/0b0c2c] process > 1A_prepare_genome_samtools [100%] 1 of 1, failed: 1 WARN: Killing pending tasks (3) ERROR ~ Error executing process > '1B_prepare_genome_picard (genome)'

Caused by: Process 1B_prepare_genome_picard (genome) terminated with an error exit status (1)

Command executed:

PICARD=which picard.jar java -jar $PICARD CreateSequenceDictionary R= genome.fa O= genome.dict

Command exit status: 1

Command output: (empty)

Work dir: /mnt/volume1/data/todo/rnaseq/work/6c/73da36c9a0400e4514e65534e58d6d

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

-- Check '.nextflow.log' file for details (base) ubuntu$ which picard /home/ubuntu/anaconda3/bin/picard (base) ubuntu$ which picard.jar (base) ubuntu$

[pditommaso]

The latest version used picard bundled with gatk4. See #14.