[2023-06-26 23:44:50,848] [INFO] DFAST_QC pipeline started.
[2023-06-26 23:44:50,850] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 23:44:50,850] [INFO] DQC Reference Directory: /var/lib/cwl/stg262a5f78-3e75-4232-a106-79a85ecd0199/dqc_reference
[2023-06-26 23:44:52,119] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 23:44:52,120] [INFO] Task started: Prodigal
[2023-06-26 23:44:52,120] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb299224-6feb-47b8-adff-2550178ff6a2/GCA_002683455.1_ASM268345v1_genomic.fna.gz | prodigal -d GCA_002683455.1_ASM268345v1_genomic.fna/cds.fna -a GCA_002683455.1_ASM268345v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 23:45:04,580] [INFO] Task succeeded: Prodigal
[2023-06-26 23:45:04,581] [INFO] Task started: HMMsearch
[2023-06-26 23:45:04,581] [INFO] Running command: hmmsearch --tblout GCA_002683455.1_ASM268345v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg262a5f78-3e75-4232-a106-79a85ecd0199/dqc_reference/reference_markers.hmm GCA_002683455.1_ASM268345v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 23:45:04,882] [INFO] Task succeeded: HMMsearch
[2023-06-26 23:45:04,884] [INFO] Found 6/6 markers.
[2023-06-26 23:45:04,925] [INFO] Query marker FASTA was written to GCA_002683455.1_ASM268345v1_genomic.fna/markers.fasta
[2023-06-26 23:45:04,926] [INFO] Task started: Blastn
[2023-06-26 23:45:04,926] [INFO] Running command: blastn -query GCA_002683455.1_ASM268345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg262a5f78-3e75-4232-a106-79a85ecd0199/dqc_reference/reference_markers.fasta -out GCA_002683455.1_ASM268345v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:45:05,702] [INFO] Task succeeded: Blastn
[2023-06-26 23:45:05,706] [INFO] Selected 28 target genomes.
[2023-06-26 23:45:05,706] [INFO] Target genome list was writen to GCA_002683455.1_ASM268345v1_genomic.fna/target_genomes.txt
[2023-06-26 23:45:05,722] [INFO] Task started: fastANI
[2023-06-26 23:45:05,722] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb299224-6feb-47b8-adff-2550178ff6a2/GCA_002683455.1_ASM268345v1_genomic.fna.gz --refList GCA_002683455.1_ASM268345v1_genomic.fna/target_genomes.txt --output GCA_002683455.1_ASM268345v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 23:45:25,711] [INFO] Task succeeded: fastANI
[2023-06-26 23:45:25,712] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg262a5f78-3e75-4232-a106-79a85ecd0199/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 23:45:25,712] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg262a5f78-3e75-4232-a106-79a85ecd0199/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 23:45:25,733] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 23:45:25,733] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-26 23:45:25,733] [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
Marinobacter algicola	strain=DG893	GCA_000170835.1	236100	236100	type	True	78.4333	255	1439	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	78.4092	226	1439	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	78.3886	440	1439	95	below_threshold
Marinobacter bohaiensis	strain=T17	GCA_003258515.1	2201898	2201898	type	True	78.3027	418	1439	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	78.2943	199	1439	95	below_threshold
Marinobacter nanhaiticus	strain=D15-8W	GCA_000364845.1	1305740	1305740	type	True	78.2555	380	1439	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	78.2054	415	1439	95	below_threshold
Marinobacter fonticola	strain=CS412	GCA_008122265.1	2603215	2603215	type	True	78.1705	396	1439	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	77.8862	243	1439	95	below_threshold
Marinobacter litoralis	strain=Sw-45	GCA_003336705.1	187981	187981	type	True	77.7999	178	1439	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	77.7949	242	1439	95	below_threshold
Marinobacter lipolyticus	strain=SM19	GCA_000397065.2	209639	209639	type	True	77.7833	239	1439	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	77.7541	234	1439	95	below_threshold
Marinobacter changyiensis	strain=CLL7-20	GCA_009193265.1	2604091	2604091	type	True	77.7128	212	1439	95	below_threshold
Marinobacter zhejiangensis	strain=CGMCC 1.7061	GCA_900114775.1	488535	488535	type	True	77.6756	208	1439	95	below_threshold
Marinobacter halotolerans	strain=NBRC 110910	GCA_008795985.1	1569211	1569211	type	True	77.6119	218	1439	95	below_threshold
Marinobacter vulgaris	strain=F01	GCA_007559285.1	1928331	1928331	type	True	77.581	221	1439	95	below_threshold
Marinobacter profundi	strain=PWS21	GCA_002744715.1	2666256	2666256	type	True	77.553	270	1439	95	below_threshold
Marinobacter zhanjiangensis	strain=KCTC 22280	GCA_014651935.1	578215	578215	type	True	77.5492	205	1439	95	below_threshold
Marinobacter maroccanus	strain=N4	GCA_002933275.1	2055143	2055143	type	True	77.544	230	1439	95	below_threshold
Marinobacter vulgaris	strain=F01	GCA_003344045.1	1928331	1928331	type	True	77.4943	223	1439	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	77.437	227	1439	95	below_threshold
Pseudomonas pohangensis	strain=DSM 17875	GCA_900105995.1	364197	364197	type	True	76.2546	50	1439	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	75.6502	52	1439	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 23:45:25,752] [INFO] DFAST Taxonomy check result was written to GCA_002683455.1_ASM268345v1_genomic.fna/tc_result.tsv
[2023-06-26 23:45:25,753] [INFO] ===== Taxonomy check completed =====
[2023-06-26 23:45:25,753] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 23:45:25,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg262a5f78-3e75-4232-a106-79a85ecd0199/dqc_reference/checkm_data
[2023-06-26 23:45:25,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 23:45:25,803] [INFO] Task started: CheckM
[2023-06-26 23:45:25,803] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002683455.1_ASM268345v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002683455.1_ASM268345v1_genomic.fna/checkm_input GCA_002683455.1_ASM268345v1_genomic.fna/checkm_result
[2023-06-26 23:46:07,337] [INFO] Task succeeded: CheckM
[2023-06-26 23:46:07,338] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 12.50%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-26 23:46:07,374] [INFO] ===== Completeness check finished =====
[2023-06-26 23:46:07,374] [INFO] ===== Start GTDB Search =====
[2023-06-26 23:46:07,375] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002683455.1_ASM268345v1_genomic.fna/markers.fasta)
[2023-06-26 23:46:07,375] [INFO] Task started: Blastn
[2023-06-26 23:46:07,375] [INFO] Running command: blastn -query GCA_002683455.1_ASM268345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg262a5f78-3e75-4232-a106-79a85ecd0199/dqc_reference/reference_markers_gtdb.fasta -out GCA_002683455.1_ASM268345v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:46:08,613] [INFO] Task succeeded: Blastn
[2023-06-26 23:46:08,618] [INFO] Selected 20 target genomes.
[2023-06-26 23:46:08,619] [INFO] Target genome list was writen to GCA_002683455.1_ASM268345v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 23:46:08,639] [INFO] Task started: fastANI
[2023-06-26 23:46:08,640] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb299224-6feb-47b8-adff-2550178ff6a2/GCA_002683455.1_ASM268345v1_genomic.fna.gz --refList GCA_002683455.1_ASM268345v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002683455.1_ASM268345v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 23:46:23,149] [INFO] Task succeeded: fastANI
[2023-06-26 23:46:23,173] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-26 23:46:23,173] [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
GCA_002717955.1	s__Marinobacter_A sp002717955	99.9535	1302	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	99.94	99.88	0.97	0.95	4	conclusive
GCF_000170835.1	s__Marinobacter algicola	78.4137	257	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258515.1	s__Marinobacter_A bohaiensis	78.2948	419	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	98.52	98.52	0.96	0.96	2	-
GCF_000364845.1	s__Marinobacter_A nanhaiticus	78.244	382	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003789045.1	s__Marinobacter_A sp003789045	78.2335	434	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	97.70	97.70	0.91	0.91	2	-
GCF_004327985.1	s__Marinobacter_A halodurans	78.2069	415	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122265.1	s__Marinobacter_A fonticola	78.1608	397	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018424605.1	s__Marinobacter lipolyticus_B	77.8081	260	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359475.1	s__Marinobacter sp014359475	77.7619	211	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193265.1	s__Marinobacter changyiensis	77.7051	214	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114775.1	s__Marinobacter zhejiangensis	77.6687	210	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686085.1	s__Marinobacter sp000686085	77.6463	238	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003315345.1	s__Marinobacter pelagius_A	77.6018	243	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002744715.1	s__Marinobacter profundi	77.5515	271	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.28	99.28	0.94	0.94	2	-
GCF_002933275.1	s__Marinobacter maroccanus	77.5437	231	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344045.1	s__Marinobacter vulgaris	77.4894	225	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900114925.1	s__Marinobacter pelagius	77.4372	228	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860765.1	s__Marinobacter salexigens_A	77.3583	144	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792665.1	s__Marinobacter orientalis	77.2475	187	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014762755.1	s__Marinobacter sp014762755	77.0183	166	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-26 23:46:23,176] [INFO] GTDB search result was written to GCA_002683455.1_ASM268345v1_genomic.fna/result_gtdb.tsv
[2023-06-26 23:46:23,176] [INFO] ===== GTDB Search completed =====
[2023-06-26 23:46:23,181] [INFO] DFAST_QC result json was written to GCA_002683455.1_ASM268345v1_genomic.fna/dqc_result.json
[2023-06-26 23:46:23,181] [INFO] DFAST_QC completed!
[2023-06-26 23:46:23,181] [INFO] Total running time: 0h1m32s