[2023-06-30 19:32:18,118] [INFO] DFAST_QC pipeline started.
[2023-06-30 19:32:18,120] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 19:32:18,121] [INFO] DQC Reference Directory: /var/lib/cwl/stg1133d489-4fac-4978-a4d6-5023e603fa48/dqc_reference
[2023-06-30 19:32:19,758] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 19:32:19,759] [INFO] Task started: Prodigal
[2023-06-30 19:32:19,759] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb5b8e70-60d0-4ca5-b191-a35f318735cc/GCA_019100385.1_ASM1910038v1_genomic.fna.gz | prodigal -d GCA_019100385.1_ASM1910038v1_genomic.fna/cds.fna -a GCA_019100385.1_ASM1910038v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 19:32:32,987] [INFO] Task succeeded: Prodigal
[2023-06-30 19:32:32,988] [INFO] Task started: HMMsearch
[2023-06-30 19:32:32,988] [INFO] Running command: hmmsearch --tblout GCA_019100385.1_ASM1910038v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1133d489-4fac-4978-a4d6-5023e603fa48/dqc_reference/reference_markers.hmm GCA_019100385.1_ASM1910038v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 19:32:33,284] [INFO] Task succeeded: HMMsearch
[2023-06-30 19:32:33,285] [INFO] Found 6/6 markers.
[2023-06-30 19:32:33,377] [INFO] Query marker FASTA was written to GCA_019100385.1_ASM1910038v1_genomic.fna/markers.fasta
[2023-06-30 19:32:33,377] [INFO] Task started: Blastn
[2023-06-30 19:32:33,378] [INFO] Running command: blastn -query GCA_019100385.1_ASM1910038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1133d489-4fac-4978-a4d6-5023e603fa48/dqc_reference/reference_markers.fasta -out GCA_019100385.1_ASM1910038v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:32:34,197] [INFO] Task succeeded: Blastn
[2023-06-30 19:32:34,202] [INFO] Selected 34 target genomes.
[2023-06-30 19:32:34,202] [INFO] Target genome list was writen to GCA_019100385.1_ASM1910038v1_genomic.fna/target_genomes.txt
[2023-06-30 19:32:34,206] [INFO] Task started: fastANI
[2023-06-30 19:32:34,207] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb5b8e70-60d0-4ca5-b191-a35f318735cc/GCA_019100385.1_ASM1910038v1_genomic.fna.gz --refList GCA_019100385.1_ASM1910038v1_genomic.fna/target_genomes.txt --output GCA_019100385.1_ASM1910038v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 19:32:58,375] [INFO] Task succeeded: fastANI
[2023-06-30 19:32:58,376] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1133d489-4fac-4978-a4d6-5023e603fa48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 19:32:58,376] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1133d489-4fac-4978-a4d6-5023e603fa48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 19:32:58,398] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 19:32:58,398] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 19:32:58,398] [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
Sedimenticola selenatireducens	strain=DSM 17993	GCA_000428045.1	191960	191960	type	True	78.5483	140	1534	95	below_threshold
Thiolapillus brandeum	strain=Hiromi 1	GCA_000828615.1	1076588	1076588	type	True	77.7853	62	1534	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	77.3027	132	1534	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	77.2447	138	1534	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	77.2362	106	1534	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	77.0779	93	1534	95	below_threshold
Sedimenticola thiotaurini	strain=SIP-G1	GCA_001007875.1	1543721	1543721	type	True	77.0401	144	1534	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	76.9972	112	1534	95	below_threshold
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	76.9909	115	1534	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.9693	114	1534	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	76.9448	78	1534	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	76.9337	96	1534	95	below_threshold
Thiocystis violascens	strain=DSM 198	GCA_000227745.3	73141	73141	type	True	76.8223	100	1534	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.8111	97	1534	95	below_threshold
Aquisalimonas asiatica	strain=CGMCC 1.6291	GCA_900110585.1	406100	406100	type	True	76.7812	52	1534	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	76.5802	105	1534	95	below_threshold
Methyloterricola oryzae	strain=73a	GCA_000934725.1	1495050	1495050	type	True	76.5356	57	1534	95	below_threshold
Halochromatium roseum	strain=DSM 18859	GCA_016653315.1	391920	391920	type	True	76.4977	94	1534	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	76.4736	62	1534	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.3687	69	1534	95	below_threshold
Pseudomonas cavernicola	strain=K1S02-6	GCA_003596405.1	2320866	2320866	type	True	76.3229	51	1534	95	below_threshold
Pseudomonas maumuensis	strain=COW77	GCA_019139675.1	2842354	2842354	type	True	76.2059	55	1534	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	76.1218	61	1534	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	76.1015	71	1534	95	below_threshold
Natronocella acetinitrilica	strain=ANL 6-2	GCA_024170285.1	414046	414046	type	True	75.7809	54	1534	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	75.5327	63	1534	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	75.4795	56	1534	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	75.4201	54	1534	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 19:32:58,401] [INFO] DFAST Taxonomy check result was written to GCA_019100385.1_ASM1910038v1_genomic.fna/tc_result.tsv
[2023-06-30 19:32:58,401] [INFO] ===== Taxonomy check completed =====
[2023-06-30 19:32:58,402] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 19:32:58,402] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1133d489-4fac-4978-a4d6-5023e603fa48/dqc_reference/checkm_data
[2023-06-30 19:32:58,404] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 19:32:58,449] [INFO] Task started: CheckM
[2023-06-30 19:32:58,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019100385.1_ASM1910038v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019100385.1_ASM1910038v1_genomic.fna/checkm_input GCA_019100385.1_ASM1910038v1_genomic.fna/checkm_result
[2023-06-30 19:33:39,469] [INFO] Task succeeded: CheckM
[2023-06-30 19:33:39,470] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 19:33:39,491] [INFO] ===== Completeness check finished =====
[2023-06-30 19:33:39,491] [INFO] ===== Start GTDB Search =====
[2023-06-30 19:33:39,491] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019100385.1_ASM1910038v1_genomic.fna/markers.fasta)
[2023-06-30 19:33:39,492] [INFO] Task started: Blastn
[2023-06-30 19:33:39,492] [INFO] Running command: blastn -query GCA_019100385.1_ASM1910038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1133d489-4fac-4978-a4d6-5023e603fa48/dqc_reference/reference_markers_gtdb.fasta -out GCA_019100385.1_ASM1910038v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:33:40,901] [INFO] Task succeeded: Blastn
[2023-06-30 19:33:40,906] [INFO] Selected 9 target genomes.
[2023-06-30 19:33:40,906] [INFO] Target genome list was writen to GCA_019100385.1_ASM1910038v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 19:33:40,907] [INFO] Task started: fastANI
[2023-06-30 19:33:40,907] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb5b8e70-60d0-4ca5-b191-a35f318735cc/GCA_019100385.1_ASM1910038v1_genomic.fna.gz --refList GCA_019100385.1_ASM1910038v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019100385.1_ASM1910038v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 19:33:49,051] [INFO] Task succeeded: fastANI
[2023-06-30 19:33:49,064] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 19:33:49,064] [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_003094535.1	s__Thiodiazotropha sp003094535	99.628	1285	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.75	99.58	0.95	0.90	13	conclusive
GCA_003058495.1	s__Thiodiazotropha sp003058495	91.0222	1266	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.61	99.54	0.96	0.95	6	-
GCA_003094555.1	s__Thiodiazotropha sp003094555	81.075	808	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.74	99.69	0.92	0.89	3	-
GCA_003058525.1	s__Thiodiazotropha sp003058525	80.6187	840	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.55	99.55	0.93	0.93	2	-
GCF_001715975.1	s__Thiodiazotropha endolucinida_A	80.5599	840	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	98.81	98.44	0.92	0.86	30	-
GCA_019100305.1	s__Thiodiazotropha sp019100305	78.6246	304	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016842065.1	s__Thiodiazotropha sp016842065	78.0953	385	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001708965.1	s__Thiodiazotropha endoloripes	77.8609	374	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.62	99.43	0.97	0.94	9	-
GCA_016756855.1	s__QGON01 sp016756855	77.2318	178	1534	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__QGON01	95.0	99.16	98.34	0.94	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-30 19:33:49,066] [INFO] GTDB search result was written to GCA_019100385.1_ASM1910038v1_genomic.fna/result_gtdb.tsv
[2023-06-30 19:33:49,067] [INFO] ===== GTDB Search completed =====
[2023-06-30 19:33:49,071] [INFO] DFAST_QC result json was written to GCA_019100385.1_ASM1910038v1_genomic.fna/dqc_result.json
[2023-06-30 19:33:49,072] [INFO] DFAST_QC completed!
[2023-06-30 19:33:49,072] [INFO] Total running time: 0h1m31s