04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `threads' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `extension_paired' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `extension' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `gene_call_type' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `bypass_assembly' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `bypass_gene_calling' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `bypass_gene_catalog' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `output_basename' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `output' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `input' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `config' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `jobs' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `grid_jobs' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `grid' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `grid_partition' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `grid_benchmark' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `grid_options' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `grid_environment' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `grid_scratch' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `dry_run' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `skip_nothing' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `quit_early' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `until_task' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `exclude_task' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `target' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `exclude_target' = `INFO' 04/04/2022 08:01:24 AM - anadama2.cli - INFO: Command line argument `log_level' = `INFO' 04/04/2022 08:01:24 AM - metawibele.config - INFO: ###### Start assembly module ###### 04/04/2022 08:01:24 AM - metawibele.config - INFO: ###### Start gene_calling module ###### 04/04/2022 08:01:24 AM - metawibele.config - INFO: ###### Start gene_catalog module ###### 04/04/2022 08:01:24 AM - LoggerReporter - INFO: Beginning AnADAMA run with 66 tasks. 04/04/2022 08:01:24 AM - LoggerReporter - INFO: Workflow description = A workflow to preprocess shotgun sequencing reads of metagenomes with tasks of metagenomic assembly, gene calling, building gene catalogs and generating gene abundance for each sample. 04/04/2022 08:01:24 AM - LoggerReporter - INFO: Workflow version = 0.4.4 04/04/2022 08:01:24 AM - LoggerReporter - INFO: Workflow configuration options 04/04/2022 08:01:24 AM - LoggerReporter - INFO: threads = None 04/04/2022 08:01:24 AM - LoggerReporter - INFO: extension_paired = _1.fastq,_2.fastq 04/04/2022 08:01:24 AM - LoggerReporter - INFO: extension = .fastq 04/04/2022 08:01:24 AM - LoggerReporter - INFO: gene_call_type = prodigal 04/04/2022 08:01:24 AM - LoggerReporter - INFO: bypass_assembly = False 04/04/2022 08:01:24 AM - LoggerReporter - INFO: bypass_gene_calling = False 04/04/2022 08:01:24 AM - LoggerReporter - INFO: bypass_gene_catalog = False 04/04/2022 08:01:24 AM - LoggerReporter - INFO: output_basename = batch_22 04/04/2022 08:01:24 AM - LoggerReporter - INFO: output = preprocess/ 04/04/2022 08:01:24 AM - LoggerReporter - INFO: input = fastq/ 04/04/2022 08:01:24 AM - LoggerReporter - INFO: config = None 04/04/2022 08:01:24 AM - LoggerReporter - INFO: jobs = 1 04/04/2022 08:01:24 AM - LoggerReporter - INFO: grid_jobs = 0 04/04/2022 08:01:24 AM - LoggerReporter - INFO: grid = aws 04/04/2022 08:01:24 AM - LoggerReporter - INFO: grid_partition = general 04/04/2022 08:01:24 AM - LoggerReporter - INFO: grid_benchmark = on 04/04/2022 08:01:24 AM - LoggerReporter - INFO: grid_options = None 04/04/2022 08:01:24 AM - LoggerReporter - INFO: grid_environment = None 04/04/2022 08:01:24 AM - LoggerReporter - INFO: grid_scratch = None 04/04/2022 08:01:24 AM - LoggerReporter - INFO: dry_run = False 04/04/2022 08:01:24 AM - LoggerReporter - INFO: skip_nothing = False 04/04/2022 08:01:24 AM - LoggerReporter - INFO: quit_early = False 04/04/2022 08:01:24 AM - LoggerReporter - INFO: until_task = None 04/04/2022 08:01:24 AM - LoggerReporter - INFO: exclude_task = None 04/04/2022 08:01:24 AM - LoggerReporter - INFO: target = None 04/04/2022 08:01:24 AM - LoggerReporter - INFO: exclude_target = None 04/04/2022 08:01:24 AM - LoggerReporter - INFO: log_level = INFO 04/04/2022 08:01:25 AM - LoggerReporter - INFO: task 4, B22A002S004F2_1_kneaddata_paired__megahit : ready and waiting for resources 04/04/2022 08:01:25 AM - LoggerReporter - INFO: task 4, B22A002S004F2_1_kneaddata_paired__megahit : starting to run 04/04/2022 08:01:25 AM - LoggerReporter - INFO: Tracked executable version: MEGAHIT v1.1.3 04/04/2022 08:01:25 AM - LoggerReporter - INFO: Executing with shell: rm -rf /usr/data/preprocess/assembly/B22A002S004F2_1_kneaddata_paired && megahit -1 /usr/data/fastq/B22A002S004F2_1_kneaddata_paired_1.fastq -2 /usr/data/fastq/B22A002S004F2_1_kneaddata_paired_2.fastq -t 8 -o /usr/data/preprocess/assembly/B22A002S004F2_1_kneaddata_paired --out-prefix B22A002S004F2_1_kneaddata_paired >/usr/data/preprocess/assembly/B22A002S004F2_1_kneaddata_paired.log 2>&1 04/04/2022 08:54:02 AM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 08:54:02 AM - LoggerReporter - INFO: task 4, B22A002S004F2_1_kneaddata_paired__megahit : completed successfully 04/04/2022 08:54:02 AM - LoggerReporter - INFO: task 14, ln__B22A002S004F2_1_kneaddata_paired.contigs.fa : ready and waiting for resources 04/04/2022 08:54:02 AM - LoggerReporter - INFO: task 14, ln__B22A002S004F2_1_kneaddata_paired.contigs.fa : starting to run 04/04/2022 08:54:02 AM - LoggerReporter - INFO: Executing with shell: ln -fs /usr/data/preprocess/assembly/B22A002S004F2_1_kneaddata_paired/B22A002S004F2_1_kneaddata_paired.contigs.fa /usr/data/preprocess/assembly/B22A002S004F2_1_kneaddata_paired.contigs.fa 04/04/2022 08:54:02 AM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 08:54:02 AM - LoggerReporter - INFO: task 14, ln__B22A002S004F2_1_kneaddata_paired.contigs.fa : completed successfully 04/04/2022 08:54:02 AM - LoggerReporter - INFO: task 21, B22A002S004F2_1_kneaddata_paired__prodigal : ready and waiting for resources 04/04/2022 08:54:02 AM - LoggerReporter - INFO: task 21, B22A002S004F2_1_kneaddata_paired__prodigal : starting to run 04/04/2022 08:54:02 AM - LoggerReporter - INFO: Executing with shell: prodigal -m -p meta -i /usr/data/preprocess/assembly/B22A002S004F2_1_kneaddata_paired/B22A002S004F2_1_kneaddata_paired.contigs.fa -f gff -o /usr/data/preprocess/gene_calls/B22A002S004F2_1_kneaddata_paired/B22A002S004F2_1_kneaddata_paired.gff -d /usr/data/preprocess/gene_calls/B22A002S004F2_1_kneaddata_paired/B22A002S004F2_1_kneaddata_paired.fna -s /usr/data/preprocess/gene_calls/B22A002S004F2_1_kneaddata_paired/B22A002S004F2_1_kneaddata_paired.gene_score.txt -a /usr/data/preprocess/gene_calls/B22A002S004F2_1_kneaddata_paired/B22A002S004F2_1_kneaddata_paired.faa >/usr/data/preprocess/gene_calls/B22A002S004F2_1_kneaddata_paired/B22A002S004F2_1_kneaddata_paired.stdout.log 2>&1 04/04/2022 09:09:32 AM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 09:09:32 AM - LoggerReporter - INFO: task 21, B22A002S004F2_1_kneaddata_paired__prodigal : completed successfully 04/04/2022 09:09:32 AM - LoggerReporter - INFO: task 27, ln__B22A002S004F2_1_kneaddata_paired.faa : ready and waiting for resources 04/04/2022 09:09:32 AM - LoggerReporter - INFO: task 27, ln__B22A002S004F2_1_kneaddata_paired.faa : starting to run 04/04/2022 09:09:32 AM - LoggerReporter - INFO: Executing with shell: ln -fs /usr/data/preprocess/gene_calls/B22A002S004F2_1_kneaddata_paired/B22A002S004F2_1_kneaddata_paired.faa /usr/data/preprocess/gene_calls/B22A002S004F2_1_kneaddata_paired.faa 04/04/2022 09:09:32 AM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 09:09:32 AM - LoggerReporter - INFO: task 27, ln__B22A002S004F2_1_kneaddata_paired.faa : completed successfully 04/04/2022 09:09:32 AM - LoggerReporter - INFO: task 28, ln__B22A002S004F2_1_kneaddata_paired.faa : ready and waiting for resources 04/04/2022 09:09:32 AM - LoggerReporter - INFO: task 28, ln__B22A002S004F2_1_kneaddata_paired.faa : starting to run 04/04/2022 09:09:32 AM - LoggerReporter - INFO: Executing with shell: ln -fs /usr/data/preprocess/gene_calls/B22A002S004F2_1_kneaddata_paired/B22A002S004F2_1_kneaddata_paired.fna /usr/data/preprocess/gene_calls/B22A002S004F2_1_kneaddata_paired.fna 04/04/2022 09:09:32 AM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 09:09:32 AM - LoggerReporter - INFO: task 28, ln__B22A002S004F2_1_kneaddata_paired.faa : completed successfully 04/04/2022 09:09:32 AM - LoggerReporter - INFO: task 29, ln__B22A002S004F2_1_kneaddata_paired.faa : ready and waiting for resources 04/04/2022 09:09:32 AM - LoggerReporter - INFO: task 29, ln__B22A002S004F2_1_kneaddata_paired.faa : starting to run 04/04/2022 09:09:32 AM - LoggerReporter - INFO: Executing with shell: ln -fs /usr/data/preprocess/gene_calls/B22A002S004F2_1_kneaddata_paired/B22A002S004F2_1_kneaddata_paired.gff /usr/data/preprocess/gene_calls/B22A002S004F2_1_kneaddata_paired.gff 04/04/2022 09:09:32 AM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 09:09:32 AM - LoggerReporter - INFO: task 29, ln__B22A002S004F2_1_kneaddata_paired.faa : completed successfully 04/04/2022 09:09:32 AM - LoggerReporter - INFO: task 7, B22BME001103_1_kneaddata_paired__megahit : ready and waiting for resources 04/04/2022 09:09:32 AM - LoggerReporter - INFO: task 7, B22BME001103_1_kneaddata_paired__megahit : starting to run 04/04/2022 09:09:32 AM - LoggerReporter - INFO: Tracked executable version: MEGAHIT v1.1.3 04/04/2022 09:09:32 AM - LoggerReporter - INFO: Executing with shell: rm -rf /usr/data/preprocess/assembly/B22BME001103_1_kneaddata_paired && megahit -1 /usr/data/fastq/B22BME001103_1_kneaddata_paired_1.fastq -2 /usr/data/fastq/B22BME001103_1_kneaddata_paired_2.fastq -t 8 -o /usr/data/preprocess/assembly/B22BME001103_1_kneaddata_paired --out-prefix B22BME001103_1_kneaddata_paired >/usr/data/preprocess/assembly/B22BME001103_1_kneaddata_paired.log 2>&1 04/04/2022 10:50:37 AM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 10:50:37 AM - LoggerReporter - INFO: task 7, B22BME001103_1_kneaddata_paired__megahit : completed successfully 04/04/2022 10:50:37 AM - LoggerReporter - INFO: task 15, ln__B22BME001103_1_kneaddata_paired.contigs.fa : ready and waiting for resources 04/04/2022 10:50:37 AM - LoggerReporter - INFO: task 15, ln__B22BME001103_1_kneaddata_paired.contigs.fa : starting to run 04/04/2022 10:50:37 AM - LoggerReporter - INFO: Executing with shell: ln -fs /usr/data/preprocess/assembly/B22BME001103_1_kneaddata_paired/B22BME001103_1_kneaddata_paired.contigs.fa /usr/data/preprocess/assembly/B22BME001103_1_kneaddata_paired.contigs.fa 04/04/2022 10:50:37 AM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 10:50:37 AM - LoggerReporter - INFO: task 15, ln__B22BME001103_1_kneaddata_paired.contigs.fa : completed successfully 04/04/2022 10:50:37 AM - LoggerReporter - INFO: task 22, B22BME001103_1_kneaddata_paired__prodigal : ready and waiting for resources 04/04/2022 10:50:37 AM - LoggerReporter - INFO: task 22, B22BME001103_1_kneaddata_paired__prodigal : starting to run 04/04/2022 10:50:37 AM - LoggerReporter - INFO: Executing with shell: prodigal -m -p meta -i /usr/data/preprocess/assembly/B22BME001103_1_kneaddata_paired/B22BME001103_1_kneaddata_paired.contigs.fa -f gff -o /usr/data/preprocess/gene_calls/B22BME001103_1_kneaddata_paired/B22BME001103_1_kneaddata_paired.gff -d /usr/data/preprocess/gene_calls/B22BME001103_1_kneaddata_paired/B22BME001103_1_kneaddata_paired.fna -s /usr/data/preprocess/gene_calls/B22BME001103_1_kneaddata_paired/B22BME001103_1_kneaddata_paired.gene_score.txt -a /usr/data/preprocess/gene_calls/B22BME001103_1_kneaddata_paired/B22BME001103_1_kneaddata_paired.faa >/usr/data/preprocess/gene_calls/B22BME001103_1_kneaddata_paired/B22BME001103_1_kneaddata_paired.stdout.log 2>&1 04/04/2022 11:16:21 AM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 11:16:21 AM - LoggerReporter - INFO: task 22, B22BME001103_1_kneaddata_paired__prodigal : completed successfully 04/04/2022 11:16:21 AM - LoggerReporter - INFO: task 30, ln__B22BME001103_1_kneaddata_paired.faa : ready and waiting for resources 04/04/2022 11:16:21 AM - LoggerReporter - INFO: task 30, ln__B22BME001103_1_kneaddata_paired.faa : starting to run 04/04/2022 11:16:21 AM - LoggerReporter - INFO: Executing with shell: ln -fs /usr/data/preprocess/gene_calls/B22BME001103_1_kneaddata_paired/B22BME001103_1_kneaddata_paired.faa /usr/data/preprocess/gene_calls/B22BME001103_1_kneaddata_paired.faa 04/04/2022 11:16:21 AM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 11:16:21 AM - LoggerReporter - INFO: task 30, ln__B22BME001103_1_kneaddata_paired.faa : completed successfully 04/04/2022 11:16:21 AM - LoggerReporter - INFO: task 31, ln__B22BME001103_1_kneaddata_paired.faa : ready and waiting for resources 04/04/2022 11:16:21 AM - LoggerReporter - INFO: task 31, ln__B22BME001103_1_kneaddata_paired.faa : starting to run 04/04/2022 11:16:21 AM - LoggerReporter - INFO: Executing with shell: ln -fs /usr/data/preprocess/gene_calls/B22BME001103_1_kneaddata_paired/B22BME001103_1_kneaddata_paired.fna /usr/data/preprocess/gene_calls/B22BME001103_1_kneaddata_paired.fna 04/04/2022 11:16:21 AM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 11:16:21 AM - LoggerReporter - INFO: task 31, ln__B22BME001103_1_kneaddata_paired.faa : completed successfully 04/04/2022 11:16:21 AM - LoggerReporter - INFO: task 32, ln__B22BME001103_1_kneaddata_paired.faa : ready and waiting for resources 04/04/2022 11:16:21 AM - LoggerReporter - INFO: task 32, ln__B22BME001103_1_kneaddata_paired.faa : starting to run 04/04/2022 11:16:21 AM - LoggerReporter - INFO: Executing with shell: ln -fs /usr/data/preprocess/gene_calls/B22BME001103_1_kneaddata_paired/B22BME001103_1_kneaddata_paired.gff /usr/data/preprocess/gene_calls/B22BME001103_1_kneaddata_paired.gff 04/04/2022 11:16:21 AM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 11:16:21 AM - LoggerReporter - INFO: task 32, ln__B22BME001103_1_kneaddata_paired.faa : completed successfully 04/04/2022 11:16:21 AM - LoggerReporter - INFO: task 10, B22BME001104_1_kneaddata_paired__megahit : ready and waiting for resources 04/04/2022 11:16:21 AM - LoggerReporter - INFO: task 10, B22BME001104_1_kneaddata_paired__megahit : starting to run 04/04/2022 11:16:21 AM - LoggerReporter - INFO: Tracked executable version: MEGAHIT v1.1.3 04/04/2022 11:16:21 AM - LoggerReporter - INFO: Executing with shell: rm -rf /usr/data/preprocess/assembly/B22BME001104_1_kneaddata_paired && megahit -1 /usr/data/fastq/B22BME001104_1_kneaddata_paired_1.fastq -2 /usr/data/fastq/B22BME001104_1_kneaddata_paired_2.fastq -t 8 -o /usr/data/preprocess/assembly/B22BME001104_1_kneaddata_paired --out-prefix B22BME001104_1_kneaddata_paired >/usr/data/preprocess/assembly/B22BME001104_1_kneaddata_paired.log 2>&1 04/04/2022 12:29:23 PM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 12:29:23 PM - LoggerReporter - INFO: task 10, B22BME001104_1_kneaddata_paired__megahit : completed successfully 04/04/2022 12:29:23 PM - LoggerReporter - INFO: task 16, ln__B22BME001104_1_kneaddata_paired.contigs.fa : ready and waiting for resources 04/04/2022 12:29:23 PM - LoggerReporter - INFO: task 16, ln__B22BME001104_1_kneaddata_paired.contigs.fa : starting to run 04/04/2022 12:29:23 PM - LoggerReporter - INFO: Executing with shell: ln -fs /usr/data/preprocess/assembly/B22BME001104_1_kneaddata_paired/B22BME001104_1_kneaddata_paired.contigs.fa /usr/data/preprocess/assembly/B22BME001104_1_kneaddata_paired.contigs.fa 04/04/2022 12:29:23 PM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 12:29:23 PM - LoggerReporter - INFO: task 16, ln__B22BME001104_1_kneaddata_paired.contigs.fa : completed successfully 04/04/2022 12:29:23 PM - LoggerReporter - INFO: task 23, B22BME001104_1_kneaddata_paired__prodigal : ready and waiting for resources 04/04/2022 12:29:23 PM - LoggerReporter - INFO: task 23, B22BME001104_1_kneaddata_paired__prodigal : starting to run 04/04/2022 12:29:23 PM - LoggerReporter - INFO: Executing with shell: prodigal -m -p meta -i /usr/data/preprocess/assembly/B22BME001104_1_kneaddata_paired/B22BME001104_1_kneaddata_paired.contigs.fa -f gff -o /usr/data/preprocess/gene_calls/B22BME001104_1_kneaddata_paired/B22BME001104_1_kneaddata_paired.gff -d /usr/data/preprocess/gene_calls/B22BME001104_1_kneaddata_paired/B22BME001104_1_kneaddata_paired.fna -s /usr/data/preprocess/gene_calls/B22BME001104_1_kneaddata_paired/B22BME001104_1_kneaddata_paired.gene_score.txt -a /usr/data/preprocess/gene_calls/B22BME001104_1_kneaddata_paired/B22BME001104_1_kneaddata_paired.faa >/usr/data/preprocess/gene_calls/B22BME001104_1_kneaddata_paired/B22BME001104_1_kneaddata_paired.stdout.log 2>&1 04/04/2022 12:49:42 PM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 12:49:42 PM - LoggerReporter - INFO: task 23, B22BME001104_1_kneaddata_paired__prodigal : completed successfully 04/04/2022 12:49:42 PM - LoggerReporter - INFO: task 33, ln__B22BME001104_1_kneaddata_paired.faa : ready and waiting for resources 04/04/2022 12:49:42 PM - LoggerReporter - INFO: task 33, ln__B22BME001104_1_kneaddata_paired.faa : starting to run 04/04/2022 12:49:42 PM - LoggerReporter - INFO: Executing with shell: ln -fs /usr/data/preprocess/gene_calls/B22BME001104_1_kneaddata_paired/B22BME001104_1_kneaddata_paired.faa /usr/data/preprocess/gene_calls/B22BME001104_1_kneaddata_paired.faa 04/04/2022 12:49:42 PM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 12:49:42 PM - LoggerReporter - INFO: task 33, ln__B22BME001104_1_kneaddata_paired.faa : completed successfully 04/04/2022 12:49:42 PM - LoggerReporter - INFO: task 34, ln__B22BME001104_1_kneaddata_paired.faa : ready and waiting for resources 04/04/2022 12:49:42 PM - LoggerReporter - INFO: task 34, ln__B22BME001104_1_kneaddata_paired.faa : starting to run 04/04/2022 12:49:42 PM - LoggerReporter - INFO: Executing with shell: ln -fs /usr/data/preprocess/gene_calls/B22BME001104_1_kneaddata_paired/B22BME001104_1_kneaddata_paired.fna /usr/data/preprocess/gene_calls/B22BME001104_1_kneaddata_paired.fna 04/04/2022 12:49:42 PM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 12:49:42 PM - LoggerReporter - INFO: task 34, ln__B22BME001104_1_kneaddata_paired.faa : completed successfully 04/04/2022 12:49:42 PM - LoggerReporter - INFO: task 35, ln__B22BME001104_1_kneaddata_paired.faa : ready and waiting for resources 04/04/2022 12:49:42 PM - LoggerReporter - INFO: task 35, ln__B22BME001104_1_kneaddata_paired.faa : starting to run 04/04/2022 12:49:42 PM - LoggerReporter - INFO: Executing with shell: ln -fs /usr/data/preprocess/gene_calls/B22BME001104_1_kneaddata_paired/B22BME001104_1_kneaddata_paired.gff /usr/data/preprocess/gene_calls/B22BME001104_1_kneaddata_paired.gff 04/04/2022 12:49:42 PM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 12:49:42 PM - LoggerReporter - INFO: task 35, ln__B22BME001104_1_kneaddata_paired.faa : completed successfully 04/04/2022 12:49:42 PM - LoggerReporter - INFO: task 0, B22A002S003F2_1_kneaddata_paired__megahit : ready and waiting for resources 04/04/2022 12:49:42 PM - LoggerReporter - INFO: task 0, B22A002S003F2_1_kneaddata_paired__megahit : starting to run 04/04/2022 12:49:42 PM - LoggerReporter - INFO: Tracked executable version: MEGAHIT v1.1.3 04/04/2022 12:49:42 PM - LoggerReporter - INFO: Executing with shell: rm -rf /usr/data/preprocess/assembly/B22A002S003F2_1_kneaddata_paired && megahit -1 /usr/data/fastq/B22A002S003F2_1_kneaddata_paired_1.fastq -2 /usr/data/fastq/B22A002S003F2_1_kneaddata_paired_2.fastq -t 8 -o /usr/data/preprocess/assembly/B22A002S003F2_1_kneaddata_paired --out-prefix B22A002S003F2_1_kneaddata_paired >/usr/data/preprocess/assembly/B22A002S003F2_1_kneaddata_paired.log 2>&1 04/04/2022 01:52:43 PM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 01:52:43 PM - LoggerReporter - INFO: task 0, B22A002S003F2_1_kneaddata_paired__megahit : completed successfully 04/04/2022 01:52:43 PM - LoggerReporter - INFO: task 13, ln__B22A002S003F2_1_kneaddata_paired.contigs.fa : ready and waiting for resources 04/04/2022 01:52:43 PM - LoggerReporter - INFO: task 13, ln__B22A002S003F2_1_kneaddata_paired.contigs.fa : starting to run 04/04/2022 01:52:43 PM - LoggerReporter - INFO: Executing with shell: ln -fs /usr/data/preprocess/assembly/B22A002S003F2_1_kneaddata_paired/B22A002S003F2_1_kneaddata_paired.contigs.fa /usr/data/preprocess/assembly/B22A002S003F2_1_kneaddata_paired.contigs.fa 04/04/2022 01:52:43 PM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 01:52:43 PM - LoggerReporter - INFO: task 13, ln__B22A002S003F2_1_kneaddata_paired.contigs.fa : completed successfully 04/04/2022 01:52:43 PM - LoggerReporter - INFO: task 17, format_contig_table : ready and waiting for resources 04/04/2022 01:52:43 PM - LoggerReporter - INFO: task 17, format_contig_table : starting to run 04/04/2022 01:52:43 PM - LoggerReporter - INFO: Executing with shell: metawibele_format_contig_sequences -p /usr/data/preprocess/assembly -e contigs.fa -o /usr/data/preprocess/finalized/batch_22_contig_sequence.fasta > /usr/data/preprocess/finalized/batch_22_contig_sequence.fasta.log 2>&1 04/04/2022 01:52:53 PM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 01:52:53 PM - LoggerReporter - INFO: task 17, format_contig_table : completed successfully 04/04/2022 01:52:53 PM - LoggerReporter - INFO: task 19, B22A002S003F2_1_kneaddata_paired__prodigal : ready and waiting for resources 04/04/2022 01:52:53 PM - LoggerReporter - INFO: task 19, B22A002S003F2_1_kneaddata_paired__prodigal : starting to run 04/04/2022 01:52:53 PM - LoggerReporter - INFO: Executing with shell: prodigal -m -p meta -i /usr/data/preprocess/assembly/B22A002S003F2_1_kneaddata_paired/B22A002S003F2_1_kneaddata_paired.contigs.fa -f gff -o /usr/data/preprocess/gene_calls/B22A002S003F2_1_kneaddata_paired/B22A002S003F2_1_kneaddata_paired.gff -d /usr/data/preprocess/gene_calls/B22A002S003F2_1_kneaddata_paired/B22A002S003F2_1_kneaddata_paired.fna -s /usr/data/preprocess/gene_calls/B22A002S003F2_1_kneaddata_paired/B22A002S003F2_1_kneaddata_paired.gene_score.txt -a /usr/data/preprocess/gene_calls/B22A002S003F2_1_kneaddata_paired/B22A002S003F2_1_kneaddata_paired.faa >/usr/data/preprocess/gene_calls/B22A002S003F2_1_kneaddata_paired/B22A002S003F2_1_kneaddata_paired.stdout.log 2>&1 04/04/2022 02:08:44 PM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 02:08:44 PM - LoggerReporter - INFO: task 19, B22A002S003F2_1_kneaddata_paired__prodigal : completed successfully 04/04/2022 02:08:44 PM - LoggerReporter - INFO: task 24, ln__B22A002S003F2_1_kneaddata_paired.faa : ready and waiting for resources 04/04/2022 02:08:44 PM - LoggerReporter - INFO: task 24, ln__B22A002S003F2_1_kneaddata_paired.faa : starting to run 04/04/2022 02:08:44 PM - LoggerReporter - INFO: Executing with shell: ln -fs /usr/data/preprocess/gene_calls/B22A002S003F2_1_kneaddata_paired/B22A002S003F2_1_kneaddata_paired.faa /usr/data/preprocess/gene_calls/B22A002S003F2_1_kneaddata_paired.faa 04/04/2022 02:08:44 PM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 02:08:44 PM - LoggerReporter - INFO: task 24, ln__B22A002S003F2_1_kneaddata_paired.faa : completed successfully 04/04/2022 02:08:44 PM - LoggerReporter - INFO: task 38, format_protein_sequences : ready and waiting for resources 04/04/2022 02:08:44 PM - LoggerReporter - INFO: task 38, format_protein_sequences : starting to run 04/04/2022 02:08:44 PM - LoggerReporter - INFO: Executing with shell: metawibele_format_protein_sequences -p /usr/data/preprocess/gene_calls -q /usr/data/preprocess/gene_calls -e faa -o /usr/data/preprocess/finalized/batch_22_combined_protein.faa -m /usr/data/preprocess/finalized/batch_22_gene_info.tsv >/usr/data/preprocess/finalized/batch_22_combined_protein.log 2>&1 04/04/2022 02:09:36 PM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 02:09:36 PM - LoggerReporter - INFO: task 38, format_protein_sequences : completed successfully 04/04/2022 02:09:36 PM - LoggerReporter - INFO: task 40, usearch__sorting : ready and waiting for resources 04/04/2022 02:09:36 PM - LoggerReporter - INFO: task 40, usearch__sorting : starting to run 04/04/2022 02:09:37 PM - LoggerReporter - INFO: Tracked executable version: usearch v9.0.2132_i86linux32 04/04/2022 02:09:37 PM - LoggerReporter - INFO: Executing with shell: usearch -sortbylength /usr/data/preprocess/finalized/batch_22_combined_protein.faa -fastaout /usr/data/preprocess/finalized/batch_22_combined_protein.sorted.faa -minseqlength 0 >/usr/data/preprocess/finalized/batch_22_combined_protein.sorted.log 2>&1 04/04/2022 02:09:40 PM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 02:09:40 PM - LoggerReporter - INFO: task 40, usearch__sorting : completed successfully 04/04/2022 02:09:40 PM - LoggerReporter - INFO: task 46, extract_complete_ORF_seq : ready and waiting for resources 04/04/2022 02:09:40 PM - LoggerReporter - INFO: task 46, extract_complete_ORF_seq : starting to run 04/04/2022 02:09:40 PM - LoggerReporter - INFO: Executing with shell: metawibele_extract_complete_ORF_seq -t complete -m /usr/data/preprocess/finalized/batch_22_gene_info.tsv -i /usr/data/preprocess/finalized/batch_22_combined_protein.sorted.faa -o /usr/data/preprocess/finalized/batch_22_combined_protein.complete.sorted.faa >/usr/data/preprocess/finalized/batch_22_combined_protein.complete.sorted.log 2>&1 04/04/2022 02:09:48 PM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 02:09:48 PM - LoggerReporter - INFO: task 46, extract_complete_ORF_seq : completed successfully 04/04/2022 02:09:48 PM - LoggerReporter - INFO: task 25, ln__B22A002S003F2_1_kneaddata_paired.faa : ready and waiting for resources 04/04/2022 02:09:48 PM - LoggerReporter - INFO: task 25, ln__B22A002S003F2_1_kneaddata_paired.faa : starting to run 04/04/2022 02:09:48 PM - LoggerReporter - INFO: Executing with shell: ln -fs /usr/data/preprocess/gene_calls/B22A002S003F2_1_kneaddata_paired/B22A002S003F2_1_kneaddata_paired.fna /usr/data/preprocess/gene_calls/B22A002S003F2_1_kneaddata_paired.fna 04/04/2022 02:09:48 PM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 02:09:48 PM - LoggerReporter - INFO: task 25, ln__B22A002S003F2_1_kneaddata_paired.faa : completed successfully 04/04/2022 02:09:48 PM - LoggerReporter - INFO: task 36, combine_gene_sequences : ready and waiting for resources 04/04/2022 02:09:48 PM - LoggerReporter - INFO: task 36, combine_gene_sequences : starting to run 04/04/2022 02:09:48 PM - LoggerReporter - INFO: Executing with shell: metawibele_combine_gene_sequences -p /usr/data/preprocess/gene_calls -e fna -o /usr/data/preprocess/finalized/batch_22_combined_gene.fna > /usr/data/preprocess/finalized/batch_22_combined_gene.log 2>&1 04/04/2022 02:10:56 PM - LoggerReporter - ERROR: task 36, combine_gene_sequences : Failed! Error message : Error executing action 0. Original Exception: Traceback (most recent call last): File "/usr/local/lib/python3.6/dist-packages/anadama2/runners.py", line 201, in _run_task_locally action_func(task) File "/usr/local/lib/python3.6/dist-packages/anadama2/helpers.py", line 89, in actually_sh ret = _sh(s, **kwargs) File "/usr/local/lib/python3.6/dist-packages/anadama2/util/__init__.py", line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1])) anadama2.util.ShellException: [Errno 1] Command `metawibele_combine_gene_sequences -p /usr/data/preprocess/gene_calls -e fna -o /usr/data/preprocess/finalized/batch_22_combined_gene.fna > /usr/data/preprocess/finalized/batch_22_combined_gene.log 2>&1 ' failed. Out: b'' Err: b'' (Apr 04 08:01:25) [ 0/44 - 0.00%] **Ready ** Task 4: B22A002S004F2_1_kneaddata_paired__megahit (Apr 04 08:01:25) [ 0/44 - 0.00%] **Started ** Task 4: B22A002S004F2_1_kneaddata_paired__megahit (Apr 04 08:54:02) [ 1/44 - 2.27%] **Completed** Task 4: B22A002S004F2_1_kneaddata_paired__megahit (Apr 04 08:54:02) [ 1/44 - 2.27%] **Ready ** Task 14: ln__B22A002S004F2_1_kneaddata_paired.contigs.fa (Apr 04 08:54:02) [ 1/44 - 2.27%] **Started ** Task 14: ln__B22A002S004F2_1_kneaddata_paired.contigs.fa (Apr 04 08:54:02) [ 2/44 - 4.55%] **Completed** Task 14: ln__B22A002S004F2_1_kneaddata_paired.contigs.fa (Apr 04 08:54:02) [ 2/44 - 4.55%] **Ready ** Task 21: B22A002S004F2_1_kneaddata_paired__prodigal (Apr 04 08:54:02) [ 2/44 - 4.55%] **Started ** Task 21: B22A002S004F2_1_kneaddata_paired__prodigal (Apr 04 09:09:32) [ 3/44 - 6.82%] **Completed** Task 21: B22A002S004F2_1_kneaddata_paired__prodigal (Apr 04 09:09:32) [ 3/44 - 6.82%] **Ready ** Task 27: ln__B22A002S004F2_1_kneaddata_paired.faa (Apr 04 09:09:32) [ 3/44 - 6.82%] **Started ** Task 27: ln__B22A002S004F2_1_kneaddata_paired.faa (Apr 04 09:09:32) [ 4/44 - 9.09%] **Completed** Task 27: ln__B22A002S004F2_1_kneaddata_paired.faa (Apr 04 09:09:32) [ 4/44 - 9.09%] **Ready ** Task 28: ln__B22A002S004F2_1_kneaddata_paired.faa (Apr 04 09:09:32) [ 4/44 - 9.09%] **Started ** Task 28: ln__B22A002S004F2_1_kneaddata_paired.faa (Apr 04 09:09:32) [ 5/44 - 11.36%] **Completed** Task 28: ln__B22A002S004F2_1_kneaddata_paired.faa (Apr 04 09:09:32) [ 5/44 - 11.36%] **Ready ** Task 29: ln__B22A002S004F2_1_kneaddata_paired.faa (Apr 04 09:09:32) [ 5/44 - 11.36%] **Started ** Task 29: ln__B22A002S004F2_1_kneaddata_paired.faa (Apr 04 09:09:32) [ 6/44 - 13.64%] **Completed** Task 29: ln__B22A002S004F2_1_kneaddata_paired.faa (Apr 04 09:09:32) [ 6/44 - 13.64%] **Ready ** Task 7: B22BME001103_1_kneaddata_paired__megahit (Apr 04 09:09:32) [ 6/44 - 13.64%] **Started ** Task 7: B22BME001103_1_kneaddata_paired__megahit (Apr 04 10:50:37) [ 7/44 - 15.91%] **Completed** Task 7: B22BME001103_1_kneaddata_paired__megahit (Apr 04 10:50:37) [ 7/44 - 15.91%] **Ready ** Task 15: ln__B22BME001103_1_kneaddata_paired.contigs.fa (Apr 04 10:50:37) [ 7/44 - 15.91%] **Started ** Task 15: ln__B22BME001103_1_kneaddata_paired.contigs.fa (Apr 04 10:50:37) [ 8/44 - 18.18%] **Completed** Task 15: ln__B22BME001103_1_kneaddata_paired.contigs.fa (Apr 04 10:50:37) [ 8/44 - 18.18%] **Ready ** Task 22: B22BME001103_1_kneaddata_paired__prodigal (Apr 04 10:50:37) [ 8/44 - 18.18%] **Started ** Task 22: B22BME001103_1_kneaddata_paired__prodigal (Apr 04 11:16:20) [ 9/44 - 20.45%] **Completed** Task 22: B22BME001103_1_kneaddata_paired__prodigal (Apr 04 11:16:20) [ 9/44 - 20.45%] **Ready ** Task 30: ln__B22BME001103_1_kneaddata_paired.faa (Apr 04 11:16:20) [ 9/44 - 20.45%] **Started ** Task 30: ln__B22BME001103_1_kneaddata_paired.faa (Apr 04 11:16:21) [10/44 - 22.73%] **Completed** Task 30: ln__B22BME001103_1_kneaddata_paired.faa (Apr 04 11:16:21) [10/44 - 22.73%] **Ready ** Task 31: ln__B22BME001103_1_kneaddata_paired.faa (Apr 04 11:16:21) [10/44 - 22.73%] **Started ** Task 31: ln__B22BME001103_1_kneaddata_paired.faa (Apr 04 11:16:21) [11/44 - 25.00%] **Completed** Task 31: ln__B22BME001103_1_kneaddata_paired.faa (Apr 04 11:16:21) [11/44 - 25.00%] **Ready ** Task 32: ln__B22BME001103_1_kneaddata_paired.faa (Apr 04 11:16:21) [11/44 - 25.00%] **Started ** Task 32: ln__B22BME001103_1_kneaddata_paired.faa (Apr 04 11:16:21) [12/44 - 27.27%] **Completed** Task 32: ln__B22BME001103_1_kneaddata_paired.faa (Apr 04 11:16:21) [12/44 - 27.27%] **Ready ** Task 10: B22BME001104_1_kneaddata_paired__megahit (Apr 04 11:16:21) [12/44 - 27.27%] **Started ** Task 10: B22BME001104_1_kneaddata_paired__megahit (Apr 04 12:29:23) [13/44 - 29.55%] **Completed** Task 10: B22BME001104_1_kneaddata_paired__megahit (Apr 04 12:29:23) [13/44 - 29.55%] **Ready ** Task 16: ln__B22BME001104_1_kneaddata_paired.contigs.fa (Apr 04 12:29:23) [13/44 - 29.55%] **Started ** Task 16: ln__B22BME001104_1_kneaddata_paired.contigs.fa (Apr 04 12:29:23) [14/44 - 31.82%] **Completed** Task 16: ln__B22BME001104_1_kneaddata_paired.contigs.fa (Apr 04 12:29:23) [14/44 - 31.82%] **Ready ** Task 23: B22BME001104_1_kneaddata_paired__prodigal (Apr 04 12:29:23) [14/44 - 31.82%] **Started ** Task 23: B22BME001104_1_kneaddata_paired__prodigal (Apr 04 12:49:42) [15/44 - 34.09%] **Completed** Task 23: B22BME001104_1_kneaddata_paired__prodigal (Apr 04 12:49:42) [15/44 - 34.09%] **Ready ** Task 33: ln__B22BME001104_1_kneaddata_paired.faa (Apr 04 12:49:42) [15/44 - 34.09%] **Started ** Task 33: ln__B22BME001104_1_kneaddata_paired.faa (Apr 04 12:49:42) [16/44 - 36.36%] **Completed** Task 33: ln__B22BME001104_1_kneaddata_paired.faa (Apr 04 12:49:42) [16/44 - 36.36%] **Ready ** Task 34: ln__B22BME001104_1_kneaddata_paired.faa (Apr 04 12:49:42) [16/44 - 36.36%] **Started ** Task 34: ln__B22BME001104_1_kneaddata_paired.faa (Apr 04 12:49:42) [17/44 - 38.64%] **Completed** Task 34: ln__B22BME001104_1_kneaddata_paired.faa (Apr 04 12:49:42) [17/44 - 38.64%] **Ready ** Task 35: ln__B22BME001104_1_kneaddata_paired.faa (Apr 04 12:49:42) [17/44 - 38.64%] **Started ** Task 35: ln__B22BME001104_1_kneaddata_paired.faa (Apr 04 12:49:42) [18/44 - 40.91%] **Completed** Task 35: ln__B22BME001104_1_kneaddata_paired.faa (Apr 04 12:49:42) [18/44 - 40.91%] **Ready ** Task 0: B22A002S003F2_1_kneaddata_paired__megahit (Apr 04 12:49:42) [18/44 - 40.91%] **Started ** Task 0: B22A002S003F2_1_kneaddata_paired__megahit (Apr 04 13:52:43) [19/44 - 43.18%] **Completed** Task 0: B22A002S003F2_1_kneaddata_paired__megahit (Apr 04 13:52:43) [19/44 - 43.18%] **Ready ** Task 13: ln__B22A002S003F2_1_kneaddata_paired.contigs.fa (Apr 04 13:52:43) [19/44 - 43.18%] **Started ** Task 13: ln__B22A002S003F2_1_kneaddata_paired.contigs.fa (Apr 04 13:52:43) [20/44 - 45.45%] **Completed** Task 13: ln__B22A002S003F2_1_kneaddata_paired.contigs.fa (Apr 04 13:52:43) [20/44 - 45.45%] **Ready ** Task 17: format_contig_table (Apr 04 13:52:43) [20/44 - 45.45%] **Started ** Task 17: format_contig_table (Apr 04 13:52:53) [21/44 - 47.73%] **Completed** Task 17: format_contig_table (Apr 04 13:52:53) [21/44 - 47.73%] **Ready ** Task 19: B22A002S003F2_1_kneaddata_paired__prodigal (Apr 04 13:52:53) [21/44 - 47.73%] **Started ** Task 19: B22A002S003F2_1_kneaddata_paired__prodigal (Apr 04 14:08:44) [22/44 - 50.00%] **Completed** Task 19: B22A002S003F2_1_kneaddata_paired__prodigal (Apr 04 14:08:44) [22/44 - 50.00%] **Ready ** Task 24: ln__B22A002S003F2_1_kneaddata_paired.faa (Apr 04 14:08:44) [22/44 - 50.00%] **Started ** Task 24: ln__B22A002S003F2_1_kneaddata_paired.faa (Apr 04 14:08:44) [23/44 - 52.27%] **Completed** Task 24: ln__B22A002S003F2_1_kneaddata_paired.faa (Apr 04 14:08:44) [23/44 - 52.27%] **Ready ** Task 38: format_protein_sequences (Apr 04 14:08:44) [23/44 - 52.27%] **Started ** Task 38: format_protein_sequences (Apr 04 14:09:36) [24/44 - 54.55%] **Completed** Task 38: format_protein_sequences (Apr 04 14:09:36) [24/44 - 54.55%] **Ready ** Task 40: usearch__sorting (Apr 04 14:09:36) [24/44 - 54.55%] **Started ** Task 40: usearch__sorting (Apr 04 14:09:40) [25/44 - 56.82%] **Completed** Task 40: usearch__sorting (Apr 04 14:09:40) [25/44 - 56.82%] **Ready ** Task 46: extract_complete_ORF_seq (Apr 04 14:09:40) [25/44 - 56.82%] **Started ** Task 46: extract_complete_ORF_seq (Apr 04 14:09:48) [26/44 - 59.09%] **Completed** Task 46: extract_complete_ORF_seq (Apr 04 14:09:48) [26/44 - 59.09%] **Ready ** Task 25: ln__B22A002S003F2_1_kneaddata_paired.faa (Apr 04 14:09:48) [26/44 - 59.09%] **Started ** Task 25: ln__B22A002S003F2_1_kneaddata_paired.faa (Apr 04 14:09:48) [27/44 - 61.36%] **Completed** Task 25: ln__B22A002S003F2_1_kneaddata_paired.faa (Apr 04 14:09:48) [27/44 - 61.36%] **Ready ** Task 36: combine_gene_sequences (Apr 04 14:09:48) [27/44 - 61.36%] **Started ** Task 36: combine_gene_sequences (Apr 04 14:10:56) [28/44 - 63.64%] **Failed ** Task 36: combine_gene_sequences 04/04/2022 02:10:56 PM - LoggerReporter - ERROR: task 42, extract_protein_coding_genes : Failed! Error message : Task failed because parent task `36' failed 04/04/2022 02:10:56 PM - LoggerReporter - ERROR: task 44, extract_complete_ORF_seq : Failed! Error message : Task failed because parent task `42' failed 04/04/2022 02:10:56 PM - LoggerReporter - ERROR: task 47, cd-hit-est : Failed! Error message : Task failed because parent task `44' failed 04/04/2022 02:10:56 PM - LoggerReporter - ERROR: task 49, extract_cluster_CD-hit : Failed! Error message : Task failed because parent task `47' failed 04/04/2022 02:10:56 PM - LoggerReporter - ERROR: task 51, extract_non_redundance_seq : Failed! Error message : Task failed because parent task `47' failed 04/04/2022 02:10:56 PM - LoggerReporter - ERROR: task 53, gene_abundance_indexRef : Failed! Error message : Task failed because parent task `47' failed 04/04/2022 02:10:56 PM - LoggerReporter - ERROR: task 55, B22A002S003F2_1_kneaddata_paired__gene_abundance : Failed! Error message : Task failed because parent task `53' failed 04/04/2022 02:10:56 PM - LoggerReporter - ERROR: task 60, ln__B22A002S003F2_1_kneaddata_paired.sort.bed : Failed! Error message : Task failed because parent task `55' failed 04/04/2022 02:10:56 PM - LoggerReporter - ERROR: task 57, B22A002S004F2_1_kneaddata_paired__gene_abundance : Failed! Error message : Task failed because parent task `53' failed 04/04/2022 02:10:56 PM - LoggerReporter - ERROR: task 61, ln__B22A002S004F2_1_kneaddata_paired.sort.bed : Failed! Error message : Task failed because parent task `57' failed 04/04/2022 02:10:56 PM - LoggerReporter - ERROR: task 58, B22BME001103_1_kneaddata_paired__gene_abundance : Failed! Error message : Task failed because parent task `53' failed 04/04/2022 02:10:56 PM - LoggerReporter - ERROR: task 62, ln__B22BME001103_1_kneaddata_paired.sort.bed : Failed! Error message : Task failed because parent task `58' failed 04/04/2022 02:10:56 PM - LoggerReporter - ERROR: task 59, B22BME001104_1_kneaddata_paired__gene_abundance : Failed! Error message : Task failed because parent task `53' failed 04/04/2022 02:10:56 PM - LoggerReporter - ERROR: task 63, ln__B22BME001104_1_kneaddata_paired.sort.bed : Failed! Error message : Task failed because parent task `59' failed 04/04/2022 02:10:56 PM - LoggerReporter - ERROR: task 64, gene_catalog_abundance : Failed! Error message : Task failed because parent task `60' failed 04/04/2022 02:10:56 PM - LoggerReporter - INFO: task 26, ln__B22A002S003F2_1_kneaddata_paired.faa : ready and waiting for resources 04/04/2022 02:10:56 PM - LoggerReporter - INFO: task 26, ln__B22A002S003F2_1_kneaddata_paired.faa : starting to run 04/04/2022 02:10:56 PM - LoggerReporter - INFO: Executing with shell: ln -fs /usr/data/preprocess/gene_calls/B22A002S003F2_1_kneaddata_paired/B22A002S003F2_1_kneaddata_paired.gff /usr/data/preprocess/gene_calls/B22A002S003F2_1_kneaddata_paired.gff 04/04/2022 02:10:56 PM - anadama2.helpers - INFO: Execution complete. Stdout: Stderr: 04/04/2022 02:10:56 PM - LoggerReporter - INFO: task 26, ln__B22A002S003F2_1_kneaddata_paired.faa : completed successfully 04/04/2022 02:10:56 PM - LoggerReporter - ERROR: AnADAMA run finished with errors. (Apr 04 14:10:56) [29/44 - 65.91%] **Failed ** Task 42: extract_protein_coding_genes (Apr 04 14:10:56) [30/44 - 68.18%] **Failed ** Task 44: extract_complete_ORF_seq (Apr 04 14:10:56) [31/44 - 70.45%] **Failed ** Task 47: cd-hit-est (Apr 04 14:10:56) [32/44 - 72.73%] **Failed ** Task 49: extract_cluster_CD-hit (Apr 04 14:10:56) [33/44 - 75.00%] **Failed ** Task 51: extract_non_redundance_seq (Apr 04 14:10:56) [34/44 - 77.27%] **Failed ** Task 53: gene_abundance_indexRef (Apr 04 14:10:56) [35/44 - 79.55%] **Failed ** Task 55: B22A002S003F2_1_kneaddata_paired__gene_abundance (Apr 04 14:10:56) [36/44 - 81.82%] **Failed ** Task 60: ln__B22A002S003F2_1_kneaddata_paired.sort.bed (Apr 04 14:10:56) [37/44 - 84.09%] **Failed ** Task 57: B22A002S004F2_1_kneaddata_paired__gene_abundance (Apr 04 14:10:56) [38/44 - 86.36%] **Failed ** Task 61: ln__B22A002S004F2_1_kneaddata_paired.sort.bed (Apr 04 14:10:56) [39/44 - 88.64%] **Failed ** Task 58: B22BME001103_1_kneaddata_paired__gene_abundance (Apr 04 14:10:56) [40/44 - 90.91%] **Failed ** Task 62: ln__B22BME001103_1_kneaddata_paired.sort.bed (Apr 04 14:10:56) [41/44 - 93.18%] **Failed ** Task 59: B22BME001104_1_kneaddata_paired__gene_abundance (Apr 04 14:10:56) [42/44 - 95.45%] **Failed ** Task 63: ln__B22BME001104_1_kneaddata_paired.sort.bed (Apr 04 14:10:56) [43/44 - 97.73%] **Failed ** Task 64: gene_catalog_abundance (Apr 04 14:10:56) [43/44 - 97.73%] **Ready ** Task 26: ln__B22A002S003F2_1_kneaddata_paired.faa (Apr 04 14:10:56) [43/44 - 97.73%] **Started ** Task 26: ln__B22A002S003F2_1_kneaddata_paired.faa (Apr 04 14:10:56) [44/44 - 100.00%] **Completed** Task 26: ln__B22A002S003F2_1_kneaddata_paired.faa Run Finished Task 36 failed Name: combine_gene_sequences Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File "/usr/local/lib/python3.6/dist-packages/anadama2/runners.py", line 201, in _run_task_locally action_func(task) File "/usr/local/lib/python3.6/dist-packages/anadama2/helpers.py", line 89, in actually_sh ret = _sh(s, **kwargs) File "/usr/local/lib/python3.6/dist-packages/anadama2/util/__init__.py", line 320, in sh raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1])) anadama2.util.ShellException: [Errno 1] Command `metawibele_combine_gene_sequences -p /usr/data/preprocess/gene_calls -e fna -o /usr/data/preprocess/finalized/batch_22_combined_gene.fna > /usr/data/preprocess/finalized/batch_22_combined_gene.log 2>&1 ' failed. Out: b'' Err: b'' Task 42 failed Name: extract_protein_coding_genes Original error: Task failed because parent task `36' failed Task 44 failed Name: extract_complete_ORF_seq Original error: Task failed because parent task `42' failed Task 47 failed Name: cd-hit-est Original error: Task failed because parent task `44' failed Task 49 failed Name: extract_cluster_CD-hit Original error: Task failed because parent task `47' failed Task 51 failed Name: extract_non_redundance_seq Original error: Task failed because parent task `47' failed Task 53 failed Name: gene_abundance_indexRef Original error: Task failed because parent task `47' failed Task 55 failed Name: B22A002S003F2_1_kneaddata_paired__gene_abundance Original error: Task failed because parent task `53' failed Task 60 failed Name: ln__B22A002S003F2_1_kneaddata_paired.sort.bed Original error: Task failed because parent task `55' failed Task 57 failed Name: B22A002S004F2_1_kneaddata_paired__gene_abundance Original error: Task failed because parent task `53' failed Task 61 failed Name: ln__B22A002S004F2_1_kneaddata_paired.sort.bed Original error: Task failed because parent task `57' failed Task 58 failed Name: B22BME001103_1_kneaddata_paired__gene_abundance Original error: Task failed because parent task `53' failed Task 62 failed Name: ln__B22BME001103_1_kneaddata_paired.sort.bed Original error: Task failed because parent task `58' failed Task 59 failed Name: B22BME001104_1_kneaddata_paired__gene_abundance Original error: Task failed because parent task `53' failed Task 63 failed Name: ln__B22BME001104_1_kneaddata_paired.sort.bed Original error: Task failed because parent task `59' failed Task 64 failed Name: gene_catalog_abundance Original error: Task failed because parent task `60' failed Traceback (most recent call last): File "/usr/local/bin/preprocess.py", line 175, in main(parse_cli_arguments()) File "/usr/local/bin/preprocess.py", line 172, in main workflow.go() File "/usr/local/lib/python3.6/dist-packages/anadama2/workflow.py", line 801, in go self._handle_finished() File "/usr/local/lib/python3.6/dist-packages/anadama2/workflow.py", line 833, in _handle_finished raise RunFailed() anadama2.workflow.RunFailed