[2024-01-24 12:06:33,942] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:33,945] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:33,945] [INFO] DQC Reference Directory: /var/lib/cwl/stgb239b364-dd1a-4c6b-b7f2-b96e37d6f58c/dqc_reference
[2024-01-24 12:06:35,413] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:35,414] [INFO] Task started: Prodigal
[2024-01-24 12:06:35,414] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d66f1f1-0c0e-469b-9acb-580b7879dbee/GCF_008795985.1_ASM879598v1_genomic.fna.gz | prodigal -d GCF_008795985.1_ASM879598v1_genomic.fna/cds.fna -a GCF_008795985.1_ASM879598v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:46,990] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:46,990] [INFO] Task started: HMMsearch
[2024-01-24 12:06:46,990] [INFO] Running command: hmmsearch --tblout GCF_008795985.1_ASM879598v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb239b364-dd1a-4c6b-b7f2-b96e37d6f58c/dqc_reference/reference_markers.hmm GCF_008795985.1_ASM879598v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:47,278] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:47,280] [INFO] Found 6/6 markers.
[2024-01-24 12:06:47,324] [INFO] Query marker FASTA was written to GCF_008795985.1_ASM879598v1_genomic.fna/markers.fasta
[2024-01-24 12:06:47,325] [INFO] Task started: Blastn
[2024-01-24 12:06:47,325] [INFO] Running command: blastn -query GCF_008795985.1_ASM879598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb239b364-dd1a-4c6b-b7f2-b96e37d6f58c/dqc_reference/reference_markers.fasta -out GCF_008795985.1_ASM879598v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:48,190] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:48,194] [INFO] Selected 19 target genomes.
[2024-01-24 12:06:48,194] [INFO] Target genome list was writen to GCF_008795985.1_ASM879598v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:48,207] [INFO] Task started: fastANI
[2024-01-24 12:06:48,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d66f1f1-0c0e-469b-9acb-580b7879dbee/GCF_008795985.1_ASM879598v1_genomic.fna.gz --refList GCF_008795985.1_ASM879598v1_genomic.fna/target_genomes.txt --output GCF_008795985.1_ASM879598v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:02,839] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:02,840] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb239b364-dd1a-4c6b-b7f2-b96e37d6f58c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:02,840] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb239b364-dd1a-4c6b-b7f2-b96e37d6f58c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:02,868] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:02,868] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:02,868] [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 halotolerans	strain=NBRC 110910	GCA_008795985.1	1569211	1569211	type	True	100.0	1258	1258	95	conclusive
Marinobacter confluentis	strain=HJM-18	GCA_004785685.1	1697557	1697557	type	True	81.4729	760	1258	95	below_threshold
Marinobacter confluentis	strain=KCTC 42705	GCA_008795935.1	1697557	1697557	type	True	81.399	767	1258	95	below_threshold
Marinobacter vulgaris	strain=F01	GCA_007559285.1	1928331	1928331	type	True	79.6601	575	1258	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	79.6241	560	1258	95	below_threshold
Marinobacter algicola	strain=DG893	GCA_000170835.1	236100	236100	type	True	79.594	553	1258	95	below_threshold
Marinobacter vulgaris	strain=F01	GCA_003344045.1	1928331	1928331	type	True	79.5558	577	1258	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_012956055.1	1928859	1928859	type	True	79.366	549	1258	95	below_threshold
Marinobacter adhaerens	strain=HP15	GCA_000166295.1	1033846	1033846	type	True	79.299	482	1258	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	79.2463	473	1258	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_004792665.1	1928859	1928859	type	True	79.187	545	1258	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	79.107	456	1258	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	79.0757	463	1258	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	78.8188	476	1258	95	below_threshold
Marinobacter profundi	strain=PWS21	GCA_002744715.1	2666256	2666256	type	True	78.8078	429	1258	95	below_threshold
Marinobacter oulmenensis	strain=DSM 22359	GCA_014201735.1	643747	643747	type	True	78.7403	383	1258	95	below_threshold
Marinobacter maritimus	strain=CK47	GCA_007671675.1	277961	277961	type	True	78.2797	330	1258	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	76.5787	101	1258	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	76.4962	96	1258	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:02,870] [INFO] DFAST Taxonomy check result was written to GCF_008795985.1_ASM879598v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:02,871] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:02,871] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:02,871] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb239b364-dd1a-4c6b-b7f2-b96e37d6f58c/dqc_reference/checkm_data
[2024-01-24 12:07:02,872] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:02,913] [INFO] Task started: CheckM
[2024-01-24 12:07:02,913] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008795985.1_ASM879598v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008795985.1_ASM879598v1_genomic.fna/checkm_input GCF_008795985.1_ASM879598v1_genomic.fna/checkm_result
[2024-01-24 12:07:39,142] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:39,143] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:39,161] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:39,161] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:39,162] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008795985.1_ASM879598v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:39,162] [INFO] Task started: Blastn
[2024-01-24 12:07:39,162] [INFO] Running command: blastn -query GCF_008795985.1_ASM879598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb239b364-dd1a-4c6b-b7f2-b96e37d6f58c/dqc_reference/reference_markers_gtdb.fasta -out GCF_008795985.1_ASM879598v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:40,493] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:40,501] [INFO] Selected 19 target genomes.
[2024-01-24 12:07:40,501] [INFO] Target genome list was writen to GCF_008795985.1_ASM879598v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:40,519] [INFO] Task started: fastANI
[2024-01-24 12:07:40,520] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d66f1f1-0c0e-469b-9acb-580b7879dbee/GCF_008795985.1_ASM879598v1_genomic.fna.gz --refList GCF_008795985.1_ASM879598v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008795985.1_ASM879598v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:54,703] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:54,730] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:54,731] [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_008795985.1	s__Marinobacter halotolerans	100.0	1258	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004785685.1	s__Marinobacter confluentis	81.4636	761	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005298175.1	s__Marinobacter sp005298175	79.9868	619	1258	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	79.8811	609	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008795955.1	s__Marinobacter sp008795955	79.6242	559	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000831005.1	s__Marinobacter salarius	79.5996	582	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.84	96.73	0.88	0.79	21	-
GCF_000170835.1	s__Marinobacter algicola	79.594	553	1258	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	79.5558	577	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003994855.1	s__Marinobacter sp003994855	79.3461	481	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166295.1	s__Marinobacter adhaerens	79.292	485	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	98.39	97.71	0.91	0.87	5	-
GCF_004792665.1	s__Marinobacter orientalis	79.187	545	1258	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	79.1288	486	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002258215.1	s__Marinobacter vinifirmus	79.1121	455	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCA_017643965.1	s__Marinobacter sp017643965	78.9381	383	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820575.1	s__Marinobacter sediminum	78.8447	461	1258	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	78.8078	429	1258	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	78.6223	393	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762755.1	s__Marinobacter sp014762755	78.3755	339	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007671675.1	s__Marinobacter maritimus	78.2797	330	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.91	98.91	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:54,732] [INFO] GTDB search result was written to GCF_008795985.1_ASM879598v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:54,733] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:54,737] [INFO] DFAST_QC result json was written to GCF_008795985.1_ASM879598v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:54,737] [INFO] DFAST_QC completed!
[2024-01-24 12:07:54,738] [INFO] Total running time: 0h1m21s