[2023-06-18 18:53:20,098] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:53:20,104] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:53:20,104] [INFO] DQC Reference Directory: /var/lib/cwl/stg3db32f39-f0d1-4efd-8766-00dc6991aade/dqc_reference
[2023-06-18 18:53:21,580] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:53:21,580] [INFO] Task started: Prodigal
[2023-06-18 18:53:21,581] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1f57ea4-726c-4124-9431-977df861dc18/GCA_018267705.1_ASM1826770v1_genomic.fna.gz | prodigal -d GCA_018267705.1_ASM1826770v1_genomic.fna/cds.fna -a GCA_018267705.1_ASM1826770v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:53:30,745] [INFO] Task succeeded: Prodigal
[2023-06-18 18:53:30,745] [INFO] Task started: HMMsearch
[2023-06-18 18:53:30,745] [INFO] Running command: hmmsearch --tblout GCA_018267705.1_ASM1826770v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3db32f39-f0d1-4efd-8766-00dc6991aade/dqc_reference/reference_markers.hmm GCA_018267705.1_ASM1826770v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:53:31,055] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:53:31,057] [INFO] Found 6/6 markers.
[2023-06-18 18:53:31,084] [INFO] Query marker FASTA was written to GCA_018267705.1_ASM1826770v1_genomic.fna/markers.fasta
[2023-06-18 18:53:31,084] [INFO] Task started: Blastn
[2023-06-18 18:53:31,084] [INFO] Running command: blastn -query GCA_018267705.1_ASM1826770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3db32f39-f0d1-4efd-8766-00dc6991aade/dqc_reference/reference_markers.fasta -out GCA_018267705.1_ASM1826770v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:53:31,737] [INFO] Task succeeded: Blastn
[2023-06-18 18:53:31,741] [INFO] Selected 21 target genomes.
[2023-06-18 18:53:31,742] [INFO] Target genome list was writen to GCA_018267705.1_ASM1826770v1_genomic.fna/target_genomes.txt
[2023-06-18 18:53:31,745] [INFO] Task started: fastANI
[2023-06-18 18:53:31,745] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1f57ea4-726c-4124-9431-977df861dc18/GCA_018267705.1_ASM1826770v1_genomic.fna.gz --refList GCA_018267705.1_ASM1826770v1_genomic.fna/target_genomes.txt --output GCA_018267705.1_ASM1826770v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:53:52,409] [INFO] Task succeeded: fastANI
[2023-06-18 18:53:52,410] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3db32f39-f0d1-4efd-8766-00dc6991aade/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:53:52,410] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3db32f39-f0d1-4efd-8766-00dc6991aade/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:53:52,423] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 18:53:52,423] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 18:53:52,424] [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
Hydrotalea lipotrueae	strain=TMF_100	GCA_019249625.1	2803817	2803817	type	True	76.856	159	866	95	below_threshold
Hydrotalea flava	strain=CCUG 51397	GCA_001623405.1	714549	714549	suspected-type	True	76.761	158	866	95	below_threshold
Hydrotalea sandarakina	strain=DSM 23241	GCA_003254115.1	1004304	1004304	type	True	76.722	180	866	95	below_threshold
Sediminibacterium salmoneum	strain=NBRC 103935	GCA_000511175.1	426421	426421	type	True	76.2859	86	866	95	below_threshold
Parafilimonas terrae	strain=DSM 28286	GCA_900115755.1	1465490	1465490	type	True	76.0567	84	866	95	below_threshold
Limnovirga soli	strain=KCS-6	GCA_013106755.1	2656915	2656915	type	True	75.8816	124	866	95	below_threshold
Pinibacter aurantiacus	strain=MAH-26	GCA_019130065.1	2851599	2851599	type	True	75.8677	54	866	95	below_threshold
Arachidicoccus soli	strain=KIS59-12	GCA_003600625.1	2341117	2341117	type	True	75.8321	79	866	95	below_threshold
Lacibacter luteus	strain=TTM-7	GCA_004118265.1	2508719	2508719	type	True	75.8031	72	866	95	below_threshold
Segetibacter koreensis	strain=DSM 18137	GCA_000374045.1	398037	398037	type	True	75.6379	75	866	95	below_threshold
Niabella ginsengisoli	strain=GR10-1	GCA_022513635.1	522298	522298	type	True	75.6088	70	866	95	below_threshold
Hanamia caeni	strain=BO-59	GCA_003721595.1	2294116	2294116	type	True	75.3598	55	866	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 18:53:52,426] [INFO] DFAST Taxonomy check result was written to GCA_018267705.1_ASM1826770v1_genomic.fna/tc_result.tsv
[2023-06-18 18:53:52,427] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:53:52,427] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:53:52,427] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3db32f39-f0d1-4efd-8766-00dc6991aade/dqc_reference/checkm_data
[2023-06-18 18:53:52,429] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:53:52,462] [INFO] Task started: CheckM
[2023-06-18 18:53:52,462] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018267705.1_ASM1826770v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018267705.1_ASM1826770v1_genomic.fna/checkm_input GCA_018267705.1_ASM1826770v1_genomic.fna/checkm_result
[2023-06-18 18:54:23,220] [INFO] Task succeeded: CheckM
[2023-06-18 18:54:23,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 18:54:23,242] [INFO] ===== Completeness check finished =====
[2023-06-18 18:54:23,242] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:54:23,242] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018267705.1_ASM1826770v1_genomic.fna/markers.fasta)
[2023-06-18 18:54:23,243] [INFO] Task started: Blastn
[2023-06-18 18:54:23,243] [INFO] Running command: blastn -query GCA_018267705.1_ASM1826770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3db32f39-f0d1-4efd-8766-00dc6991aade/dqc_reference/reference_markers_gtdb.fasta -out GCA_018267705.1_ASM1826770v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:54:24,250] [INFO] Task succeeded: Blastn
[2023-06-18 18:54:24,255] [INFO] Selected 12 target genomes.
[2023-06-18 18:54:24,255] [INFO] Target genome list was writen to GCA_018267705.1_ASM1826770v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:54:24,260] [INFO] Task started: fastANI
[2023-06-18 18:54:24,261] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1f57ea4-726c-4124-9431-977df861dc18/GCA_018267705.1_ASM1826770v1_genomic.fna.gz --refList GCA_018267705.1_ASM1826770v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018267705.1_ASM1826770v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:54:31,872] [INFO] Task succeeded: fastANI
[2023-06-18 18:54:31,891] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 18:54:31,891] [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
GCA_018267705.1	s__CW01 sp018267705	100.0	866	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CW01	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCA_018267725.1	s__CW01 sp018267725	88.833	735	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CW01	95.0	97.77	97.12	0.93	0.90	5	-
GCA_004028795.1	s__CW01 sp004028795	80.4177	571	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CW01	95.0	99.97	99.97	0.97	0.97	2	-
GCA_903881425.1	s__CAILAF01 sp903881425	77.7005	266	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.80	99.80	0.95	0.95	2	-
GCA_017304675.1	s__CW01 sp017304675	77.2046	247	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903870685.1	s__CAILAF01 sp903870685	77.0856	280	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.70	99.46	0.92	0.91	5	-
GCA_018061385.1	s__UBA1930 sp018061385	77.0328	171	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__UBA1930	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001623405.1	s__Hydrotalea flava	76.7748	157	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Hydrotalea	95.0	95.88	95.18	0.90	0.86	13	-
GCA_011362875.1	s__Hydrotalea flava_A	76.7242	185	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Hydrotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018335935.1	s__CAIVPM01 sp018335935	76.7152	195	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAIVPM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254115.1	s__Hydrotalea sandarakina	76.6974	181	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Hydrotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337145.1	s__UBA1930 sp002337145	76.1695	110	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__UBA1930	95.0	99.95	99.95	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-18 18:54:31,894] [INFO] GTDB search result was written to GCA_018267705.1_ASM1826770v1_genomic.fna/result_gtdb.tsv
[2023-06-18 18:54:31,894] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:54:31,898] [INFO] DFAST_QC result json was written to GCA_018267705.1_ASM1826770v1_genomic.fna/dqc_result.json
[2023-06-18 18:54:31,898] [INFO] DFAST_QC completed!
[2023-06-18 18:54:31,898] [INFO] Total running time: 0h1m12s