Error --pilon polish contigs

[GeonhoCho]

Hello, i am running the following command:

!/bin/bash

SBATCH -J metacom_CJ_Car

SBATCH -t UNLIMITED

SBATCH -p Node2

SBATCH -n 12

python3 /home/geonho/tools/MetaCompass-2.0-beta/go_metacompass.py -r /home/geonho/WGS/REF_ACP/REF_GENOMES/C_rudii_JRPAMB4_complete_genome_NZ_CP041245/ACP_C_rudii.ref.fas -1 /home/geonho/WGS/trimmed/CJ_S7_L003_R1_001.fastq.gz -2 /home/geonho/WGS/trimmed/CJ_S7_L003_R2_001.fastq.gz -o /home/geonho/WGS/trimmed/metacompass/Carsonella/CJ -t 12 -y 12

and i get the following error:

[Sat Oct 16 17:25:58 2021] Building DAG of jobs... [Sat Oct 16 17:25:58 2021] Provided cores: 12 [Sat Oct 16 17:25:58 2021] Rules claiming more threads will be scaled down. [Sat Oct 16 17:25:58 2021] Job counts: [Sat Oct 16 17:25:58 2021] count jobs [Sat Oct 16 17:25:58 2021] 1 all [Sat Oct 16 17:25:58 2021] 1 assemble_unmapped [Sat Oct 16 17:25:58 2021] 1 assembled_references [Sat Oct 16 17:25:58 2021] 1 bam_sort [Sat Oct 16 17:25:58 2021] 1 bowtie2_map [Sat Oct 16 17:25:58 2021] 1 build_contigs [Sat Oct 16 17:25:58 2021] 1 create_tsv [Sat Oct 16 17:25:58 2021] 1 join_contigs [Sat Oct 16 17:25:58 2021] 1 mapping_stats [Sat Oct 16 17:25:58 2021] 1 pilon_contigs [Sat Oct 16 17:25:58 2021] 1 pilon_map [Sat Oct 16 17:25:58 2021] 1 sam_to_bam [Sat Oct 16 17:25:58 2021] 1 stats_all [Sat Oct 16 17:25:58 2021] 1 stats_genome [Sat Oct 16 17:25:58 2021] 14

[Sat Oct 16 17:25:58 2021] Job 10: ---Build index .

[Sat Oct 16 17:25:58 2021] bowtie2-build -o 3 --threads 12 -q /home/geonho/WGS/REF_ACP/REF_GENOMES/C_rudii_JRPAMB4_co$ [Sat Oct 16 17:46:20 2021] Finished job 10. [Sat Oct 16 17:46:20 2021] 1 of 14 steps (7%) done

[Sat Oct 16 17:46:20 2021] Job 7: ---Build contigs .

[Sat Oct 16 17:46:20 2021] /home/geonho/tools/MetaCompass-2.0-beta/bin/buildcontig -r /home/geonho/WGS/REF_ACP/REF_GE$ [Sat Oct 16 17:46:24 2021] Finished job 7. [Sat Oct 16 17:46:24 2021] 2 of 14 steps (14%) done

[Sat Oct 16 17:46:24 2021] Job 11: ---Map reads for pilon polishing.

[Sat Oct 16 17:46:24 2021] bowtie2-build --threads 12 -q /home/geonho/WGS/trimmed/metacompass/Carsonella/CJ/assembly/$ [Sat Oct 16 18:34:32 2021] Finished job 11. [Sat Oct 16 18:34:32 2021] 3 of 14 steps (21%) done [Sat Oct 16 18:34:32 2021] Job 9: ---Assembled references .

[Sat Oct 16 18:34:33 2021] grep '>' /home/geonho/WGS/trimmed/metacompass/Carsonella/CJ/assembly/contigs.fasta |rev| c$

[Sat Oct 16 18:34:33 2021] Job 13: ---Convert sam to bam .

[Sat Oct 16 18:34:33 2021] samtools view -bS /home/geonho/WGS/trimmed/metacompass/Carsonella/CJ/error_correction/mc.s$ [Sat Oct 16 18:34:41 2021] Finished job 9. [Sat Oct 16 18:34:41 2021] 4 of 14 steps (29%) done

[Sat Oct 16 18:34:41 2021] Job 3: ---mapping stats per genome in reference-guided contigs

[Sat Oct 16 18:34:44 2021] grep '>' /home/geonho/WGS/REF_ACP/REF_GENOMES/C_rudii_JRPAMB4_complete_genome_NZ_CP041245/$ [Sat Oct 16 18:34:53 2021] Finished job 13. [Sat Oct 16 18:34:53 2021] 5 of 14 steps (36%) done [Sat Oct 16 18:35:27 2021] Finished job 3. [Sat Oct 16 18:35:27 2021] 6 of 14 steps (43%) done

[Sat Oct 16 18:35:27 2021] Job 12: ---Sort bam .

[Sat Oct 16 18:35:27 2021] samtools sort -@ 12 /home/geonho/WGS/trimmed/metacompass/Carsonella/CJ/error_correction/mc$ [Sat Oct 16 18:36:01 2021] Finished job 12. [Sat Oct 16 18:36:02 2021] 7 of 14 steps (50%) done

[Sat Oct 16 18:36:02 2021] Job 5: ---Assemble unmapped reads .

[Sat Oct 16 18:36:03 2021] if [[ -s /home/geonho/WGS/trimmed/metacompass/Carsonella/CJ/error_correction/mc.sam.unmapp$ [Mon Oct 18 17:16:58 2021] Finished job 5. [Mon Oct 18 17:16:58 2021] 8 of 14 steps (57%) done

[Mon Oct 18 17:16:58 2021] Job 6: ---Pilon polish contigs .

[Mon Oct 18 17:16:58 2021] java -Xmx12G -jar /home/geonho/tools/MetaCompass-2.0-beta/bin/pilon-1.23.jar --flank 5 --t$ [Mon Oct 18 17:16:58 2021] Error in rule pilon_contigs: [Mon Oct 18 17:16:58 2021] jobid: 6 [Mon Oct 18 17:16:58 2021] output: /home/geonho/WGS/trimmed/metacompass/Carsonella/CJ/error_correction/contigs.pi$ [Mon Oct 18 17:16:58 2021] log: /home/geonho/WGS/trimmed/metacompass/Carsonella/CJ/logs/pilon.log

[Mon Oct 18 17:16:58 2021] RuleException: [Mon Oct 18 17:16:58 2021] CalledProcessError in line 130 of /home/geonho/tools/MetaCompass-2.0-beta/snakemake/metaco$ [Mon Oct 18 17:16:58 2021] Command ' set -euo pipefail; java -Xmx12G -jar /home/geonho/tools/MetaCompass-2.0-beta/bi$ [Mon Oct 18 17:16:58 2021] File "/home/geonho/tools/MetaCompass-2.0-beta/snakemake/metacompass.ref.paired.py", line$ [Mon Oct 18 17:16:58 2021] File "/home/geonho/conda/metacompass/lib/python3.6/concurrent/futures/thread.py", line 5$ [Mon Oct 18 17:16:58 2021] Will exit after finishing currently running jobs. [Mon Oct 18 17:16:58 2021] Exiting because a job execution failed. Look above for error message [Mon Oct 18 17:16:58 2021] Complete log: .snakemake/log/2021-10-16T172558.569258.snakemake.log

Here's the log file pilon.log:

/bin/bash: java: command not found

Do you have any solution for this problem?

Thanks : )

[vcepeda]

check your java installation. I didn't include it in the requirements but is needed by pilon