[2024-01-24 12:23:50,496] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:50,498] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:50,499] [INFO] DQC Reference Directory: /var/lib/cwl/stg3998fea6-9002-421f-98fb-8f2cd124710f/dqc_reference
[2024-01-24 12:23:51,879] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:51,880] [INFO] Task started: Prodigal
[2024-01-24 12:23:51,880] [INFO] Running command: gunzip -c /var/lib/cwl/stgc36bf183-1f0c-431b-880b-d5f4dddf173e/GCF_019903425.1_ASM1990342v1_genomic.fna.gz | prodigal -d GCF_019903425.1_ASM1990342v1_genomic.fna/cds.fna -a GCF_019903425.1_ASM1990342v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:24:02,693] [INFO] Task succeeded: Prodigal
[2024-01-24 12:24:02,694] [INFO] Task started: HMMsearch
[2024-01-24 12:24:02,694] [INFO] Running command: hmmsearch --tblout GCF_019903425.1_ASM1990342v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3998fea6-9002-421f-98fb-8f2cd124710f/dqc_reference/reference_markers.hmm GCF_019903425.1_ASM1990342v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:24:03,011] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:24:03,013] [INFO] Found 6/6 markers.
[2024-01-24 12:24:03,047] [INFO] Query marker FASTA was written to GCF_019903425.1_ASM1990342v1_genomic.fna/markers.fasta
[2024-01-24 12:24:03,047] [INFO] Task started: Blastn
[2024-01-24 12:24:03,047] [INFO] Running command: blastn -query GCF_019903425.1_ASM1990342v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3998fea6-9002-421f-98fb-8f2cd124710f/dqc_reference/reference_markers.fasta -out GCF_019903425.1_ASM1990342v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:03,863] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:03,867] [INFO] Selected 30 target genomes.
[2024-01-24 12:24:03,867] [INFO] Target genome list was writen to GCF_019903425.1_ASM1990342v1_genomic.fna/target_genomes.txt
[2024-01-24 12:24:03,877] [INFO] Task started: fastANI
[2024-01-24 12:24:03,877] [INFO] Running command: fastANI --query /var/lib/cwl/stgc36bf183-1f0c-431b-880b-d5f4dddf173e/GCF_019903425.1_ASM1990342v1_genomic.fna.gz --refList GCF_019903425.1_ASM1990342v1_genomic.fna/target_genomes.txt --output GCF_019903425.1_ASM1990342v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:22,519] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:22,520] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3998fea6-9002-421f-98fb-8f2cd124710f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:22,520] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3998fea6-9002-421f-98fb-8f2cd124710f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:22,546] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:24:22,546] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:24:22,546] [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
Tamilnaduibacter salinus	strain=DSM 28688	GCA_003096655.1	1484056	1484056	type	True	77.671	184	1168	95	below_threshold
Tamilnaduibacter salinus	strain=Mi-7	GCA_002287355.1	1484056	1484056	type	True	77.6184	180	1168	95	below_threshold
Marinobacter bohaiensis	strain=T17	GCA_003258515.1	2201898	2201898	type	True	77.5845	274	1168	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	77.4516	224	1168	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	77.3636	251	1168	95	below_threshold
Marinobacter lutaoensis	strain=T5054	GCA_001981305.1	135739	135739	type	True	77.2064	210	1168	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	77.1905	185	1168	95	below_threshold
Marinobacter persicus	strain=KCTC 23561	GCA_014652295.1	930118	930118	type	True	77.1674	171	1168	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	77.1464	213	1168	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	77.143	176	1168	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	77.065	135	1168	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	76.9842	147	1168	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	76.9694	194	1168	95	below_threshold
Marinobacter halophilus	strain=JCM 30472	GCA_003007685.1	1323740	1323740	type	True	76.9467	120	1168	95	below_threshold
Marinobacter adhaerens	strain=HP15	GCA_000166295.1	1033846	1033846	type	True	76.9329	145	1168	95	below_threshold
Marinobacter algicola	strain=DG893	GCA_000170835.1	236100	236100	type	True	76.9168	141	1168	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	76.8211	135	1168	95	below_threshold
Marinobacter halophilus	strain=CGMCC 1.12481	GCA_014637865.1	1323740	1323740	type	True	76.8018	119	1168	95	below_threshold
Marinobacter oulmenensis	strain=DSM 22359	GCA_014201735.1	643747	643747	type	True	76.7896	184	1168	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	76.7695	184	1168	95	below_threshold
Marinobacter nauticus	strain=DSM 50418	GCA_003634635.1	2743	2743	type	True	76.7444	152	1168	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	76.7381	112	1168	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.6526	111	1168	95	below_threshold
Microbulbifer taiwanensis	strain=LMG 26125	GCA_014904815.1	986746	986746	type	True	76.5228	97	1168	95	below_threshold
Pseudomonas triticicola	strain=SWRI88	GCA_019145375.1	2842345	2842345	type	True	76.3601	72	1168	95	below_threshold
Marinobacter piscensis	strain=Abdou3	GCA_007671655.1	1562308	1562308	type	True	76.1809	79	1168	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	76.0929	91	1168	95	below_threshold
[Pseudomonas] zhaodongensis	strain=DSM 27559T	GCA_024448735.1	1176257	1176257	suspected-type	True	76.0303	68	1168	95	below_threshold
[Pseudomonas] zhaodongensis	strain=NEAU-ST5-21	GCA_003696365.1	1176257	1176257	suspected-type	True	76.0061	69	1168	95	below_threshold
Aeromonas piscicola	strain=LMG 24783	GCA_000820005.1	600645	600645	type	True	75.9428	57	1168	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:22,549] [INFO] DFAST Taxonomy check result was written to GCF_019903425.1_ASM1990342v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:22,550] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:22,550] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:22,550] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3998fea6-9002-421f-98fb-8f2cd124710f/dqc_reference/checkm_data
[2024-01-24 12:24:22,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:22,586] [INFO] Task started: CheckM
[2024-01-24 12:24:22,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019903425.1_ASM1990342v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019903425.1_ASM1990342v1_genomic.fna/checkm_input GCF_019903425.1_ASM1990342v1_genomic.fna/checkm_result
[2024-01-24 12:24:57,360] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:57,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:57,386] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:57,387] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:57,387] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019903425.1_ASM1990342v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:57,387] [INFO] Task started: Blastn
[2024-01-24 12:24:57,388] [INFO] Running command: blastn -query GCF_019903425.1_ASM1990342v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3998fea6-9002-421f-98fb-8f2cd124710f/dqc_reference/reference_markers_gtdb.fasta -out GCF_019903425.1_ASM1990342v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:58,832] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:58,837] [INFO] Selected 11 target genomes.
[2024-01-24 12:24:58,837] [INFO] Target genome list was writen to GCF_019903425.1_ASM1990342v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:58,845] [INFO] Task started: fastANI
[2024-01-24 12:24:58,846] [INFO] Running command: fastANI --query /var/lib/cwl/stgc36bf183-1f0c-431b-880b-d5f4dddf173e/GCF_019903425.1_ASM1990342v1_genomic.fna.gz --refList GCF_019903425.1_ASM1990342v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019903425.1_ASM1990342v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:07,193] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:07,206] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:07,206] [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_900162675.1	s__Halospina utahensis_A	100.0	1168	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Halospina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009856365.1	s__Halospina utahensis_B	89.5471	919	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Halospina	95.0	99.12	98.25	0.93	0.87	3	-
GCF_002286965.1	s__Halospina salipaludis	89.1243	916	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Halospina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364635.1	s__Halospina denitrificans	80.4822	502	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Halospina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258515.1	s__Marinobacter_A bohaiensis	77.5897	275	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	98.52	98.52	0.96	0.96	2	-
GCA_007135745.1	s__Halospina sp007135745	77.4849	154	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Halospina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004327985.1	s__Marinobacter_A halodurans	77.331	254	1168	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_015645095.1	s__Halomonas_F sp015645095	76.7859	166	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692645.1	s__REBR01 sp007692645	76.7057	172	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__REBR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012044895.1	s__Aquisalimonas sp012044895	76.5632	115	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337735.1	s__Thioalbus denitrificans	76.4503	135	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:07,208] [INFO] GTDB search result was written to GCF_019903425.1_ASM1990342v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:07,208] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:07,213] [INFO] DFAST_QC result json was written to GCF_019903425.1_ASM1990342v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:07,213] [INFO] DFAST_QC completed!
[2024-01-24 12:25:07,213] [INFO] Total running time: 0h1m17s