[2023-06-05 00:14:25,890] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:14:25,892] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:14:25,892] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f030932-9acf-4200-86ae-0daf84370a37/dqc_reference
[2023-06-05 00:14:27,306] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:14:27,307] [INFO] Task started: Prodigal
[2023-06-05 00:14:27,307] [INFO] Running command: gunzip -c /var/lib/cwl/stg189f9c6a-0b55-4dac-a640-3788e2f4608b/GCA_001657385.1_ASM165738v1_genomic.fna.gz | prodigal -d GCA_001657385.1_ASM165738v1_genomic.fna/cds.fna -a GCA_001657385.1_ASM165738v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:14:38,399] [INFO] Task succeeded: Prodigal
[2023-06-05 00:14:38,399] [INFO] Task started: HMMsearch
[2023-06-05 00:14:38,400] [INFO] Running command: hmmsearch --tblout GCA_001657385.1_ASM165738v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f030932-9acf-4200-86ae-0daf84370a37/dqc_reference/reference_markers.hmm GCA_001657385.1_ASM165738v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:14:38,730] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:14:38,731] [INFO] Found 6/6 markers.
[2023-06-05 00:14:38,767] [INFO] Query marker FASTA was written to GCA_001657385.1_ASM165738v1_genomic.fna/markers.fasta
[2023-06-05 00:14:38,768] [INFO] Task started: Blastn
[2023-06-05 00:14:38,768] [INFO] Running command: blastn -query GCA_001657385.1_ASM165738v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f030932-9acf-4200-86ae-0daf84370a37/dqc_reference/reference_markers.fasta -out GCA_001657385.1_ASM165738v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:14:39,767] [INFO] Task succeeded: Blastn
[2023-06-05 00:14:39,771] [INFO] Selected 22 target genomes.
[2023-06-05 00:14:39,772] [INFO] Target genome list was writen to GCA_001657385.1_ASM165738v1_genomic.fna/target_genomes.txt
[2023-06-05 00:14:39,778] [INFO] Task started: fastANI
[2023-06-05 00:14:39,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg189f9c6a-0b55-4dac-a640-3788e2f4608b/GCA_001657385.1_ASM165738v1_genomic.fna.gz --refList GCA_001657385.1_ASM165738v1_genomic.fna/target_genomes.txt --output GCA_001657385.1_ASM165738v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:14:56,021] [INFO] Task succeeded: fastANI
[2023-06-05 00:14:56,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f030932-9acf-4200-86ae-0daf84370a37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:14:56,022] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f030932-9acf-4200-86ae-0daf84370a37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:14:56,039] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:14:56,039] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 00:14:56,039] [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
Marinicaulis flavus	strain=SY-3-19	GCA_002943565.1	2058213	2058213	type	True	78.3176	505	1395	95	below_threshold
Amphiplicatus metriothermophilus	strain=CGMCC 1.12710	GCA_900199215.1	1519374	1519374	type	True	77.5926	406	1395	95	below_threshold
Amphiplicatus metriothermophilus	strain=DSM 105738	GCA_014199495.1	1519374	1519374	type	True	77.5912	408	1395	95	below_threshold
Aquisalinus luteolus	strain=NH6-79	GCA_009712425.2	1566827	1566827	type	True	77.346	186	1395	95	below_threshold
Aquisalinus luteolus	strain=CGMCC 1.14984	GCA_014640455.1	1566827	1566827	type	True	77.329	186	1395	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	77.1937	195	1395	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_014534785.1	1526572	1526572	type	True	77.1606	205	1395	95	below_threshold
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	77.1246	207	1395	95	below_threshold
Parvularcula dongshanensis	strain=DSM 102850	GCA_014199615.1	1173995	1173995	type	True	76.7818	177	1395	95	below_threshold
Parvularcula marina	strain=SM1705	GCA_003399445.1	2292771	2292771	type	True	76.6315	100	1395	95	below_threshold
Methyloceanibacter marginalis	strain=R-67177	GCA_001723295.1	1774971	1774971	type	True	76.4959	77	1395	95	below_threshold
Kaustia mangrovi	strain=R1DC25	GCA_015482775.1	2593653	2593653	type	True	76.1925	166	1395	95	below_threshold
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	76.0519	131	1395	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	75.9777	143	1395	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	75.9315	132	1395	95	below_threshold
Mesorhizobium wenxiniae	strain=WYCCWR 10195	GCA_002284535.1	2014805	2014805	type	True	75.9227	120	1395	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	75.9218	207	1395	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	75.8703	177	1395	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	75.7376	107	1395	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.622	236	1395	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	75.6207	148	1395	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.2578	142	1395	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 00:14:56,041] [INFO] DFAST Taxonomy check result was written to GCA_001657385.1_ASM165738v1_genomic.fna/tc_result.tsv
[2023-06-05 00:14:56,042] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:14:56,042] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:14:56,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f030932-9acf-4200-86ae-0daf84370a37/dqc_reference/checkm_data
[2023-06-05 00:14:56,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:14:56,100] [INFO] Task started: CheckM
[2023-06-05 00:14:56,100] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001657385.1_ASM165738v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001657385.1_ASM165738v1_genomic.fna/checkm_input GCA_001657385.1_ASM165738v1_genomic.fna/checkm_result
[2023-06-05 00:15:31,189] [INFO] Task succeeded: CheckM
[2023-06-05 00:15:31,190] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:15:31,214] [INFO] ===== Completeness check finished =====
[2023-06-05 00:15:31,214] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:15:31,215] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001657385.1_ASM165738v1_genomic.fna/markers.fasta)
[2023-06-05 00:15:31,215] [INFO] Task started: Blastn
[2023-06-05 00:15:31,215] [INFO] Running command: blastn -query GCA_001657385.1_ASM165738v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f030932-9acf-4200-86ae-0daf84370a37/dqc_reference/reference_markers_gtdb.fasta -out GCA_001657385.1_ASM165738v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:15:32,945] [INFO] Task succeeded: Blastn
[2023-06-05 00:15:32,950] [INFO] Selected 15 target genomes.
[2023-06-05 00:15:32,951] [INFO] Target genome list was writen to GCA_001657385.1_ASM165738v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:15:33,002] [INFO] Task started: fastANI
[2023-06-05 00:15:33,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg189f9c6a-0b55-4dac-a640-3788e2f4608b/GCA_001657385.1_ASM165738v1_genomic.fna.gz --refList GCA_001657385.1_ASM165738v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001657385.1_ASM165738v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:15:42,668] [INFO] Task succeeded: fastANI
[2023-06-05 00:15:42,684] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 00:15:42,684] [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_001657385.1	s__Marinicaulis sp001657385	100.0	1391	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002943565.1	s__Marinicaulis flavus	78.3489	501	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704915.1	s__Marinicaulis sp002704915	77.6685	375	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199215.1	s__Amphiplicatus metriothermophilus	77.5617	411	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014640095.1	s__Aquisalinus flavus	77.1241	207	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013389105.1	s__JACADZ01 sp013389105	77.0498	243	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__JACADZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125425.1	s__Amphiplicatus sp016125425	76.9907	245	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767925.1	s__CV81 sp001767925	76.8126	255	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013389125.1	s__CV81 sp013389125	76.6664	179	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826095.1	s__CV81 sp902826095	76.6226	280	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002535.1	s__Marinicaulis sp013002535	76.4608	125	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	99.52	99.49	0.97	0.96	3	-
GCA_013003675.1	s__JABDIP01 sp013003675	75.993	113	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__JABDIP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577315.1	s__Aquamicrobium_A sp003577315	75.9423	190	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002937075.1	s__Rhodoblastus sphagnicola	75.9106	150	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhodoblastus	95.0	99.97	99.97	0.98	0.98	2	-
GCF_014197695.1	s__Rhodoblastus acidophilus_B	75.7129	157	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhodoblastus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 00:15:42,686] [INFO] GTDB search result was written to GCA_001657385.1_ASM165738v1_genomic.fna/result_gtdb.tsv
[2023-06-05 00:15:42,687] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:15:42,691] [INFO] DFAST_QC result json was written to GCA_001657385.1_ASM165738v1_genomic.fna/dqc_result.json
[2023-06-05 00:15:42,692] [INFO] DFAST_QC completed!
[2023-06-05 00:15:42,692] [INFO] Total running time: 0h1m17s