[2023-07-01 01:02:18,838] [INFO] DFAST_QC pipeline started.
[2023-07-01 01:02:18,842] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 01:02:18,842] [INFO] DQC Reference Directory: /var/lib/cwl/stg81113e33-e7a8-4ba3-8b85-b2dd487f3018/dqc_reference
[2023-07-01 01:02:20,267] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 01:02:20,268] [INFO] Task started: Prodigal
[2023-07-01 01:02:20,269] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d231572-7246-4dea-8339-99c46c3ab634/GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna.gz | prodigal -d GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna/cds.fna -a GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 01:02:44,079] [INFO] Task succeeded: Prodigal
[2023-07-01 01:02:44,080] [INFO] Task started: HMMsearch
[2023-07-01 01:02:44,080] [INFO] Running command: hmmsearch --tblout GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81113e33-e7a8-4ba3-8b85-b2dd487f3018/dqc_reference/reference_markers.hmm GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna/protein.faa > /dev/null
[2023-07-01 01:02:44,439] [INFO] Task succeeded: HMMsearch
[2023-07-01 01:02:44,440] [INFO] Found 6/6 markers.
[2023-07-01 01:02:44,484] [INFO] Query marker FASTA was written to GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna/markers.fasta
[2023-07-01 01:02:44,484] [INFO] Task started: Blastn
[2023-07-01 01:02:44,484] [INFO] Running command: blastn -query GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna/markers.fasta -db /var/lib/cwl/stg81113e33-e7a8-4ba3-8b85-b2dd487f3018/dqc_reference/reference_markers.fasta -out GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:02:45,078] [INFO] Task succeeded: Blastn
[2023-07-01 01:02:45,084] [INFO] Selected 23 target genomes.
[2023-07-01 01:02:45,084] [INFO] Target genome list was writen to GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna/target_genomes.txt
[2023-07-01 01:02:45,088] [INFO] Task started: fastANI
[2023-07-01 01:02:45,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d231572-7246-4dea-8339-99c46c3ab634/GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna.gz --refList GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna/target_genomes.txt --output GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 01:03:05,216] [INFO] Task succeeded: fastANI
[2023-07-01 01:03:05,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81113e33-e7a8-4ba3-8b85-b2dd487f3018/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 01:03:05,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81113e33-e7a8-4ba3-8b85-b2dd487f3018/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 01:03:05,223] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 01:03:05,224] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 01:03:05,224] [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
Flavipsychrobacter stenotrophus	strain=RB1R16	GCA_002954265.1	2077091	2077091	type	True	75.9389	104	1800	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 01:03:05,227] [INFO] DFAST Taxonomy check result was written to GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna/tc_result.tsv
[2023-07-01 01:03:05,227] [INFO] ===== Taxonomy check completed =====
[2023-07-01 01:03:05,228] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 01:03:05,228] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81113e33-e7a8-4ba3-8b85-b2dd487f3018/dqc_reference/checkm_data
[2023-07-01 01:03:05,230] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 01:03:05,282] [INFO] Task started: CheckM
[2023-07-01 01:03:05,282] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna/checkm_input GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna/checkm_result
[2023-07-01 01:04:12,355] [INFO] Task succeeded: CheckM
[2023-07-01 01:04:12,357] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 01:04:12,381] [INFO] ===== Completeness check finished =====
[2023-07-01 01:04:12,381] [INFO] ===== Start GTDB Search =====
[2023-07-01 01:04:12,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna/markers.fasta)
[2023-07-01 01:04:12,382] [INFO] Task started: Blastn
[2023-07-01 01:04:12,382] [INFO] Running command: blastn -query GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna/markers.fasta -db /var/lib/cwl/stg81113e33-e7a8-4ba3-8b85-b2dd487f3018/dqc_reference/reference_markers_gtdb.fasta -out GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:04:13,130] [INFO] Task succeeded: Blastn
[2023-07-01 01:04:13,135] [INFO] Selected 15 target genomes.
[2023-07-01 01:04:13,135] [INFO] Target genome list was writen to GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 01:04:13,139] [INFO] Task started: fastANI
[2023-07-01 01:04:13,139] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d231572-7246-4dea-8339-99c46c3ab634/GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna.gz --refList GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna/target_genomes_gtdb.txt --output GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 01:04:25,307] [INFO] Task succeeded: fastANI
[2023-07-01 01:04:25,324] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 01:04:25,324] [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_903835005.1	s__Flavipsychrobacter sp903835005	99.9795	1749	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	99.41	96.14	0.96	0.85	8	conclusive
GCA_903904855.1	s__Flavipsychrobacter sp903904855	81.0808	973	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	99.94	99.91	0.94	0.93	3	-
GCA_903903635.1	s__Flavipsychrobacter sp903903635	77.4596	365	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013288445.1	s__Flavipsychrobacter sp013288445	77.108	123	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903887415.1	s__Flavipsychrobacter sp903887415	76.9032	208	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	99.97	99.94	0.98	0.97	4	-
GCA_903905065.1	s__Flavipsychrobacter sp903905065	76.8872	169	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	99.97	99.97	0.97	0.97	2	-
GCA_903881585.1	s__Flavipsychrobacter sp903881585	76.8326	182	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839875.1	s__Flavipsychrobacter sp903839875	76.7541	226	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	99.93	99.93	0.96	0.95	3	-
GCA_013285595.1	s__Flavipsychrobacter sp013285595	76.6993	126	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903821975.1	s__Flavipsychrobacter sp903821975	76.6857	146	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903887005.1	s__Flavipsychrobacter sp903887005	76.6726	207	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903882805.1	s__Flavipsychrobacter sp903882805	76.4861	163	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903906615.1	s__Flavipsychrobacter sp903906615	76.2804	147	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013815385.1	s__Flavipsychrobacter sp013815385	76.1435	83	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 01:04:25,327] [INFO] GTDB search result was written to GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna/result_gtdb.tsv
[2023-07-01 01:04:25,327] [INFO] ===== GTDB Search completed =====
[2023-07-01 01:04:25,330] [INFO] DFAST_QC result json was written to GCA_903828735.1_freshwater_MAG_---_AM-2014_bin-0949_genomic.fna/dqc_result.json
[2023-07-01 01:04:25,330] [INFO] DFAST_QC completed!
[2023-07-01 01:04:25,330] [INFO] Total running time: 0h2m6s