[2024-01-24 15:02:33,102] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:33,105] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:33,105] [INFO] DQC Reference Directory: /var/lib/cwl/stg364fc40e-a03a-4232-ac2f-31a2eb58bea1/dqc_reference
[2024-01-24 15:02:34,417] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:34,418] [INFO] Task started: Prodigal
[2024-01-24 15:02:34,418] [INFO] Running command: gunzip -c /var/lib/cwl/stg31167f26-e435-4062-a39b-b85e414808e5/GCF_014861485.1_ASM1486148v1_genomic.fna.gz | prodigal -d GCF_014861485.1_ASM1486148v1_genomic.fna/cds.fna -a GCF_014861485.1_ASM1486148v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:41,923] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:41,924] [INFO] Task started: HMMsearch
[2024-01-24 15:02:41,924] [INFO] Running command: hmmsearch --tblout GCF_014861485.1_ASM1486148v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg364fc40e-a03a-4232-ac2f-31a2eb58bea1/dqc_reference/reference_markers.hmm GCF_014861485.1_ASM1486148v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:42,175] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:42,176] [INFO] Found 6/6 markers.
[2024-01-24 15:02:42,209] [INFO] Query marker FASTA was written to GCF_014861485.1_ASM1486148v1_genomic.fna/markers.fasta
[2024-01-24 15:02:42,210] [INFO] Task started: Blastn
[2024-01-24 15:02:42,210] [INFO] Running command: blastn -query GCF_014861485.1_ASM1486148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg364fc40e-a03a-4232-ac2f-31a2eb58bea1/dqc_reference/reference_markers.fasta -out GCF_014861485.1_ASM1486148v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:43,073] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:43,078] [INFO] Selected 23 target genomes.
[2024-01-24 15:02:43,078] [INFO] Target genome list was writen to GCF_014861485.1_ASM1486148v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:43,087] [INFO] Task started: fastANI
[2024-01-24 15:02:43,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg31167f26-e435-4062-a39b-b85e414808e5/GCF_014861485.1_ASM1486148v1_genomic.fna.gz --refList GCF_014861485.1_ASM1486148v1_genomic.fna/target_genomes.txt --output GCF_014861485.1_ASM1486148v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:03,628] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:03,629] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg364fc40e-a03a-4232-ac2f-31a2eb58bea1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:03,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg364fc40e-a03a-4232-ac2f-31a2eb58bea1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:03,647] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:03,647] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:03,648] [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
Phaeovibrio sulfidiphilus	strain=DSM 23193	GCA_014861485.1	1220600	1220600	type	True	100.0	849	850	95	conclusive
Pararhodospirillum oryzae	strain=NBRC 107573	GCA_007992075.1	478448	478448	type	True	77.8809	193	850	95	below_threshold
Pararhodospirillum photometricum	strain=DSM 122	GCA_000284415.2	1084	1084	type	True	77.7491	171	850	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	77.5459	152	850	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	77.22	177	850	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	77.2116	161	850	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	77.1732	155	850	95	below_threshold
Rhodospirillum rubrum	strain=ATCC 11170	GCA_000013085.1	1085	1085	type	True	77.157	156	850	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	77.021	91	850	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014203135.1	140057	140057	type	True	76.9801	129	850	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.8468	161	850	95	below_threshold
Methylobacterium jeotgali	strain=LMG 23639	GCA_022179345.1	381630	381630	type	True	76.5103	83	850	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.3196	90	850	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.3161	89	850	95	below_threshold
Acuticoccus kandeliae	strain=J103	GCA_003073115.1	2073160	2073160	type	True	76.2993	64	850	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	76.2098	70	850	95	below_threshold
Methylobacterium aerolatum	strain=DSM 19013	GCA_022179085.1	418708	418708	type	True	76.1936	99	850	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	76.1593	71	850	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	76.0941	83	850	95	below_threshold
Jannaschia rubra	strain=CECT 5088	GCA_001403735.1	282197	282197	type	True	76.0054	54	850	95	below_threshold
Jannaschia rubra	strain=DSM 16279	GCA_900113265.1	282197	282197	type	True	75.9534	55	850	95	below_threshold
Phreatobacter stygius	strain=KCTC 52518	GCA_005144885.1	1940610	1940610	type	True	75.9042	73	850	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:03,661] [INFO] DFAST Taxonomy check result was written to GCF_014861485.1_ASM1486148v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:03,662] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:03,662] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:03,662] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg364fc40e-a03a-4232-ac2f-31a2eb58bea1/dqc_reference/checkm_data
[2024-01-24 15:03:03,665] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:03,699] [INFO] Task started: CheckM
[2024-01-24 15:03:03,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014861485.1_ASM1486148v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014861485.1_ASM1486148v1_genomic.fna/checkm_input GCF_014861485.1_ASM1486148v1_genomic.fna/checkm_result
[2024-01-24 15:03:33,913] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:33,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:33,935] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:33,936] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:33,936] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014861485.1_ASM1486148v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:33,936] [INFO] Task started: Blastn
[2024-01-24 15:03:33,937] [INFO] Running command: blastn -query GCF_014861485.1_ASM1486148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg364fc40e-a03a-4232-ac2f-31a2eb58bea1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014861485.1_ASM1486148v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:35,580] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:35,584] [INFO] Selected 19 target genomes.
[2024-01-24 15:03:35,584] [INFO] Target genome list was writen to GCF_014861485.1_ASM1486148v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:35,598] [INFO] Task started: fastANI
[2024-01-24 15:03:35,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg31167f26-e435-4062-a39b-b85e414808e5/GCF_014861485.1_ASM1486148v1_genomic.fna.gz --refList GCF_014861485.1_ASM1486148v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014861485.1_ASM1486148v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:51,119] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:51,139] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:51,140] [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_014861485.1	s__Phaeovibrio sulfidiphilus	100.0	849	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Phaeovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007992075.1	s__Pararhodospirillum oryzae	77.8809	193	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Pararhodospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284415.1	s__Pararhodospirillum photometricum	77.7681	170	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Pararhodospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961745.1	s__BRH-c57 sp000961745	77.2307	99	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__BRH-c57	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009601025.1	s__Rhodospira navarrensis	77.2045	177	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197795.1	s__Rhodospira goensis	77.1805	163	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013085.1	s__Rhodospirillum rubrum	77.1571	156	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospirillum	95.0	98.74	96.31	0.98	0.96	7	-
GCF_014197915.1	s__Rhodospira visakhapatnamensis	77.109	164	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729435.1	s__Magnetospirillum sp902729435	76.9716	144	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232485.1	s__JADFZP01 sp015232485	76.6817	97	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	96.70	95.97	0.70	0.69	3	-
GCF_014692675.1	s__Roseibium aggregatum_C	76.5703	57	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786295.1	s__Pseudooceanicola marinus	76.2168	70	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCA_001898425.1	s__69-11 sp001898425	76.0629	74	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__69-11	95.0	99.84	99.84	0.96	0.96	2	-
GCA_015232025.1	s__JADFZP01 sp015232025	76.0237	79	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403735.1	s__Jannaschia rubra	76.0054	54	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_005144885.1	s__Phreatobacter stygius	75.9042	73	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794005.1	s__Tagaea sp016794005	75.5935	61	850	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__Tagaea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:51,142] [INFO] GTDB search result was written to GCF_014861485.1_ASM1486148v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:51,142] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:51,147] [INFO] DFAST_QC result json was written to GCF_014861485.1_ASM1486148v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:51,147] [INFO] DFAST_QC completed!
[2024-01-24 15:03:51,147] [INFO] Total running time: 0h1m18s