[2024-01-24 14:28:02,459] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:02,466] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:02,466] [INFO] DQC Reference Directory: /var/lib/cwl/stg93bc8ab6-28ae-4570-bcab-2fb88526aff5/dqc_reference
[2024-01-24 14:28:03,703] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:03,704] [INFO] Task started: Prodigal
[2024-01-24 14:28:03,704] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e854702-60d7-4eae-9cf7-61ece83cffaa/GCF_000381985.1_ASM38198v1_genomic.fna.gz | prodigal -d GCF_000381985.1_ASM38198v1_genomic.fna/cds.fna -a GCF_000381985.1_ASM38198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:15,883] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:15,883] [INFO] Task started: HMMsearch
[2024-01-24 14:28:15,883] [INFO] Running command: hmmsearch --tblout GCF_000381985.1_ASM38198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93bc8ab6-28ae-4570-bcab-2fb88526aff5/dqc_reference/reference_markers.hmm GCF_000381985.1_ASM38198v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:16,191] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:16,192] [INFO] Found 6/6 markers.
[2024-01-24 14:28:16,231] [INFO] Query marker FASTA was written to GCF_000381985.1_ASM38198v1_genomic.fna/markers.fasta
[2024-01-24 14:28:16,232] [INFO] Task started: Blastn
[2024-01-24 14:28:16,232] [INFO] Running command: blastn -query GCF_000381985.1_ASM38198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93bc8ab6-28ae-4570-bcab-2fb88526aff5/dqc_reference/reference_markers.fasta -out GCF_000381985.1_ASM38198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:17,325] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:17,329] [INFO] Selected 24 target genomes.
[2024-01-24 14:28:17,329] [INFO] Target genome list was writen to GCF_000381985.1_ASM38198v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:17,361] [INFO] Task started: fastANI
[2024-01-24 14:28:17,361] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e854702-60d7-4eae-9cf7-61ece83cffaa/GCF_000381985.1_ASM38198v1_genomic.fna.gz --refList GCF_000381985.1_ASM38198v1_genomic.fna/target_genomes.txt --output GCF_000381985.1_ASM38198v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:39,408] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:39,409] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93bc8ab6-28ae-4570-bcab-2fb88526aff5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:39,409] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93bc8ab6-28ae-4570-bcab-2fb88526aff5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:39,428] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:39,429] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:39,429] [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
Novispirillum itersonii subsp. itersonii	strain=ATCC 12639	GCA_000381985.1	180199	189	type	True	100.0	1408	1412	95	conclusive
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	77.1092	228	1412	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.945	209	1412	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.9141	174	1412	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	76.857	216	1412	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.7542	189	1412	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	76.5838	198	1412	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	76.5491	189	1412	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.4704	199	1412	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	76.4257	204	1412	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	76.3885	217	1412	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	76.3792	207	1412	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	76.3283	172	1412	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	76.3101	215	1412	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	76.2984	263	1412	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.2017	195	1412	95	below_threshold
Rhodospirillum rubrum	strain=ATCC 11170	GCA_000013085.1	1085	1085	type	True	76.1929	185	1412	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	76.1834	186	1412	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	76.1563	217	1412	95	below_threshold
Kordiimonas marina	strain=A6E486	GCA_023006325.1	2872312	2872312	type	True	76.1283	77	1412	95	below_threshold
Telmatospirillum siberiense	strain=26-4b1	GCA_002845745.1	382514	382514	type	True	75.9994	118	1412	95	below_threshold
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	75.8707	77	1412	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	75.6104	93	1412	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	75.1874	65	1412	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:39,431] [INFO] DFAST Taxonomy check result was written to GCF_000381985.1_ASM38198v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:39,432] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:39,432] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:39,433] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93bc8ab6-28ae-4570-bcab-2fb88526aff5/dqc_reference/checkm_data
[2024-01-24 14:28:39,434] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:39,480] [INFO] Task started: CheckM
[2024-01-24 14:28:39,480] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000381985.1_ASM38198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000381985.1_ASM38198v1_genomic.fna/checkm_input GCF_000381985.1_ASM38198v1_genomic.fna/checkm_result
[2024-01-24 14:29:20,570] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:20,572] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:20,593] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:20,594] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:20,594] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000381985.1_ASM38198v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:20,594] [INFO] Task started: Blastn
[2024-01-24 14:29:20,595] [INFO] Running command: blastn -query GCF_000381985.1_ASM38198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93bc8ab6-28ae-4570-bcab-2fb88526aff5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000381985.1_ASM38198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:22,342] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:22,346] [INFO] Selected 16 target genomes.
[2024-01-24 14:29:22,346] [INFO] Target genome list was writen to GCF_000381985.1_ASM38198v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:22,395] [INFO] Task started: fastANI
[2024-01-24 14:29:22,395] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e854702-60d7-4eae-9cf7-61ece83cffaa/GCF_000381985.1_ASM38198v1_genomic.fna.gz --refList GCF_000381985.1_ASM38198v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000381985.1_ASM38198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:34,819] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:34,834] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:34,834] [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_000381985.1	s__Novispirillum itersonii	100.0	1410	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Novispirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014205675.1	s__Novispirillum itersonii_A	86.3216	1157	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Novispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156605.1	s__Insolitispirillum peregrinum	78.196	397	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Insolitispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961745.1	s__BRH-c57 sp000961745	77.5198	214	1412	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_900230255.1	s__Caenispirillum bisanense	77.3714	279	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315795.1	s__Caenispirillum salinarum	77.1445	225	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012102745.1	s__Haematospirillum sp012102745	76.7816	97	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Haematospirillum	95.0	99.64	99.29	0.98	0.97	3	-
GCF_012102705.1	s__Haematospirillum sp012102705	76.7744	89	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Haematospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001603335.1	s__Alpha-05 sp001603335	76.5828	92	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Alpha-05	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100455.1	s__Roseospirillum parvum	76.4704	199	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Roseospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900079695.1	s__Alpha-05 sp900079695	76.4399	139	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Alpha-05	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232025.1	s__JADFZP01 sp015232025	76.4236	94	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013085.1	s__Rhodospirillum rubrum	76.1834	186	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospirillum	95.0	98.74	96.31	0.98	0.96	7	-
GCF_017876155.1	s__Azospirillum rugosum	76.1706	218	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003574685.1	s__SYSU-D60007 sp003574685	75.702	82	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002079305.1	s__Rhodovulum sp002079305	75.2979	87	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:34,836] [INFO] GTDB search result was written to GCF_000381985.1_ASM38198v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:34,837] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:34,841] [INFO] DFAST_QC result json was written to GCF_000381985.1_ASM38198v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:34,841] [INFO] DFAST_QC completed!
[2024-01-24 14:29:34,841] [INFO] Total running time: 0h1m32s