[2024-01-24 13:57:44,010] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:44,012] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:44,012] [INFO] DQC Reference Directory: /var/lib/cwl/stg050ad7ba-e03d-49d9-85b1-7198edcbfaac/dqc_reference
[2024-01-24 13:57:45,271] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:45,272] [INFO] Task started: Prodigal
[2024-01-24 13:57:45,272] [INFO] Running command: gunzip -c /var/lib/cwl/stg9eb13c9c-9550-46cc-a52e-7987099eb6cd/GCF_001007875.1_ASM100787v1_genomic.fna.gz | prodigal -d GCF_001007875.1_ASM100787v1_genomic.fna/cds.fna -a GCF_001007875.1_ASM100787v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:56,971] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:56,971] [INFO] Task started: HMMsearch
[2024-01-24 13:57:56,971] [INFO] Running command: hmmsearch --tblout GCF_001007875.1_ASM100787v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg050ad7ba-e03d-49d9-85b1-7198edcbfaac/dqc_reference/reference_markers.hmm GCF_001007875.1_ASM100787v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:57,261] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:57,263] [INFO] Found 6/6 markers.
[2024-01-24 13:57:57,300] [INFO] Query marker FASTA was written to GCF_001007875.1_ASM100787v1_genomic.fna/markers.fasta
[2024-01-24 13:57:57,301] [INFO] Task started: Blastn
[2024-01-24 13:57:57,301] [INFO] Running command: blastn -query GCF_001007875.1_ASM100787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg050ad7ba-e03d-49d9-85b1-7198edcbfaac/dqc_reference/reference_markers.fasta -out GCF_001007875.1_ASM100787v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:58,101] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:58,106] [INFO] Selected 25 target genomes.
[2024-01-24 13:57:58,106] [INFO] Target genome list was writen to GCF_001007875.1_ASM100787v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:58,152] [INFO] Task started: fastANI
[2024-01-24 13:57:58,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg9eb13c9c-9550-46cc-a52e-7987099eb6cd/GCF_001007875.1_ASM100787v1_genomic.fna.gz --refList GCF_001007875.1_ASM100787v1_genomic.fna/target_genomes.txt --output GCF_001007875.1_ASM100787v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:15,521] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:15,522] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg050ad7ba-e03d-49d9-85b1-7198edcbfaac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:15,522] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg050ad7ba-e03d-49d9-85b1-7198edcbfaac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:15,540] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:15,540] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:15,540] [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 thiotaurini	strain=SIP-G1	GCA_001007875.1	1543721	1543721	type	True	100.0	1319	1320	95	conclusive
Sedimenticola selenatireducens	strain=DSM 17993	GCA_000428045.1	191960	191960	type	True	81.2349	836	1320	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	77.0973	113	1320	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	77.0399	161	1320	95	below_threshold
Pseudomonas oryzicola	strain=RD9SR1	GCA_014269185.2	485876	485876	type	True	76.9745	51	1320	95	below_threshold
Sulfuriflexus mobilis	strain=aks1	GCA_003967195.1	1811807	1811807	type	True	76.632	70	1320	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.6194	116	1320	95	below_threshold
Aeromonas finlandensis	strain=4287D	GCA_000764645.1	1543375	1543375	type	True	76.5839	51	1320	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	76.5749	117	1320	95	below_threshold
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	76.567	110	1320	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	76.5417	125	1320	95	below_threshold
Ectothiorhodospira magna	strain=B7-7	GCA_900110965.1	867345	867345	type	True	76.5231	81	1320	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	76.5093	93	1320	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	76.4493	123	1320	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.3576	89	1320	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.3297	82	1320	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	76.2799	70	1320	95	below_threshold
Aeromonas sanarellii	strain=LMG 24682	GCA_000820085.1	633415	633415	type	True	76.1076	73	1320	95	below_threshold
Aeromonas australiensis	strain=CECT 8023	GCA_000819725.1	1114880	1114880	type	True	76.0329	55	1320	95	below_threshold
Ferrimonas futtsuensis	strain=DSM 18154	GCA_000422645.1	364764	364764	type	True	75.846	54	1320	95	below_threshold
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	75.6982	82	1320	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	75.5558	59	1320	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	75.3086	59	1320	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:15,542] [INFO] DFAST Taxonomy check result was written to GCF_001007875.1_ASM100787v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:15,543] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:15,543] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:15,543] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg050ad7ba-e03d-49d9-85b1-7198edcbfaac/dqc_reference/checkm_data
[2024-01-24 13:58:15,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:15,588] [INFO] Task started: CheckM
[2024-01-24 13:58:15,588] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001007875.1_ASM100787v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001007875.1_ASM100787v1_genomic.fna/checkm_input GCF_001007875.1_ASM100787v1_genomic.fna/checkm_result
[2024-01-24 13:58:54,307] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:54,308] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:54,326] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:54,326] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:54,327] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001007875.1_ASM100787v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:54,327] [INFO] Task started: Blastn
[2024-01-24 13:58:54,327] [INFO] Running command: blastn -query GCF_001007875.1_ASM100787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg050ad7ba-e03d-49d9-85b1-7198edcbfaac/dqc_reference/reference_markers_gtdb.fasta -out GCF_001007875.1_ASM100787v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:55,552] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:55,556] [INFO] Selected 12 target genomes.
[2024-01-24 13:58:55,556] [INFO] Target genome list was writen to GCF_001007875.1_ASM100787v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:55,744] [INFO] Task started: fastANI
[2024-01-24 13:58:55,744] [INFO] Running command: fastANI --query /var/lib/cwl/stg9eb13c9c-9550-46cc-a52e-7987099eb6cd/GCF_001007875.1_ASM100787v1_genomic.fna.gz --refList GCF_001007875.1_ASM100787v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001007875.1_ASM100787v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:05,208] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:05,218] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:05,219] [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_001007875.1	s__Sedimenticola thiotaurini	100.0	1319	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000428045.1	s__Sedimenticola selenatireducens	81.2479	836	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola	95.0	98.15	98.15	0.90	0.90	2	-
GCF_007625115.1	s__Sedimenticola selenatireducens_A	78.3865	281	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007713595.1	s__Sedimenticola thiotaurini_A	78.2139	345	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051715.1	s__HyVt-443 sp011051715	77.8053	283	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__HyVt-443	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002020805.1	s__GCF-002020805 sp002020805	77.5282	184	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__GCF-002020805	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869585.1	s__BM503 sp002869585	77.12	215	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__BM503	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001708965.1	s__Thiodiazotropha endoloripes	77.0869	121	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.62	99.43	0.97	0.94	9	-
GCA_001709035.1	s__Thiodiazotropha endoloripes_B	76.8202	134	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.26	97.31	0.93	0.86	11	-
GCA_016842065.1	s__Thiodiazotropha sp016842065	76.815	135	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390365.1	s__SLIM01 sp011390365	76.8148	188	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__SLIM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003676145.1	s__Thiodiazotropha endolucinida	76.6847	147	1320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	97.91	96.39	0.93	0.89	26	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:05,220] [INFO] GTDB search result was written to GCF_001007875.1_ASM100787v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:05,221] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:05,227] [INFO] DFAST_QC result json was written to GCF_001007875.1_ASM100787v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:05,227] [INFO] DFAST_QC completed!
[2024-01-24 13:59:05,227] [INFO] Total running time: 0h1m21s