[2024-01-25 19:30:21,556] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:30:21,557] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:30:21,557] [INFO] DQC Reference Directory: /var/lib/cwl/stg47675934-6c3a-4751-ba5e-e4bf7c22f894/dqc_reference
[2024-01-25 19:30:22,649] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:30:22,650] [INFO] Task started: Prodigal
[2024-01-25 19:30:22,650] [INFO] Running command: gunzip -c /var/lib/cwl/stg259278ef-451a-4374-939e-678ebb331070/GCF_030409495.1_ASM3040949v1_genomic.fna.gz | prodigal -d GCF_030409495.1_ASM3040949v1_genomic.fna/cds.fna -a GCF_030409495.1_ASM3040949v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:30:39,727] [INFO] Task succeeded: Prodigal
[2024-01-25 19:30:39,728] [INFO] Task started: HMMsearch
[2024-01-25 19:30:39,728] [INFO] Running command: hmmsearch --tblout GCF_030409495.1_ASM3040949v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47675934-6c3a-4751-ba5e-e4bf7c22f894/dqc_reference/reference_markers.hmm GCF_030409495.1_ASM3040949v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:30:39,956] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:30:39,957] [INFO] Found 6/6 markers.
[2024-01-25 19:30:39,997] [INFO] Query marker FASTA was written to GCF_030409495.1_ASM3040949v1_genomic.fna/markers.fasta
[2024-01-25 19:30:39,998] [INFO] Task started: Blastn
[2024-01-25 19:30:39,998] [INFO] Running command: blastn -query GCF_030409495.1_ASM3040949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47675934-6c3a-4751-ba5e-e4bf7c22f894/dqc_reference/reference_markers.fasta -out GCF_030409495.1_ASM3040949v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:30:40,547] [INFO] Task succeeded: Blastn
[2024-01-25 19:30:40,550] [INFO] Selected 18 target genomes.
[2024-01-25 19:30:40,550] [INFO] Target genome list was writen to GCF_030409495.1_ASM3040949v1_genomic.fna/target_genomes.txt
[2024-01-25 19:30:40,566] [INFO] Task started: fastANI
[2024-01-25 19:30:40,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg259278ef-451a-4374-939e-678ebb331070/GCF_030409495.1_ASM3040949v1_genomic.fna.gz --refList GCF_030409495.1_ASM3040949v1_genomic.fna/target_genomes.txt --output GCF_030409495.1_ASM3040949v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:30:55,554] [INFO] Task succeeded: fastANI
[2024-01-25 19:30:55,554] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47675934-6c3a-4751-ba5e-e4bf7c22f894/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:30:55,555] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47675934-6c3a-4751-ba5e-e4bf7c22f894/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:30:55,566] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:30:55,566] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:30:55,566] [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
Belliella kenyensis	strain=DSM 46651	GCA_022549675.1	1472724	1472724	type	True	99.9774	1479	1565	95	conclusive
Belliella pelovolcani	strain=DSM 46698	GCA_900156785.1	529505	529505	type	True	79.1279	397	1565	95	below_threshold
Belliella baltica	strain=DSM 15883	GCA_000265405.1	232259	232259	type	True	78.6741	338	1565	95	below_threshold
Belliella buryatensis	strain=5C	GCA_900188245.1	1500549	1500549	type	True	78.4778	372	1565	95	below_threshold
Cecembia calidifontis	strain=DSM 21411	GCA_004216715.1	1187080	1187080	type	True	78.302	169	1565	95	below_threshold
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	78.2082	186	1565	95	below_threshold
Belliella aquatica	strain=JCM 19468	GCA_022549755.1	1323734	1323734	type	True	77.9715	325	1565	95	below_threshold
Belliella aquatica	strain=CGMCC 1.12479	GCA_014637795.1	1323734	1323734	type	True	77.9023	329	1565	95	below_threshold
Algoriphagus lutimaris	strain=KCTC 22630	GCA_017051705.1	613197	613197	type	True	76.9902	101	1565	95	below_threshold
Algoriphagus zhangzhouensis	strain=CGMCC 1.11027	GCA_004366575.1	1073327	1073327	type	True	76.8786	113	1565	95	below_threshold
Algoriphagus pacificus	strain=YJ13C	GCA_017254845.1	2811234	2811234	type	True	76.8447	117	1565	95	below_threshold
Aquiflexum aquatile	strain=Z0201	GCA_003316845.1	2249427	2249427	type	True	76.8149	138	1565	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	76.7351	110	1565	95	below_threshold
Algoriphagus aquimarinus	strain=DSM 23399	GCA_900112005.1	237018	237018	type	True	76.6369	105	1565	95	below_threshold
Algoriphagus chordae	strain=DSM 19830	GCA_003254055.1	237019	237019	type	True	76.5695	95	1565	95	below_threshold
Algoriphagus yeomjeoni	strain=DSM 23446	GCA_003259505.1	291403	291403	type	True	76.5677	90	1565	95	below_threshold
Algoriphagus locisalis	strain=DSM 23445	GCA_900116615.1	305507	305507	type	True	76.4619	106	1565	95	below_threshold
Algoriphagus resistens	strain=NH1	GCA_001442615.1	1750590	1750590	type	True	76.24	91	1565	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:30:55,568] [INFO] DFAST Taxonomy check result was written to GCF_030409495.1_ASM3040949v1_genomic.fna/tc_result.tsv
[2024-01-25 19:30:55,568] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:30:55,568] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:30:55,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47675934-6c3a-4751-ba5e-e4bf7c22f894/dqc_reference/checkm_data
[2024-01-25 19:30:55,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:30:55,616] [INFO] Task started: CheckM
[2024-01-25 19:30:55,616] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409495.1_ASM3040949v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409495.1_ASM3040949v1_genomic.fna/checkm_input GCF_030409495.1_ASM3040949v1_genomic.fna/checkm_result
[2024-01-25 19:31:46,448] [INFO] Task succeeded: CheckM
[2024-01-25 19:31:46,449] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:31:46,472] [INFO] ===== Completeness check finished =====
[2024-01-25 19:31:46,472] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:31:46,473] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409495.1_ASM3040949v1_genomic.fna/markers.fasta)
[2024-01-25 19:31:46,473] [INFO] Task started: Blastn
[2024-01-25 19:31:46,473] [INFO] Running command: blastn -query GCF_030409495.1_ASM3040949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47675934-6c3a-4751-ba5e-e4bf7c22f894/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409495.1_ASM3040949v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:31:47,185] [INFO] Task succeeded: Blastn
[2024-01-25 19:31:47,191] [INFO] Selected 23 target genomes.
[2024-01-25 19:31:47,191] [INFO] Target genome list was writen to GCF_030409495.1_ASM3040949v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:31:47,225] [INFO] Task started: fastANI
[2024-01-25 19:31:47,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg259278ef-451a-4374-939e-678ebb331070/GCF_030409495.1_ASM3040949v1_genomic.fna.gz --refList GCF_030409495.1_ASM3040949v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409495.1_ASM3040949v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:32:03,989] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:04,002] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:32:04,002] [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_900156785.1	s__Belliella pelovolcani	79.1052	399	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265405.1	s__Belliella baltica	78.6746	339	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188245.1	s__Belliella buryatensis	78.4778	372	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216715.1	s__Cecembia calidifontis	78.2552	168	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637795.1	s__Belliella aquatica	77.8927	330	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000295935.2	s__Indibacter alkaliphilus	77.6994	183	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Indibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298295.1	s__Cecembia lonarensis	77.5898	141	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126775.1	s__Cecembia sp007126775	77.0257	116	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	99.59	99.59	0.88	0.88	2	-
GCF_017051705.1	s__Algoriphagus lutimaris	77.0152	100	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018500185.1	s__Litoribacter ruber	76.9796	108	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Litoribacter	95.0	98.60	98.60	0.91	0.91	2	-
GCF_004362805.1	s__Algoriphagus boseongensis	76.8228	89	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003316845.1	s__Aquiflexum_A aquatile	76.7973	138	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254845.1	s__Algoriphagus sp017254845	76.7942	119	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900148515.1	s__Algoriphagus zhangzhouensis	76.7346	109	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007692705.1	s__Mongoliibacter sp007692705	76.7187	138	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112005.1	s__Algoriphagus aquimarinus	76.6154	106	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254055.1	s__Algoriphagus chordae	76.5664	94	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429405.1	s__Algoriphagus marincola	76.5612	88	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	97.35	97.35	0.90	0.90	2	-
GCF_003259505.1	s__Algoriphagus yeomjeoni	76.5577	91	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116615.1	s__Algoriphagus locisalis	76.4392	105	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442615.1	s__Algoriphagus resistens	76.2432	91	1565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:32:04,003] [INFO] GTDB search result was written to GCF_030409495.1_ASM3040949v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:32:04,003] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:32:04,007] [INFO] DFAST_QC result json was written to GCF_030409495.1_ASM3040949v1_genomic.fna/dqc_result.json
[2024-01-25 19:32:04,007] [INFO] DFAST_QC completed!
[2024-01-25 19:32:04,007] [INFO] Total running time: 0h1m42s