[2024-01-24 15:06:36,768] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:06:36,776] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:06:36,776] [INFO] DQC Reference Directory: /var/lib/cwl/stgca650508-4832-4676-a606-b7ed1b9aa479/dqc_reference
[2024-01-24 15:06:38,222] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:06:38,224] [INFO] Task started: Prodigal
[2024-01-24 15:06:38,225] [INFO] Running command: gunzip -c /var/lib/cwl/stgc05008e8-96d0-4e36-b4ee-9c4b9d969f59/GCF_016522065.1_ASM1652206v1_genomic.fna.gz | prodigal -d GCF_016522065.1_ASM1652206v1_genomic.fna/cds.fna -a GCF_016522065.1_ASM1652206v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:06:53,862] [INFO] Task succeeded: Prodigal
[2024-01-24 15:06:53,862] [INFO] Task started: HMMsearch
[2024-01-24 15:06:53,863] [INFO] Running command: hmmsearch --tblout GCF_016522065.1_ASM1652206v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca650508-4832-4676-a606-b7ed1b9aa479/dqc_reference/reference_markers.hmm GCF_016522065.1_ASM1652206v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:06:54,158] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:06:54,159] [INFO] Found 6/6 markers.
[2024-01-24 15:06:54,191] [INFO] Query marker FASTA was written to GCF_016522065.1_ASM1652206v1_genomic.fna/markers.fasta
[2024-01-24 15:06:54,192] [INFO] Task started: Blastn
[2024-01-24 15:06:54,192] [INFO] Running command: blastn -query GCF_016522065.1_ASM1652206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca650508-4832-4676-a606-b7ed1b9aa479/dqc_reference/reference_markers.fasta -out GCF_016522065.1_ASM1652206v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:06:54,902] [INFO] Task succeeded: Blastn
[2024-01-24 15:06:54,906] [INFO] Selected 24 target genomes.
[2024-01-24 15:06:54,907] [INFO] Target genome list was writen to GCF_016522065.1_ASM1652206v1_genomic.fna/target_genomes.txt
[2024-01-24 15:06:54,917] [INFO] Task started: fastANI
[2024-01-24 15:06:54,917] [INFO] Running command: fastANI --query /var/lib/cwl/stgc05008e8-96d0-4e36-b4ee-9c4b9d969f59/GCF_016522065.1_ASM1652206v1_genomic.fna.gz --refList GCF_016522065.1_ASM1652206v1_genomic.fna/target_genomes.txt --output GCF_016522065.1_ASM1652206v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:07:18,521] [INFO] Task succeeded: fastANI
[2024-01-24 15:07:18,522] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca650508-4832-4676-a606-b7ed1b9aa479/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:07:18,522] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca650508-4832-4676-a606-b7ed1b9aa479/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:07:18,541] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:07:18,542] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:07:18,542] [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
Flavobacterium agrisoli	strain=SE-1-e	GCA_016522065.1	2793066	2793066	type	True	100.0	1227	1229	95	conclusive
Flavobacterium johnsoniae	strain=ATCC 17061	GCA_002221975.1	986	986	type	True	78.9553	465	1229	95	below_threshold
Flavobacterium seoulense	strain=EM1321	GCA_000695795.1	1492738	1492738	type	True	78.7783	388	1229	95	below_threshold
Flavobacterium nitrogenifigens	strain=DSM 29982	GCA_900182675.1	1617283	1617283	type	True	78.7301	439	1229	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.7248	454	1229	95	below_threshold
Flavobacterium glycines	strain=NBRC 105008	GCA_007989005.1	551990	551990	type	True	78.7223	356	1229	95	below_threshold
Flavobacterium hibernum	strain=ATCC 51468	GCA_002217315.1	37752	37752	type	True	78.7212	501	1229	95	below_threshold
Flavobacterium nitrogenifigens	strain=NXU-44	GCA_003254565.1	1617283	1617283	type	True	78.7109	439	1229	95	below_threshold
Flavobacterium chungbukense	strain=CS100	GCA_020805785.1	877464	877464	type	True	78.6858	473	1229	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.67	464	1229	95	below_threshold
Flavobacterium hibernum	strain=NCTC13514	GCA_900450525.1	37752	37752	type	True	78.6676	506	1229	95	below_threshold
Flavobacterium denitrificans	strain=DSM 15936	GCA_000425445.1	281361	281361	type	True	78.6483	436	1229	95	below_threshold
Flavobacterium zhairuonense	strain=A5.7	GCA_004352915.1	2493631	2493631	type	True	78.6343	458	1229	95	below_threshold
Flavobacterium hibernum	strain=DSM 12611	GCA_000832125.1	37752	37752	type	True	78.634	499	1229	95	below_threshold
Flavobacterium sufflavum	strain=BBQ-12	GCA_004016525.1	1921138	1921138	type	True	78.609	392	1229	95	below_threshold
Flavobacterium sharifuzzamanii	strain=A7.6	GCA_003254585.1	2211133	2211133	type	True	78.5667	443	1229	95	below_threshold
Flavobacterium glycines	strain=Gm-149	GCA_900100165.1	551990	551990	type	True	78.5599	355	1229	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.4948	484	1229	95	below_threshold
Flavobacterium circumlabens	strain=P5626	GCA_004345565.1	2133765	2133765	type	True	78.2635	391	1229	95	below_threshold
Flavobacterium flabelliforme	strain=P4023	GCA_017948675.1	2816119	2816119	type	True	78.1908	309	1229	95	below_threshold
Flavobacterium alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	78.1769	353	1229	95	below_threshold
Flavobacterium laiguense	strain=LB2P30	GCA_003097655.1	2169409	2169409	type	True	78.1499	308	1229	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	77.1138	138	1229	95	below_threshold
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	76.9494	146	1229	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:07:18,544] [INFO] DFAST Taxonomy check result was written to GCF_016522065.1_ASM1652206v1_genomic.fna/tc_result.tsv
[2024-01-24 15:07:18,544] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:07:18,544] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:07:18,544] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca650508-4832-4676-a606-b7ed1b9aa479/dqc_reference/checkm_data
[2024-01-24 15:07:18,545] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:07:18,583] [INFO] Task started: CheckM
[2024-01-24 15:07:18,583] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016522065.1_ASM1652206v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016522065.1_ASM1652206v1_genomic.fna/checkm_input GCF_016522065.1_ASM1652206v1_genomic.fna/checkm_result
[2024-01-24 15:08:02,464] [INFO] Task succeeded: CheckM
[2024-01-24 15:08:02,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:08:02,488] [INFO] ===== Completeness check finished =====
[2024-01-24 15:08:02,488] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:08:02,489] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016522065.1_ASM1652206v1_genomic.fna/markers.fasta)
[2024-01-24 15:08:02,489] [INFO] Task started: Blastn
[2024-01-24 15:08:02,489] [INFO] Running command: blastn -query GCF_016522065.1_ASM1652206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca650508-4832-4676-a606-b7ed1b9aa479/dqc_reference/reference_markers_gtdb.fasta -out GCF_016522065.1_ASM1652206v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:08:03,465] [INFO] Task succeeded: Blastn
[2024-01-24 15:08:03,470] [INFO] Selected 25 target genomes.
[2024-01-24 15:08:03,470] [INFO] Target genome list was writen to GCF_016522065.1_ASM1652206v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:08:03,526] [INFO] Task started: fastANI
[2024-01-24 15:08:03,527] [INFO] Running command: fastANI --query /var/lib/cwl/stgc05008e8-96d0-4e36-b4ee-9c4b9d969f59/GCF_016522065.1_ASM1652206v1_genomic.fna.gz --refList GCF_016522065.1_ASM1652206v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016522065.1_ASM1652206v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:08:24,241] [INFO] Task succeeded: fastANI
[2024-01-24 15:08:24,261] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:08:24,262] [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_016522065.1	s__Flavobacterium sp016522065	100.0	1227	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001529295.1	s__Flavobacterium sp001529295	79.1682	462	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711135.1	s__Flavobacterium sp009711135	79.04	456	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902167265.1	s__Flavobacterium anhuiense_B	78.9702	494	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	4	-
GCF_000426145.1	s__Flavobacterium sp000426145	78.945	487	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909155.2	s__Flavobacterium undicola	78.9135	380	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708595.2	s__Flavobacterium sp000708595	78.908	447	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	98.27	0.95	0.93	3	-
GCF_002304005.1	s__Flavobacterium sp002304005	78.7822	452	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000695795.1	s__Flavobacterium seoulense	78.7783	388	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254565.1	s__Flavobacterium nitrogenifigens	78.7243	437	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000425445.1	s__Flavobacterium denitrificans	78.6581	435	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000832125.1	s__Flavobacterium hibernum	78.634	499	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.99	0.99	3	-
GCA_017744675.1	s__Flavobacterium sp017744675	78.6126	473	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004016525.1	s__Flavobacterium sufflavum	78.6094	392	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015182285.1	s__Flavobacterium sp015182285	78.5592	476	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254585.1	s__Flavobacterium sharifuzzamanii	78.5522	444	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946915.1	s__Flavobacterium sp003946915	78.5437	463	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006438875.1	s__Flavobacterium pectinovorum_A	78.4867	481	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813295.1	s__Flavobacterium sp002813295	78.4234	353	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345565.1	s__Flavobacterium circumlabens	78.2775	389	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.60	96.60	0.85	0.85	2	-
GCF_000425425.1	s__Flavobacterium daejeonense	78.1996	389	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920895.1	s__Flavobacterium alvei	78.1567	355	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674775.1	s__Flavobacterium sp009674775	78.1432	384	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014281985.1	s__Flavobacterium sp014281985	78.0616	311	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.07	98.07	0.91	0.91	2	-
GCA_903839195.1	s__Flavobacterium sp903839195	77.3497	211	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.63	96.46	0.85	0.82	4	-
--------------------------------------------------------------------------------
[2024-01-24 15:08:24,263] [INFO] GTDB search result was written to GCF_016522065.1_ASM1652206v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:08:24,264] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:08:24,268] [INFO] DFAST_QC result json was written to GCF_016522065.1_ASM1652206v1_genomic.fna/dqc_result.json
[2024-01-24 15:08:24,268] [INFO] DFAST_QC completed!
[2024-01-24 15:08:24,268] [INFO] Total running time: 0h1m47s