[2024-01-25 19:04:05,667] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:04:05,668] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:04:05,668] [INFO] DQC Reference Directory: /var/lib/cwl/stgc727ebe6-180d-4016-8c2e-450219813051/dqc_reference
[2024-01-25 19:04:06,794] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:04:06,794] [INFO] Task started: Prodigal
[2024-01-25 19:04:06,794] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c8220d4-2d31-4f65-9007-803ece44d14c/GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna/cds.fna -a GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:04:31,269] [INFO] Task succeeded: Prodigal
[2024-01-25 19:04:31,269] [INFO] Task started: HMMsearch
[2024-01-25 19:04:31,269] [INFO] Running command: hmmsearch --tblout GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc727ebe6-180d-4016-8c2e-450219813051/dqc_reference/reference_markers.hmm GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:04:31,538] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:04:31,539] [INFO] Found 6/6 markers.
[2024-01-25 19:04:31,584] [INFO] Query marker FASTA was written to GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 19:04:31,584] [INFO] Task started: Blastn
[2024-01-25 19:04:31,584] [INFO] Running command: blastn -query GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc727ebe6-180d-4016-8c2e-450219813051/dqc_reference/reference_markers.fasta -out GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:32,137] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:32,140] [INFO] Selected 22 target genomes.
[2024-01-25 19:04:32,140] [INFO] Target genome list was writen to GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 19:04:32,155] [INFO] Task started: fastANI
[2024-01-25 19:04:32,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c8220d4-2d31-4f65-9007-803ece44d14c/GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna.gz --refList GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:04:51,081] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:51,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc727ebe6-180d-4016-8c2e-450219813051/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:04:51,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc727ebe6-180d-4016-8c2e-450219813051/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:04:51,093] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:04:51,093] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:04:51,093] [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
Aquiflexum balticum	strain=DSM 16537	GCA_900176595.1	280473	280473	type	True	100.0	1995	1995	95	conclusive
Aquiflexum lacus	strain=CUG 91378	GCA_015476655.1	2483805	2483805	type	True	83.8216	1143	1995	95	below_threshold
Belliella baltica	strain=DSM 15883	GCA_000265405.1	232259	232259	type	True	78.4488	221	1995	95	below_threshold
Aquiflexum aquatile	strain=Z0201	GCA_003316845.1	2249427	2249427	type	True	77.8383	462	1995	95	below_threshold
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	77.8123	192	1995	95	below_threshold
Cecembia rubra	strain=DSM 28057	GCA_003014575.1	1485585	1485585	type	True	77.6862	297	1995	95	below_threshold
Belliella aquatica	strain=JCM 19468	GCA_022549755.1	1323734	1323734	type	True	77.1939	193	1995	95	below_threshold
Cecembia lonarensis	strain=LW9	GCA_000298295.1	645110	645110	type	True	77.0946	272	1995	95	below_threshold
Mongoliitalea lutea	strain=KCTC 23224	GCA_014652135.1	849756	849756	type	True	76.9515	197	1995	95	below_threshold
Algoriphagus iocasae	strain=DSM 102044	GCA_014206875.1	1836499	1836499	type	True	76.9395	130	1995	95	below_threshold
Belliella buryatensis	strain=5C	GCA_900188245.1	1500549	1500549	type	True	76.9379	185	1995	95	below_threshold
Algoriphagus machipongonensis	strain=PR1	GCA_000166275.1	388413	388413	type	True	76.9098	103	1995	95	below_threshold
Belliella kenyensis	strain=DSM 46651	GCA_022549675.1	1472724	1472724	type	True	76.8715	147	1995	95	below_threshold
Algoriphagus boseongensis	strain=CECT 8446	GCA_004362805.1	1442587	1442587	type	True	76.8348	114	1995	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	76.557	100	1995	95	below_threshold
Algoriphagus alkaliphilus	strain=DSM 22703	GCA_900103735.1	279824	279824	type	True	76.5173	139	1995	95	below_threshold
Echinicola salinicaeni	strain=P51	GCA_014280965.1	2762757	2762757	type	True	76.3582	115	1995	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:04:51,094] [INFO] DFAST Taxonomy check result was written to GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 19:04:51,095] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:04:51,095] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:04:51,095] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc727ebe6-180d-4016-8c2e-450219813051/dqc_reference/checkm_data
[2024-01-25 19:04:51,096] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:04:51,154] [INFO] Task started: CheckM
[2024-01-25 19:04:51,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna/checkm_input GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 19:05:59,024] [INFO] Task succeeded: CheckM
[2024-01-25 19:05:59,025] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:05:59,044] [INFO] ===== Completeness check finished =====
[2024-01-25 19:05:59,045] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:05:59,046] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 19:05:59,046] [INFO] Task started: Blastn
[2024-01-25 19:05:59,046] [INFO] Running command: blastn -query GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc727ebe6-180d-4016-8c2e-450219813051/dqc_reference/reference_markers_gtdb.fasta -out GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:59,834] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:59,837] [INFO] Selected 17 target genomes.
[2024-01-25 19:05:59,837] [INFO] Target genome list was writen to GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:05:59,854] [INFO] Task started: fastANI
[2024-01-25 19:05:59,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c8220d4-2d31-4f65-9007-803ece44d14c/GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna.gz --refList GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:06:15,232] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:15,243] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:06:15,243] [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_900176595.1	s__Aquiflexum balticum	100.0	1995	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015476655.1	s__Aquiflexum lacus	83.8144	1144	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003797895.1	s__Cecembia sp003797895	81.0838	494	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265405.1	s__Belliella baltica	78.5029	222	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003316845.1	s__Aquiflexum_A aquatile	77.8573	458	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126775.1	s__Cecembia sp007126775	77.7113	262	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	99.59	99.59	0.88	0.88	2	-
GCF_003014575.1	s__Cecembia rubra	77.6758	298	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003005.1	s__Mongoliibacter ruber	77.2933	291	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298295.1	s__Cecembia lonarensis	77.1163	270	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692705.1	s__Mongoliibacter sp007692705	77.0543	243	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652135.1	s__Mongoliitalea lutea	76.962	195	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014206875.1	s__Algoriphagus iocasae	76.9582	128	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166275.1	s__Algoriphagus machipongonensis	76.9418	100	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188245.1	s__Belliella buryatensis	76.9379	185	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362805.1	s__Algoriphagus boseongensis	76.8324	114	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103735.1	s__Algoriphagus alkaliphilus	76.5286	138	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.41	99.41	0.93	0.93	2	-
GCA_013373335.1	s__Algoriphagus sp013373335	76.0839	92	1995	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 19:06:15,244] [INFO] GTDB search result was written to GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 19:06:15,245] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:06:15,249] [INFO] DFAST_QC result json was written to GCF_900176595.1_IMG-taxon_2506520046_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 19:06:15,250] [INFO] DFAST_QC completed!
[2024-01-25 19:06:15,250] [INFO] Total running time: 0h2m10s