[2024-01-24 14:22:14,699] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:14,701] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:14,702] [INFO] DQC Reference Directory: /var/lib/cwl/stg111d09bb-fba0-423c-9eb1-09219f8de2bf/dqc_reference
[2024-01-24 14:22:16,104] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:16,104] [INFO] Task started: Prodigal
[2024-01-24 14:22:16,105] [INFO] Running command: gunzip -c /var/lib/cwl/stg25377244-0473-441d-a4a7-72b72dc11449/GCF_004216895.1_ASM421689v1_genomic.fna.gz | prodigal -d GCF_004216895.1_ASM421689v1_genomic.fna/cds.fna -a GCF_004216895.1_ASM421689v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:30,014] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:30,014] [INFO] Task started: HMMsearch
[2024-01-24 14:22:30,014] [INFO] Running command: hmmsearch --tblout GCF_004216895.1_ASM421689v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg111d09bb-fba0-423c-9eb1-09219f8de2bf/dqc_reference/reference_markers.hmm GCF_004216895.1_ASM421689v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:30,285] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:30,287] [INFO] Found 6/6 markers.
[2024-01-24 14:22:30,325] [INFO] Query marker FASTA was written to GCF_004216895.1_ASM421689v1_genomic.fna/markers.fasta
[2024-01-24 14:22:30,326] [INFO] Task started: Blastn
[2024-01-24 14:22:30,326] [INFO] Running command: blastn -query GCF_004216895.1_ASM421689v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg111d09bb-fba0-423c-9eb1-09219f8de2bf/dqc_reference/reference_markers.fasta -out GCF_004216895.1_ASM421689v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:31,073] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:31,077] [INFO] Selected 21 target genomes.
[2024-01-24 14:22:31,077] [INFO] Target genome list was writen to GCF_004216895.1_ASM421689v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:31,086] [INFO] Task started: fastANI
[2024-01-24 14:22:31,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg25377244-0473-441d-a4a7-72b72dc11449/GCF_004216895.1_ASM421689v1_genomic.fna.gz --refList GCF_004216895.1_ASM421689v1_genomic.fna/target_genomes.txt --output GCF_004216895.1_ASM421689v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:46,901] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:46,901] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg111d09bb-fba0-423c-9eb1-09219f8de2bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:46,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg111d09bb-fba0-423c-9eb1-09219f8de2bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:46,919] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:46,919] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:46,920] [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
Aquimarina brevivitae	strain=DSM 17196	GCA_004216895.1	323412	323412	type	True	100.0	1286	1288	95	conclusive
Aquimarina megaterium	strain=XH134	GCA_000520975.1	1443666	1443666	type	True	77.7068	220	1288	95	below_threshold
Aquimarina latercula	strain=DSM 2041	GCA_000430645.1	987	987	type	True	77.6186	248	1288	95	below_threshold
Aquimarina muelleri	strain=DSM 19832	GCA_000430665.1	279356	279356	type	True	77.3406	208	1288	95	below_threshold
Aquimarina mytili	strain=KCTC 23302	GCA_016735115.1	874423	874423	type	True	77.34	246	1288	95	below_threshold
Aquimarina muelleri	strain=KCTC 12285	GCA_014651355.1	279356	279356	type	True	77.3178	209	1288	95	below_threshold
Aquimarina atlantica	strain=22II-S11-z7	GCA_000626715.1	1317122	1317122	type	True	77.2698	245	1288	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	77.1459	257	1288	95	below_threshold
Aquimarina pacifica	strain=SW150	GCA_000520955.1	1296415	1296415	type	True	77.0954	188	1288	95	below_threshold
Aquimarina algicola	strain=M625	GCA_006443095.1	2589995	2589995	type	True	77.0512	217	1288	95	below_threshold
Aquimarina amphilecti	strain=DSM 25232	GCA_900109375.1	1038014	1038014	type	True	77.0011	270	1288	95	below_threshold
Aquimarina sediminis	strain=w01	GCA_002895435.1	2070536	2070536	type	True	76.9937	245	1288	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.6633	68	1288	95	below_threshold
Mesonia mobilis	strain=KCTC 12708	GCA_014651475.1	369791	369791	type	True	76.6587	76	1288	95	below_threshold
Mesonia mobilis	strain=DSM 19841	GCA_000423405.1	369791	369791	type	True	76.6501	73	1288	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.4926	51	1288	95	below_threshold
Aquimarina agarilytica	strain=ZC1	GCA_000255455.1	1087449	1087449	type	True	76.4616	80	1288	95	below_threshold
Aestuariivivens sediminicola	strain=MTV5-3	GCA_022662015.1	2913560	2913560	type	True	76.3989	54	1288	95	below_threshold
Cellulophaga fucicola	strain=DSM 24786	GCA_900119145.1	76595	76595	type	True	76.2202	86	1288	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:46,926] [INFO] DFAST Taxonomy check result was written to GCF_004216895.1_ASM421689v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:46,926] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:46,926] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:46,927] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg111d09bb-fba0-423c-9eb1-09219f8de2bf/dqc_reference/checkm_data
[2024-01-24 14:22:46,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:46,966] [INFO] Task started: CheckM
[2024-01-24 14:22:46,966] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004216895.1_ASM421689v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004216895.1_ASM421689v1_genomic.fna/checkm_input GCF_004216895.1_ASM421689v1_genomic.fna/checkm_result
[2024-01-24 14:23:26,095] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:26,096] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:26,116] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:26,117] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:26,117] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004216895.1_ASM421689v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:26,117] [INFO] Task started: Blastn
[2024-01-24 14:23:26,117] [INFO] Running command: blastn -query GCF_004216895.1_ASM421689v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg111d09bb-fba0-423c-9eb1-09219f8de2bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_004216895.1_ASM421689v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:27,043] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:27,047] [INFO] Selected 20 target genomes.
[2024-01-24 14:23:27,047] [INFO] Target genome list was writen to GCF_004216895.1_ASM421689v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:27,063] [INFO] Task started: fastANI
[2024-01-24 14:23:27,063] [INFO] Running command: fastANI --query /var/lib/cwl/stg25377244-0473-441d-a4a7-72b72dc11449/GCF_004216895.1_ASM421689v1_genomic.fna.gz --refList GCF_004216895.1_ASM421689v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004216895.1_ASM421689v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:42,314] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:42,330] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:42,330] [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_004216895.1	s__Aquimarina brevivitae	100.0	1286	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002697475.1	s__Aquimarina sp002697475	78.7526	247	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000520975.1	s__Aquimarina megaterium	77.7068	220	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.79	98.77	0.92	0.92	4	-
GCF_000430645.1	s__Aquimarina latercula	77.6186	248	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.44	98.41	0.94	0.92	4	-
GCF_900312815.1	s__Aquimarina sp900312815	77.4882	223	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018100805.1	s__Aquimarina sp018100805	77.4642	265	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900299535.1	s__Aquimarina sp900299535	77.3611	211	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.11	95.11	0.81	0.81	2	-
GCF_000430665.1	s__Aquimarina muelleri	77.3545	207	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	99.98	99.98	0.99	0.99	2	-
GCF_016735115.1	s__Aquimarina mytili	77.328	247	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900299505.1	s__Aquimarina sp900299505	77.2961	234	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000626715.1	s__Aquimarina atlantica	77.2805	244	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900312745.1	s__Aquimarina sp900312745	77.2364	243	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.61	95.54	0.91	0.91	4	-
GCA_006443095.1	s__Aquimarina sp006443095	77.0512	217	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007489275.1	s__Aquimarina algiphila	77.0444	259	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.78	98.78	0.88	0.88	2	-
GCF_003443675.1	s__Aquimarina sp003443675	77.0175	259	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900109375.1	s__Aquimarina amphilecti	77.011	269	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000255455.1	s__Aquimarina agarilytica	76.4616	80	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744625.1	s__Winogradskyella sp016744625	76.3615	85	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119145.1	s__Cellulophaga fucicola	76.2202	86	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012964435.1	s__Mesonia sp012964435	75.8491	72	1288	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:42,332] [INFO] GTDB search result was written to GCF_004216895.1_ASM421689v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:42,332] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:42,336] [INFO] DFAST_QC result json was written to GCF_004216895.1_ASM421689v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:42,336] [INFO] DFAST_QC completed!
[2024-01-24 14:23:42,336] [INFO] Total running time: 0h1m28s