[2024-01-24 13:22:16,077] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:16,079] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:16,079] [INFO] DQC Reference Directory: /var/lib/cwl/stg4fc3a5fa-6213-4236-99ad-0586cd844dee/dqc_reference
[2024-01-24 13:22:17,426] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:17,427] [INFO] Task started: Prodigal
[2024-01-24 13:22:17,427] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b3ef1c4-2ddd-4af1-9fc0-f173da0da212/GCF_004327985.1_ASM432798v1_genomic.fna.gz | prodigal -d GCF_004327985.1_ASM432798v1_genomic.fna/cds.fna -a GCF_004327985.1_ASM432798v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:33,696] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:33,696] [INFO] Task started: HMMsearch
[2024-01-24 13:22:33,696] [INFO] Running command: hmmsearch --tblout GCF_004327985.1_ASM432798v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4fc3a5fa-6213-4236-99ad-0586cd844dee/dqc_reference/reference_markers.hmm GCF_004327985.1_ASM432798v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:34,130] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:34,131] [INFO] Found 6/6 markers.
[2024-01-24 13:22:34,181] [INFO] Query marker FASTA was written to GCF_004327985.1_ASM432798v1_genomic.fna/markers.fasta
[2024-01-24 13:22:34,182] [INFO] Task started: Blastn
[2024-01-24 13:22:34,182] [INFO] Running command: blastn -query GCF_004327985.1_ASM432798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fc3a5fa-6213-4236-99ad-0586cd844dee/dqc_reference/reference_markers.fasta -out GCF_004327985.1_ASM432798v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:35,227] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:35,230] [INFO] Selected 15 target genomes.
[2024-01-24 13:22:35,230] [INFO] Target genome list was writen to GCF_004327985.1_ASM432798v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:35,236] [INFO] Task started: fastANI
[2024-01-24 13:22:35,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b3ef1c4-2ddd-4af1-9fc0-f173da0da212/GCF_004327985.1_ASM432798v1_genomic.fna.gz --refList GCF_004327985.1_ASM432798v1_genomic.fna/target_genomes.txt --output GCF_004327985.1_ASM432798v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:51,166] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:51,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4fc3a5fa-6213-4236-99ad-0586cd844dee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:51,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4fc3a5fa-6213-4236-99ad-0586cd844dee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:51,182] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:51,182] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:51,182] [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 halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	100.0	1661	1668	95	conclusive
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	88.0202	1253	1668	95	below_threshold
Marinobacter bohaiensis	strain=T17	GCA_003258515.1	2201898	2201898	type	True	82.2687	979	1668	95	below_threshold
Marinobacter nanhaiticus	strain=D15-8W	GCA_000364845.1	1305740	1305740	type	True	80.384	773	1668	95	below_threshold
Marinobacter fonticola	strain=CS412	GCA_008122265.1	2603215	2603215	type	True	79.7312	646	1668	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.8158	492	1668	95	below_threshold
Marinobacter profundi	strain=PWS21	GCA_002744715.1	2666256	2666256	type	True	78.7272	448	1668	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	78.5165	428	1668	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	78.4816	372	1668	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	78.4051	404	1668	95	below_threshold
Marinobacter zhanjiangensis	strain=KCTC 22280	GCA_014651935.1	578215	578215	type	True	78.3675	425	1668	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	78.3356	359	1668	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	77.2293	202	1668	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	77.2119	238	1668	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	77.0819	210	1668	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:51,184] [INFO] DFAST Taxonomy check result was written to GCF_004327985.1_ASM432798v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:51,191] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:51,191] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:51,191] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4fc3a5fa-6213-4236-99ad-0586cd844dee/dqc_reference/checkm_data
[2024-01-24 13:22:51,193] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:51,248] [INFO] Task started: CheckM
[2024-01-24 13:22:51,248] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004327985.1_ASM432798v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004327985.1_ASM432798v1_genomic.fna/checkm_input GCF_004327985.1_ASM432798v1_genomic.fna/checkm_result
[2024-01-24 13:23:40,359] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:40,360] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:40,381] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:40,381] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:40,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004327985.1_ASM432798v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:40,382] [INFO] Task started: Blastn
[2024-01-24 13:23:40,382] [INFO] Running command: blastn -query GCF_004327985.1_ASM432798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fc3a5fa-6213-4236-99ad-0586cd844dee/dqc_reference/reference_markers_gtdb.fasta -out GCF_004327985.1_ASM432798v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:42,210] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:42,213] [INFO] Selected 10 target genomes.
[2024-01-24 13:23:42,214] [INFO] Target genome list was writen to GCF_004327985.1_ASM432798v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:42,223] [INFO] Task started: fastANI
[2024-01-24 13:23:42,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b3ef1c4-2ddd-4af1-9fc0-f173da0da212/GCF_004327985.1_ASM432798v1_genomic.fna.gz --refList GCF_004327985.1_ASM432798v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004327985.1_ASM432798v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:52,192] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:52,202] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:52,202] [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_004327985.1	s__Marinobacter_A halodurans	100.0	1661	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003789045.1	s__Marinobacter_A sp003789045	87.9051	1224	1668	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_003258515.1	s__Marinobacter_A bohaiensis	82.2687	979	1668	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	80.3485	779	1668	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	79.7195	648	1668	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_003315345.1	s__Marinobacter pelagius_A	78.9591	460	1668	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	78.7078	450	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.28	99.28	0.94	0.94	2	-
GCA_018623515.1	s__Marinobacter sp018623515	78.6336	380	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003994855.1	s__Marinobacter sp003994855	78.6238	452	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651935.1	s__Marinobacter zhanjiangensis	78.3675	425	1668	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 13:23:52,204] [INFO] GTDB search result was written to GCF_004327985.1_ASM432798v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:52,204] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:52,208] [INFO] DFAST_QC result json was written to GCF_004327985.1_ASM432798v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:52,208] [INFO] DFAST_QC completed!
[2024-01-24 13:23:52,208] [INFO] Total running time: 0h1m36s