[2024-01-25 17:42:35,744] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:42:35,745] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:42:35,745] [INFO] DQC Reference Directory: /var/lib/cwl/stge3c28d13-9f44-4689-b6db-e067c94618f8/dqc_reference
[2024-01-25 17:42:36,856] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:42:36,857] [INFO] Task started: Prodigal
[2024-01-25 17:42:36,857] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c80d0e1-82cd-4229-8784-ac4ad6068aac/GCF_000397065.2_MarLipol1.0_genomic.fna.gz | prodigal -d GCF_000397065.2_MarLipol1.0_genomic.fna/cds.fna -a GCF_000397065.2_MarLipol1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:42:47,596] [INFO] Task succeeded: Prodigal
[2024-01-25 17:42:47,597] [INFO] Task started: HMMsearch
[2024-01-25 17:42:47,597] [INFO] Running command: hmmsearch --tblout GCF_000397065.2_MarLipol1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3c28d13-9f44-4689-b6db-e067c94618f8/dqc_reference/reference_markers.hmm GCF_000397065.2_MarLipol1.0_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:42:47,828] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:42:47,829] [INFO] Found 6/6 markers.
[2024-01-25 17:42:47,861] [INFO] Query marker FASTA was written to GCF_000397065.2_MarLipol1.0_genomic.fna/markers.fasta
[2024-01-25 17:42:47,861] [INFO] Task started: Blastn
[2024-01-25 17:42:47,861] [INFO] Running command: blastn -query GCF_000397065.2_MarLipol1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stge3c28d13-9f44-4689-b6db-e067c94618f8/dqc_reference/reference_markers.fasta -out GCF_000397065.2_MarLipol1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:48,639] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:48,642] [INFO] Selected 20 target genomes.
[2024-01-25 17:42:48,642] [INFO] Target genome list was writen to GCF_000397065.2_MarLipol1.0_genomic.fna/target_genomes.txt
[2024-01-25 17:42:48,659] [INFO] Task started: fastANI
[2024-01-25 17:42:48,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c80d0e1-82cd-4229-8784-ac4ad6068aac/GCF_000397065.2_MarLipol1.0_genomic.fna.gz --refList GCF_000397065.2_MarLipol1.0_genomic.fna/target_genomes.txt --output GCF_000397065.2_MarLipol1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:43:05,300] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:05,301] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3c28d13-9f44-4689-b6db-e067c94618f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:43:05,301] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3c28d13-9f44-4689-b6db-e067c94618f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:43:05,313] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:43:05,313] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:43:05,313] [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 lipolyticus	strain=SM19	GCA_000397065.2	209639	209639	type	True	100.0	1330	1330	95	conclusive
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	80.9441	712	1330	95	below_threshold
Marinobacter maroccanus	strain=N4	GCA_002933275.1	2055143	2055143	type	True	80.3571	596	1330	95	below_threshold
Marinobacter flavimaris	strain=KCTC 12185	GCA_003363485.1	262076	262076	type	True	80.3074	558	1330	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	80.282	557	1330	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	80.2507	560	1330	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	80.1694	603	1330	95	below_threshold
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	80.1125	611	1330	95	below_threshold
Marinobacter adhaerens	strain=HP15	GCA_000166295.1	1033846	1033846	type	True	80.1041	555	1330	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	79.8893	579	1330	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	79.8731	626	1330	95	below_threshold
Marinobacter alexandrii	strain=LZ-8	GCA_005871205.1	2570351	2570351	type	True	79.7851	540	1330	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	79.7332	540	1330	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	79.6768	517	1330	95	below_threshold
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	79.652	538	1330	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	79.5627	511	1330	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	79.5105	528	1330	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.9158	423	1330	95	below_threshold
Marinobacter zhejiangensis	strain=CGMCC 1.7061	GCA_900114775.1	488535	488535	type	True	78.667	383	1330	95	below_threshold
Marinobacter maritimus	strain=CK47	GCA_007671675.1	277961	277961	type	True	78.5448	394	1330	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:43:05,315] [INFO] DFAST Taxonomy check result was written to GCF_000397065.2_MarLipol1.0_genomic.fna/tc_result.tsv
[2024-01-25 17:43:05,315] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:43:05,315] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:43:05,315] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3c28d13-9f44-4689-b6db-e067c94618f8/dqc_reference/checkm_data
[2024-01-25 17:43:05,316] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:43:05,359] [INFO] Task started: CheckM
[2024-01-25 17:43:05,359] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000397065.2_MarLipol1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000397065.2_MarLipol1.0_genomic.fna/checkm_input GCF_000397065.2_MarLipol1.0_genomic.fna/checkm_result
[2024-01-25 17:43:39,180] [INFO] Task succeeded: CheckM
[2024-01-25 17:43:39,181] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:43:39,198] [INFO] ===== Completeness check finished =====
[2024-01-25 17:43:39,198] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:43:39,199] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000397065.2_MarLipol1.0_genomic.fna/markers.fasta)
[2024-01-25 17:43:39,199] [INFO] Task started: Blastn
[2024-01-25 17:43:39,199] [INFO] Running command: blastn -query GCF_000397065.2_MarLipol1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stge3c28d13-9f44-4689-b6db-e067c94618f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000397065.2_MarLipol1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:40,584] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:40,586] [INFO] Selected 17 target genomes.
[2024-01-25 17:43:40,586] [INFO] Target genome list was writen to GCF_000397065.2_MarLipol1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:43:40,601] [INFO] Task started: fastANI
[2024-01-25 17:43:40,601] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c80d0e1-82cd-4229-8784-ac4ad6068aac/GCF_000397065.2_MarLipol1.0_genomic.fna.gz --refList GCF_000397065.2_MarLipol1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000397065.2_MarLipol1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:54,876] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:54,886] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:43:54,887] [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_000397065.2	s__Marinobacter lipolyticus	100.0	1330	1330	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_003994855.1	s__Marinobacter sp003994855	87.708	1128	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018424605.1	s__Marinobacter lipolyticus_B	81.5294	740	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643965.1	s__Marinobacter sp017643965	81.3787	548	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114925.1	s__Marinobacter pelagius	80.282	557	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933295.1	s__Marinobacter flavimaris	80.2407	561	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	97.80	96.90	0.89	0.83	14	-
GCF_003441595.1	s__Marinobacter sp003441595	80.2224	612	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002744735.1	s__Marinobacter guineae	80.1169	611	1330	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	80.0884	557	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	98.39	97.71	0.91	0.87	5	-
GCF_003315345.1	s__Marinobacter pelagius_A	80.0767	566	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005298175.1	s__Marinobacter sp005298175	80.0727	630	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115175.1	s__Marinobacter gudaonensis	80.0533	587	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188435.1	s__Marinobacter sp900188435	79.933	561	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003030785.1	s__Marinobacter sp003030785	79.9293	361	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623515.1	s__Marinobacter sp018623515	79.8826	466	1330	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	78.667	383	1330	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	78.5305	395	1330	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.91	98.91	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:43:54,888] [INFO] GTDB search result was written to GCF_000397065.2_MarLipol1.0_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:54,890] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:54,893] [INFO] DFAST_QC result json was written to GCF_000397065.2_MarLipol1.0_genomic.fna/dqc_result.json
[2024-01-25 17:43:54,893] [INFO] DFAST_QC completed!
[2024-01-25 17:43:54,893] [INFO] Total running time: 0h1m19s