[2024-01-24 13:55:19,364] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:19,366] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:19,366] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe57fc0b-b1e3-4880-8c4c-8831963e602d/dqc_reference
[2024-01-24 13:55:20,716] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:20,717] [INFO] Task started: Prodigal
[2024-01-24 13:55:20,717] [INFO] Running command: gunzip -c /var/lib/cwl/stg45eb4171-0876-41fe-99c9-621cb5c1b51b/GCF_000422425.1_ASM42242v1_genomic.fna.gz | prodigal -d GCF_000422425.1_ASM42242v1_genomic.fna/cds.fna -a GCF_000422425.1_ASM42242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:33,732] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:33,732] [INFO] Task started: HMMsearch
[2024-01-24 13:55:33,732] [INFO] Running command: hmmsearch --tblout GCF_000422425.1_ASM42242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe57fc0b-b1e3-4880-8c4c-8831963e602d/dqc_reference/reference_markers.hmm GCF_000422425.1_ASM42242v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:34,102] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:34,103] [INFO] Found 6/6 markers.
[2024-01-24 13:55:34,149] [INFO] Query marker FASTA was written to GCF_000422425.1_ASM42242v1_genomic.fna/markers.fasta
[2024-01-24 13:55:34,149] [INFO] Task started: Blastn
[2024-01-24 13:55:34,149] [INFO] Running command: blastn -query GCF_000422425.1_ASM42242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe57fc0b-b1e3-4880-8c4c-8831963e602d/dqc_reference/reference_markers.fasta -out GCF_000422425.1_ASM42242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:34,918] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:34,922] [INFO] Selected 22 target genomes.
[2024-01-24 13:55:34,922] [INFO] Target genome list was writen to GCF_000422425.1_ASM42242v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:34,931] [INFO] Task started: fastANI
[2024-01-24 13:55:34,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg45eb4171-0876-41fe-99c9-621cb5c1b51b/GCF_000422425.1_ASM42242v1_genomic.fna.gz --refList GCF_000422425.1_ASM42242v1_genomic.fna/target_genomes.txt --output GCF_000422425.1_ASM42242v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:50,701] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:50,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe57fc0b-b1e3-4880-8c4c-8831963e602d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:50,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe57fc0b-b1e3-4880-8c4c-8831963e602d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:50,715] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:50,715] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:50,715] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Oceanospirillum beijerinckii	strain=DSM 7166	GCA_000422425.1	64976	64976	type	True	100.0	1717	1724	95	conclusive
Oceanospirillum sanctuarii	strain=AK56	GCA_002150805.1	1434821	1434821	type	True	79.7385	425	1724	95	below_threshold
Oceanospirillum linum	strain=ATCC 11336	GCA_001995095.2	966	966	type	True	78.7417	330	1724	95	below_threshold
Oceanospirillum maris	strain=DSM 6286	GCA_000422865.1	64977	64977	type	True	78.4345	252	1724	95	below_threshold
Oceanospirillum multiglobuliferum	strain=ATCC 33336	GCA_900167095.1	64969	64969	type	True	78.3762	226	1724	95	below_threshold
Oceanospirillum multiglobuliferum	strain=ATCC 33336	GCA_002059185.1	64969	64969	type	True	78.3532	230	1724	95	below_threshold
Marinobacterium jannaschii	strain=DSM 6295	GCA_000620085.1	64970	64970	type	True	76.9949	122	1724	95	below_threshold
Shewanella corallii	strain=DSM 21332	GCA_023349125.1	560080	560080	type	True	76.8507	55	1724	95	below_threshold
Neptunomonas marina	strain=HPM-16	GCA_004005935.1	1815562	1815562	type	True	76.6779	50	1724	95	below_threshold
Marinobacterium litorale	strain=DSM 23545	GCA_000428985.1	404770	404770	type	True	76.3155	74	1724	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:50,719] [INFO] DFAST Taxonomy check result was written to GCF_000422425.1_ASM42242v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:50,719] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:50,720] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:50,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe57fc0b-b1e3-4880-8c4c-8831963e602d/dqc_reference/checkm_data
[2024-01-24 13:55:50,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:50,780] [INFO] Task started: CheckM
[2024-01-24 13:55:50,781] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000422425.1_ASM42242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000422425.1_ASM42242v1_genomic.fna/checkm_input GCF_000422425.1_ASM42242v1_genomic.fna/checkm_result
[2024-01-24 13:56:32,310] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:32,311] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:32,330] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:32,330] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:32,330] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000422425.1_ASM42242v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:32,331] [INFO] Task started: Blastn
[2024-01-24 13:56:32,331] [INFO] Running command: blastn -query GCF_000422425.1_ASM42242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe57fc0b-b1e3-4880-8c4c-8831963e602d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000422425.1_ASM42242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:33,573] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:33,577] [INFO] Selected 15 target genomes.
[2024-01-24 13:56:33,577] [INFO] Target genome list was writen to GCF_000422425.1_ASM42242v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:33,594] [INFO] Task started: fastANI
[2024-01-24 13:56:33,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg45eb4171-0876-41fe-99c9-621cb5c1b51b/GCF_000422425.1_ASM42242v1_genomic.fna.gz --refList GCF_000422425.1_ASM42242v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000422425.1_ASM42242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:44,454] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:44,462] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:44,462] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000422425.1	s__Oceanospirillum beijerinckii	100.0	1717	1724	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	98.77	98.77	0.90	0.90	2	conclusive
GCF_014164585.1	s__Oceanospirillum sp014164585	82.1002	597	1724	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150805.1	s__Oceanospirillum sanctuarii	79.737	426	1724	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001995095.2	s__Oceanospirillum linum	78.746	330	1724	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000422865.1	s__Oceanospirillum maris	78.4303	252	1724	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005935.1	s__Neptunomonas marina	76.5784	56	1724	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	97.03	97.03	0.93	0.93	2	-
GCF_000428985.1	s__Marinobacterium litorale	76.3641	76	1724	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	97.80	97.80	0.87	0.87	2	-
GCF_013416325.1	s__Halomonas sedimenti	75.9902	50	1724	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.54	99.54	0.90	0.90	2	-
GCF_900114775.1	s__Marinobacter zhejiangensis	75.8411	51	1724	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:44,464] [INFO] GTDB search result was written to GCF_000422425.1_ASM42242v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:44,464] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:44,473] [INFO] DFAST_QC result json was written to GCF_000422425.1_ASM42242v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:44,474] [INFO] DFAST_QC completed!
[2024-01-24 13:56:44,474] [INFO] Total running time: 0h1m25s