[2024-01-25 19:31:51,319] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:31:51,321] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:31:51,321] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d614cc9-0c78-4950-846a-42f2f1137eee/dqc_reference
[2024-01-25 19:31:52,541] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:31:52,542] [INFO] Task started: Prodigal
[2024-01-25 19:31:52,542] [INFO] Running command: gunzip -c /var/lib/cwl/stg955aea9b-c0d6-4856-a797-1ad8ac5a3fae/GCF_003014615.1_ASM301461v1_genomic.fna.gz | prodigal -d GCF_003014615.1_ASM301461v1_genomic.fna/cds.fna -a GCF_003014615.1_ASM301461v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:32:02,179] [INFO] Task succeeded: Prodigal
[2024-01-25 19:32:02,179] [INFO] Task started: HMMsearch
[2024-01-25 19:32:02,179] [INFO] Running command: hmmsearch --tblout GCF_003014615.1_ASM301461v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d614cc9-0c78-4950-846a-42f2f1137eee/dqc_reference/reference_markers.hmm GCF_003014615.1_ASM301461v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:32:02,397] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:32:02,398] [INFO] Found 6/6 markers.
[2024-01-25 19:32:02,428] [INFO] Query marker FASTA was written to GCF_003014615.1_ASM301461v1_genomic.fna/markers.fasta
[2024-01-25 19:32:02,428] [INFO] Task started: Blastn
[2024-01-25 19:32:02,428] [INFO] Running command: blastn -query GCF_003014615.1_ASM301461v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d614cc9-0c78-4950-846a-42f2f1137eee/dqc_reference/reference_markers.fasta -out GCF_003014615.1_ASM301461v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:03,140] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:03,143] [INFO] Selected 21 target genomes.
[2024-01-25 19:32:03,143] [INFO] Target genome list was writen to GCF_003014615.1_ASM301461v1_genomic.fna/target_genomes.txt
[2024-01-25 19:32:03,149] [INFO] Task started: fastANI
[2024-01-25 19:32:03,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg955aea9b-c0d6-4856-a797-1ad8ac5a3fae/GCF_003014615.1_ASM301461v1_genomic.fna.gz --refList GCF_003014615.1_ASM301461v1_genomic.fna/target_genomes.txt --output GCF_003014615.1_ASM301461v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:32:17,754] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:17,754] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d614cc9-0c78-4950-846a-42f2f1137eee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:32:17,755] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d614cc9-0c78-4950-846a-42f2f1137eee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:32:17,766] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:32:17,766] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:32:17,766] [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
Marinobacterium halophilum	strain=DSM 17586	GCA_003014615.1	267374	267374	type	True	100.0	1192	1195	95	conclusive
Marinobacterium stanieri	strain=DSM 7027	GCA_900155945.1	49186	49186	type	True	80.6036	605	1195	95	below_threshold
Marinobacterium alkalitolerans	strain=AK62	GCA_017776525.1	1542925	1542925	type	True	80.4032	534	1195	95	below_threshold
Marinobacterium georgiense	strain=DSM 11526	GCA_900107855.1	48076	48076	type	True	80.3324	504	1195	95	below_threshold
Marinobacterium ramblicola	strain=D7	GCA_019084545.1	2849041	2849041	type	True	78.5423	319	1195	95	below_threshold
Marinobacterium zhoushanense	strain=CGMCC 1.15341	GCA_014641945.1	1679163	1679163	type	True	78.4697	306	1195	95	below_threshold
Marinobacterium litorale	strain=DSM 23545	GCA_000428985.1	404770	404770	type	True	78.3878	227	1195	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	78.2982	269	1195	95	below_threshold
Marinobacterium aestuarii	strain=ST58-10	GCA_001651805.1	1821621	1821621	type	True	77.8258	239	1195	95	below_threshold
Nitrincola iocasae	strain=KXZD1103	GCA_008727795.1	2614693	2614693	type	True	77.8148	117	1195	95	below_threshold
Marinobacterium rhizophilum	strain=DSM 18822	GCA_000378045.1	420402	420402	type	True	77.7573	235	1195	95	below_threshold
Marinobacterium profundum	strain=PAMC 27536	GCA_001528745.1	1714300	1714300	type	True	77.5851	219	1195	95	below_threshold
Nitrincola lacisaponensis	strain=4CA	GCA_000691225.1	267850	267850	type	True	77.5656	144	1195	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.6194	116	1195	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	76.5869	116	1195	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	76.4569	114	1195	95	below_threshold
Larsenimonas suaedae	strain=DSM 22428	GCA_023712105.1	1851019	1851019	type	True	76.3084	52	1195	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	76.0346	61	1195	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:32:17,769] [INFO] DFAST Taxonomy check result was written to GCF_003014615.1_ASM301461v1_genomic.fna/tc_result.tsv
[2024-01-25 19:32:17,769] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:32:17,770] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:32:17,770] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d614cc9-0c78-4950-846a-42f2f1137eee/dqc_reference/checkm_data
[2024-01-25 19:32:17,771] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:32:17,809] [INFO] Task started: CheckM
[2024-01-25 19:32:17,809] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003014615.1_ASM301461v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003014615.1_ASM301461v1_genomic.fna/checkm_input GCF_003014615.1_ASM301461v1_genomic.fna/checkm_result
[2024-01-25 19:32:49,709] [INFO] Task succeeded: CheckM
[2024-01-25 19:32:49,710] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:32:49,733] [INFO] ===== Completeness check finished =====
[2024-01-25 19:32:49,733] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:32:49,734] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003014615.1_ASM301461v1_genomic.fna/markers.fasta)
[2024-01-25 19:32:49,734] [INFO] Task started: Blastn
[2024-01-25 19:32:49,734] [INFO] Running command: blastn -query GCF_003014615.1_ASM301461v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d614cc9-0c78-4950-846a-42f2f1137eee/dqc_reference/reference_markers_gtdb.fasta -out GCF_003014615.1_ASM301461v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:50,955] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:50,958] [INFO] Selected 11 target genomes.
[2024-01-25 19:32:50,959] [INFO] Target genome list was writen to GCF_003014615.1_ASM301461v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:32:50,965] [INFO] Task started: fastANI
[2024-01-25 19:32:50,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg955aea9b-c0d6-4856-a797-1ad8ac5a3fae/GCF_003014615.1_ASM301461v1_genomic.fna.gz --refList GCF_003014615.1_ASM301461v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003014615.1_ASM301461v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:32:59,437] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:59,445] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:32:59,445] [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_003014615.1	s__Marinobacterium halophilum	100.0	1192	1195	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	98.87	98.87	0.91	0.91	2	conclusive
GCF_019061305.1	s__Marinobacterium sp019061305	81.4665	681	1195	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155945.1	s__Marinobacterium stanieri	80.6071	606	1195	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	96.47	96.47	0.91	0.91	2	-
GCF_013868415.1	s__Marinobacterium sp013868415	80.4268	578	1195	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017776525.1	s__Marinobacterium alkalitolerans	80.4066	534	1195	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107855.1	s__Marinobacterium georgiense	80.3107	504	1195	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	97.23	97.23	0.75	0.75	2	-
GCF_019084545.1	s__Marinobacterium sp019084545	78.5538	316	1195	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641945.1	s__Marinobacterium zhoushanense	78.4334	308	1195	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428985.1	s__Marinobacterium litorale	78.3512	228	1195	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	97.80	97.80	0.87	0.87	2	-
GCF_907163115.1	s__Pseudomonas_A stutzeri_AL	76.6524	113	1195	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.05	96.55	0.94	0.91	6	-
GCF_003205815.1	s__Pseudomonas_A sp003205815	76.5892	121	1195	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.18	96.58	0.91	0.87	27	-
--------------------------------------------------------------------------------
[2024-01-25 19:32:59,446] [INFO] GTDB search result was written to GCF_003014615.1_ASM301461v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:32:59,447] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:32:59,450] [INFO] DFAST_QC result json was written to GCF_003014615.1_ASM301461v1_genomic.fna/dqc_result.json
[2024-01-25 19:32:59,450] [INFO] DFAST_QC completed!
[2024-01-25 19:32:59,450] [INFO] Total running time: 0h1m8s