[2023-06-29 15:10:00,443] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:10:00,445] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:10:00,445] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4ef253c-d54b-457d-9426-a2d3e8d77e65/dqc_reference
[2023-06-29 15:10:01,664] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:10:01,665] [INFO] Task started: Prodigal
[2023-06-29 15:10:01,665] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c735d13-85b8-4126-82a8-7d5348bb8aee/GCA_011375345.1_ASM1137534v1_genomic.fna.gz | prodigal -d GCA_011375345.1_ASM1137534v1_genomic.fna/cds.fna -a GCA_011375345.1_ASM1137534v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:10:09,951] [INFO] Task succeeded: Prodigal
[2023-06-29 15:10:09,952] [INFO] Task started: HMMsearch
[2023-06-29 15:10:09,952] [INFO] Running command: hmmsearch --tblout GCA_011375345.1_ASM1137534v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4ef253c-d54b-457d-9426-a2d3e8d77e65/dqc_reference/reference_markers.hmm GCA_011375345.1_ASM1137534v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:10:10,211] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:10:10,212] [INFO] Found 6/6 markers.
[2023-06-29 15:10:10,240] [INFO] Query marker FASTA was written to GCA_011375345.1_ASM1137534v1_genomic.fna/markers.fasta
[2023-06-29 15:10:10,240] [INFO] Task started: Blastn
[2023-06-29 15:10:10,240] [INFO] Running command: blastn -query GCA_011375345.1_ASM1137534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4ef253c-d54b-457d-9426-a2d3e8d77e65/dqc_reference/reference_markers.fasta -out GCA_011375345.1_ASM1137534v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:10:10,999] [INFO] Task succeeded: Blastn
[2023-06-29 15:10:11,008] [INFO] Selected 35 target genomes.
[2023-06-29 15:10:11,008] [INFO] Target genome list was writen to GCA_011375345.1_ASM1137534v1_genomic.fna/target_genomes.txt
[2023-06-29 15:10:11,011] [INFO] Task started: fastANI
[2023-06-29 15:10:11,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c735d13-85b8-4126-82a8-7d5348bb8aee/GCA_011375345.1_ASM1137534v1_genomic.fna.gz --refList GCA_011375345.1_ASM1137534v1_genomic.fna/target_genomes.txt --output GCA_011375345.1_ASM1137534v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:10:33,603] [INFO] Task succeeded: fastANI
[2023-06-29 15:10:33,604] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4ef253c-d54b-457d-9426-a2d3e8d77e65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:10:33,604] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4ef253c-d54b-457d-9426-a2d3e8d77e65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:10:33,623] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 15:10:33,623] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 15:10:33,624] [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
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	77.0457	137	812	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.7794	120	812	95	below_threshold
Methylogaea oryzae	strain=JCM 16910	GCA_001312345.1	1295382	1295382	type	True	76.6462	74	812	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.6199	120	812	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	76.5243	93	812	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	76.5078	95	812	95	below_threshold
Methylogaea oryzae	strain=E10	GCA_019669985.1	1295382	1295382	type	True	76.5061	102	812	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	76.2515	106	812	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	76.1348	54	812	95	below_threshold
Thiohalophilus thiocyanatoxydans	strain=DSM 16326	GCA_004366735.1	381308	381308	type	True	75.9785	75	812	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	75.8788	89	812	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.8111	66	812	95	below_threshold
Thiocystis violascens	strain=DSM 198	GCA_000227745.3	73141	73141	type	True	75.7387	60	812	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	75.6837	64	812	95	below_threshold
Arenimonas soli	strain=CGMCC 1.15905	GCA_014643775.1	2269504	2269504	type	True	75.6628	67	812	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	75.6418	113	812	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	75.6134	77	812	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	75.6108	116	812	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.4679	72	812	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	75.4472	115	812	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	75.4411	60	812	95	below_threshold
Pseudomonas citronellolis	strain=DSM 50332	GCA_004745455.1	53408	53408	type	True	75.4311	117	812	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	75.4226	118	812	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	75.4032	67	812	95	below_threshold
Solimonas fluminis	strain=HR-BB	GCA_002930645.1	2086571	2086571	type	True	75.2735	77	812	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 15:10:33,626] [INFO] DFAST Taxonomy check result was written to GCA_011375345.1_ASM1137534v1_genomic.fna/tc_result.tsv
[2023-06-29 15:10:33,627] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:10:33,627] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:10:33,627] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4ef253c-d54b-457d-9426-a2d3e8d77e65/dqc_reference/checkm_data
[2023-06-29 15:10:33,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:10:33,659] [INFO] Task started: CheckM
[2023-06-29 15:10:33,659] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011375345.1_ASM1137534v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011375345.1_ASM1137534v1_genomic.fna/checkm_input GCA_011375345.1_ASM1137534v1_genomic.fna/checkm_result
[2023-06-29 15:11:03,698] [INFO] Task succeeded: CheckM
[2023-06-29 15:11:03,703] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 15:11:03,750] [INFO] ===== Completeness check finished =====
[2023-06-29 15:11:03,750] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:11:03,751] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011375345.1_ASM1137534v1_genomic.fna/markers.fasta)
[2023-06-29 15:11:03,751] [INFO] Task started: Blastn
[2023-06-29 15:11:03,752] [INFO] Running command: blastn -query GCA_011375345.1_ASM1137534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4ef253c-d54b-457d-9426-a2d3e8d77e65/dqc_reference/reference_markers_gtdb.fasta -out GCA_011375345.1_ASM1137534v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:11:04,990] [INFO] Task succeeded: Blastn
[2023-06-29 15:11:05,014] [INFO] Selected 27 target genomes.
[2023-06-29 15:11:05,014] [INFO] Target genome list was writen to GCA_011375345.1_ASM1137534v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:11:05,029] [INFO] Task started: fastANI
[2023-06-29 15:11:05,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c735d13-85b8-4126-82a8-7d5348bb8aee/GCA_011375345.1_ASM1137534v1_genomic.fna.gz --refList GCA_011375345.1_ASM1137534v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011375345.1_ASM1137534v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:11:19,836] [INFO] Task succeeded: fastANI
[2023-06-29 15:11:19,866] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 15:11:19,866] [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_011375345.1	s__DRLM01 sp011375345	100.0	804	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DRLM01;f__DRLM01;g__DRLM01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015488555.1	s__S012-109 sp015488555	77.1137	135	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-140;f__SZUA-140;g__S012-109	95.0	99.64	99.60	0.87	0.87	3	-
GCA_015491615.1	s__S140-43 sp015491615	77.0887	106	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S140-43;f__S140-43;g__S140-43	95.0	99.42	99.32	0.88	0.87	3	-
GCA_011371455.1	s__DRQN01 sp011371455	77.0887	96	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__DRQN01	95.0	97.38	97.35	0.90	0.88	5	-
GCF_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	77.0634	136	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051655.1	s__DRKS01 sp011051655	77.062	118	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__DRKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377945.1	s__Thioalkalivibrio_A sulfidiphilus_A	77.0014	128	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001447805.1	s__Tenderia electrophaga	76.9452	138	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Tenderiales;f__Tenderiaceae;g__Tenderia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_015490395.1	s__S141-70 sp015490395	76.7682	108	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S141-70;f__S141-70;g__S141-70	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840095.1	s__Sulfurivermis sp002840095	76.7511	145	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001245.1	s__Sulfurivermis fontis	76.6562	118	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013348725.1	s__GCA-013348725 sp013348725	76.6401	83	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-013348725;f__GCA-013348725;g__GCA-013348725	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051685.1	s__SZUA-152 sp011051685	76.5321	115	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__SZUA-152	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000365.1	s__Thioalkalivibrio_A denitrificans	76.5243	93	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011046015.1	s__SpSt-1174 sp011046015	76.4018	77	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218375.1	s__JAHJQQ01 sp016218375	76.3859	65	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JAHJQQ01;f__JAHJQQ01;g__JAHJQQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389885.1	s__JABBTK01 sp011389885	76.3383	105	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__JABBTK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012939995.1	s__Competibacter phosphatis	76.1559	54	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Competibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002897735.1	s__BMS3Abin12 sp002897735	76.0444	59	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__21-64-14;f__21-64-14;g__BMS3Abin12	95.0	99.84	99.73	0.95	0.93	3	-
GCF_004341245.1	s__Plasticicumulans_A lactativorans	75.8111	66	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002448875.1	s__UBA6920 sp002448875	75.8035	59	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SG8-11;f__SG8-11;g__UBA6920	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380335.1	s__Azotobacter vinelandii	75.4196	80	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	99.84	99.43	0.98	0.95	5	-
GCF_002930645.1	s__Solimonas_A fluminis	75.2735	77	812	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 15:11:19,868] [INFO] GTDB search result was written to GCA_011375345.1_ASM1137534v1_genomic.fna/result_gtdb.tsv
[2023-06-29 15:11:19,868] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:11:19,873] [INFO] DFAST_QC result json was written to GCA_011375345.1_ASM1137534v1_genomic.fna/dqc_result.json
[2023-06-29 15:11:19,874] [INFO] DFAST_QC completed!
[2023-06-29 15:11:19,874] [INFO] Total running time: 0h1m19s