[2023-06-29 23:16:53,784] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:16:53,786] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:16:53,786] [INFO] DQC Reference Directory: /var/lib/cwl/stg3443b2d7-8920-4536-bc7c-acd98eeee8ef/dqc_reference
[2023-06-29 23:16:55,135] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:16:55,136] [INFO] Task started: Prodigal
[2023-06-29 23:16:55,136] [INFO] Running command: gunzip -c /var/lib/cwl/stgaeff712d-6b1b-41d0-a1a4-2858929ff6a2/GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna.gz | prodigal -d GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna/cds.fna -a GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:17:17,728] [INFO] Task succeeded: Prodigal
[2023-06-29 23:17:17,728] [INFO] Task started: HMMsearch
[2023-06-29 23:17:17,728] [INFO] Running command: hmmsearch --tblout GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3443b2d7-8920-4536-bc7c-acd98eeee8ef/dqc_reference/reference_markers.hmm GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:17:18,023] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:17:18,024] [INFO] Found 6/6 markers.
[2023-06-29 23:17:18,068] [INFO] Query marker FASTA was written to GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna/markers.fasta
[2023-06-29 23:17:18,068] [INFO] Task started: Blastn
[2023-06-29 23:17:18,068] [INFO] Running command: blastn -query GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna/markers.fasta -db /var/lib/cwl/stg3443b2d7-8920-4536-bc7c-acd98eeee8ef/dqc_reference/reference_markers.fasta -out GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:17:18,707] [INFO] Task succeeded: Blastn
[2023-06-29 23:17:18,712] [INFO] Selected 24 target genomes.
[2023-06-29 23:17:18,712] [INFO] Target genome list was writen to GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna/target_genomes.txt
[2023-06-29 23:17:18,714] [INFO] Task started: fastANI
[2023-06-29 23:17:18,715] [INFO] Running command: fastANI --query /var/lib/cwl/stgaeff712d-6b1b-41d0-a1a4-2858929ff6a2/GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna.gz --refList GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna/target_genomes.txt --output GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:17:40,438] [INFO] Task succeeded: fastANI
[2023-06-29 23:17:40,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3443b2d7-8920-4536-bc7c-acd98eeee8ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:17:40,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3443b2d7-8920-4536-bc7c-acd98eeee8ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:17:40,451] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:17:40,451] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 23:17:40,452] [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
Ginsengibacter hankyongi	strain=BR5-29	GCA_008710285.1	2607284	2607284	type	True	75.7487	60	1230	95	below_threshold
Panacibacter ginsenosidivorans	strain=Gsoil1550	GCA_007971225.1	1813871	1813871	type	True	75.6062	86	1230	95	below_threshold
Ferruginibacter albus	strain=KIS38-8	GCA_020042285.1	2875540	2875540	type	True	75.5707	62	1230	95	below_threshold
Pinibacter aurantiacus	strain=MAH-26	GCA_019130065.1	2851599	2851599	type	True	75.3653	55	1230	95	below_threshold
Niastella caeni	strain=HX-16-21	GCA_004834005.1	2569763	2569763	type	True	75.1881	60	1230	95	below_threshold
Lacibacter luteus	strain=TTM-7	GCA_004118265.1	2508719	2508719	type	True	75.1829	52	1230	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:17:40,454] [INFO] DFAST Taxonomy check result was written to GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna/tc_result.tsv
[2023-06-29 23:17:40,455] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:17:40,455] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:17:40,455] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3443b2d7-8920-4536-bc7c-acd98eeee8ef/dqc_reference/checkm_data
[2023-06-29 23:17:40,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:17:40,502] [INFO] Task started: CheckM
[2023-06-29 23:17:40,502] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna/checkm_input GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna/checkm_result
[2023-06-29 23:18:46,337] [INFO] Task succeeded: CheckM
[2023-06-29 23:18:46,338] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.86%
Contamintation: 5.56%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 23:18:46,367] [INFO] ===== Completeness check finished =====
[2023-06-29 23:18:46,367] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:18:46,368] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna/markers.fasta)
[2023-06-29 23:18:46,368] [INFO] Task started: Blastn
[2023-06-29 23:18:46,368] [INFO] Running command: blastn -query GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna/markers.fasta -db /var/lib/cwl/stg3443b2d7-8920-4536-bc7c-acd98eeee8ef/dqc_reference/reference_markers_gtdb.fasta -out GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:18:47,552] [INFO] Task succeeded: Blastn
[2023-06-29 23:18:47,557] [INFO] Selected 22 target genomes.
[2023-06-29 23:18:47,557] [INFO] Target genome list was writen to GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:18:47,568] [INFO] Task started: fastANI
[2023-06-29 23:18:47,568] [INFO] Running command: fastANI --query /var/lib/cwl/stgaeff712d-6b1b-41d0-a1a4-2858929ff6a2/GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna.gz --refList GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna/target_genomes_gtdb.txt --output GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:19:03,352] [INFO] Task succeeded: fastANI
[2023-06-29 23:19:03,372] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 23:19:03,373] [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_903927975.1	s__Puia sp903927975	99.8918	1120	1230	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	99.89	99.89	0.91	0.91	2	conclusive
GCA_018266575.1	s__Puia sp018266575	77.2078	314	1230	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013288945.1	s__Puia sp013288945	76.8681	227	1230	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266455.1	s__Puia sp018266455	76.8187	235	1230	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267575.1	s__Puia sp018267575	76.3351	169	1230	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003168265.1	s__Puia sp003168265	76.2165	61	1230	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267615.1	s__Puia sp018267615	76.0593	137	1230	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005882975.1	s__VBAS01 sp005882975	75.9793	70	1230	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__VBAS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884185.1	s__CAILAF01 sp903884185	75.8997	52	1230	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.92	99.92	0.95	0.95	2	-
GCA_013285855.1	s__Parafilimonas sp013285855	75.7824	56	1230	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Parafilimonas	95.0	99.41	99.41	0.64	0.64	2	-
GCA_903830285.1	s__CAILAF01 sp903830285	75.7791	72	1230	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.59	99.53	0.91	0.89	4	-
GCA_903832075.1	s__CAILAF01 sp903832075	75.7496	65	1230	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903881425.1	s__CAILAF01 sp903881425	75.6747	63	1230	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.80	99.80	0.95	0.95	2	-
GCA_016200915.1	s__AWTP1-9 sp016200915	75.5719	71	1230	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__AWTP1-9	95.0	99.92	99.92	0.98	0.98	2	-
GCF_019130065.1	s__Parasegetibacter sp019130065	75.3653	55	1230	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Parasegetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268035.1	s__Parafilimonas sp018268035	75.154	56	1230	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Parafilimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 23:19:03,375] [INFO] GTDB search result was written to GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna/result_gtdb.tsv
[2023-06-29 23:19:03,376] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:19:03,387] [INFO] DFAST_QC result json was written to GCA_903900005.1_freshwater_MAG_---_Umea_bin-00352_genomic.fna/dqc_result.json
[2023-06-29 23:19:03,387] [INFO] DFAST_QC completed!
[2023-06-29 23:19:03,388] [INFO] Total running time: 0h2m10s