[2023-06-30 20:35:00,481] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:35:00,483] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:35:00,483] [INFO] DQC Reference Directory: /var/lib/cwl/stg883fa982-bfb1-4ef4-90e5-a6660e6cd2b4/dqc_reference
[2023-06-30 20:35:02,198] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:35:02,199] [INFO] Task started: Prodigal
[2023-06-30 20:35:02,200] [INFO] Running command: gunzip -c /var/lib/cwl/stg93ccf9cf-15e0-482c-87d4-a378396bcfc1/GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna.gz | prodigal -d GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna/cds.fna -a GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:35:07,396] [INFO] Task succeeded: Prodigal
[2023-06-30 20:35:07,396] [INFO] Task started: HMMsearch
[2023-06-30 20:35:07,396] [INFO] Running command: hmmsearch --tblout GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg883fa982-bfb1-4ef4-90e5-a6660e6cd2b4/dqc_reference/reference_markers.hmm GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:35:07,558] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:35:07,559] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg93ccf9cf-15e0-482c-87d4-a378396bcfc1/GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna.gz]
[2023-06-30 20:35:07,581] [INFO] Query marker FASTA was written to GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna/markers.fasta
[2023-06-30 20:35:07,582] [INFO] Task started: Blastn
[2023-06-30 20:35:07,582] [INFO] Running command: blastn -query GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna/markers.fasta -db /var/lib/cwl/stg883fa982-bfb1-4ef4-90e5-a6660e6cd2b4/dqc_reference/reference_markers.fasta -out GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:35:08,053] [INFO] Task succeeded: Blastn
[2023-06-30 20:35:08,058] [INFO] Selected 8 target genomes.
[2023-06-30 20:35:08,058] [INFO] Target genome list was writen to GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna/target_genomes.txt
[2023-06-30 20:35:08,059] [INFO] Task started: fastANI
[2023-06-30 20:35:08,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg93ccf9cf-15e0-482c-87d4-a378396bcfc1/GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna.gz --refList GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna/target_genomes.txt --output GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:35:11,692] [INFO] Task succeeded: fastANI
[2023-06-30 20:35:11,692] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg883fa982-bfb1-4ef4-90e5-a6660e6cd2b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:35:11,692] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg883fa982-bfb1-4ef4-90e5-a6660e6cd2b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:35:11,698] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 20:35:11,698] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 20:35:11,698] [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
Pelodictyon phaeoclathratiforme	strain=BU-1	GCA_000020645.1	34090	34090	type	True	79.2113	255	552	95	below_threshold
Chlorobium phaeobacteroides	strain=DSM 266	GCA_000015125.1	1096	1096	type	True	78.2499	89	552	95	below_threshold
Chlorobium ferrooxidans	strain=DSM 13031	GCA_000168715.1	84205	84205	type	True	77.9462	153	552	95	below_threshold
Chlorobium limicola	strain=DSM 245	GCA_000020465.1	1092	1092	type	True	76.8442	73	552	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 20:35:11,700] [INFO] DFAST Taxonomy check result was written to GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna/tc_result.tsv
[2023-06-30 20:35:11,700] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:35:11,700] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:35:11,700] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg883fa982-bfb1-4ef4-90e5-a6660e6cd2b4/dqc_reference/checkm_data
[2023-06-30 20:35:11,701] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:35:11,726] [INFO] Task started: CheckM
[2023-06-30 20:35:11,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna/checkm_input GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna/checkm_result
[2023-06-30 20:35:43,431] [INFO] Task succeeded: CheckM
[2023-06-30 20:35:43,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.57%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 20:35:43,453] [INFO] ===== Completeness check finished =====
[2023-06-30 20:35:43,453] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:35:43,454] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna/markers.fasta)
[2023-06-30 20:35:43,454] [INFO] Task started: Blastn
[2023-06-30 20:35:43,454] [INFO] Running command: blastn -query GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna/markers.fasta -db /var/lib/cwl/stg883fa982-bfb1-4ef4-90e5-a6660e6cd2b4/dqc_reference/reference_markers_gtdb.fasta -out GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:35:43,917] [INFO] Task succeeded: Blastn
[2023-06-30 20:35:43,921] [INFO] Selected 9 target genomes.
[2023-06-30 20:35:43,921] [INFO] Target genome list was writen to GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:35:43,922] [INFO] Task started: fastANI
[2023-06-30 20:35:43,922] [INFO] Running command: fastANI --query /var/lib/cwl/stg93ccf9cf-15e0-482c-87d4-a378396bcfc1/GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna.gz --refList GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna/target_genomes_gtdb.txt --output GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:35:48,373] [INFO] Task succeeded: fastANI
[2023-06-30 20:35:48,381] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 20:35:48,381] [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_903994525.1	s__Chlorobium sp903994525	99.7959	510	552	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.83	98.94	0.92	0.84	27	conclusive
GCA_903859055.1	s__Chlorobium sp903859055	88.9385	428	552	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.70	99.65	0.94	0.92	3	-
GCA_903866255.1	s__Chlorobium sp903866255	85.7107	388	552	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.98	99.98	0.95	0.93	3	-
GCA_903994635.1	s__Chlorobium sp903994635	82.9472	306	552	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.09	98.12	0.80	0.68	12	-
GCA_005843815.1	s__Chlorobium sp005843815	82.3984	290	552	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903994365.1	s__Chlorobium sp903994365	82.3773	276	552	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.58	99.23	0.74	0.73	6	-
GCA_903915955.1	s__Chlorobium sp903915955	82.2719	329	552	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	98.74	96.45	0.88	0.78	5	-
GCA_903838095.1	s__Chlorobium sp903838095	79.0286	170	552	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013334755.1	s__Chlorobium sp013334755	77.845	166	552	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.60	99.60	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-06-30 20:35:48,383] [INFO] GTDB search result was written to GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna/result_gtdb.tsv
[2023-06-30 20:35:48,384] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:35:48,387] [INFO] DFAST_QC result json was written to GCA_903852765.1_freshwater_MAG_---_KT2_bin-079_genomic.fna/dqc_result.json
[2023-06-30 20:35:48,387] [INFO] DFAST_QC completed!
[2023-06-30 20:35:48,387] [INFO] Total running time: 0h0m48s