[2023-06-29 22:59:17,953] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:59:17,956] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:59:17,956] [INFO] DQC Reference Directory: /var/lib/cwl/stg311b9925-e66b-4205-8f8d-e641cb9cafec/dqc_reference
[2023-06-29 22:59:19,275] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:59:19,276] [INFO] Task started: Prodigal
[2023-06-29 22:59:19,276] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2e66a37-3777-462b-bebd-4b0f77f6bf01/GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna.gz | prodigal -d GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna/cds.fna -a GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:59:25,848] [INFO] Task succeeded: Prodigal
[2023-06-29 22:59:25,849] [INFO] Task started: HMMsearch
[2023-06-29 22:59:25,849] [INFO] Running command: hmmsearch --tblout GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg311b9925-e66b-4205-8f8d-e641cb9cafec/dqc_reference/reference_markers.hmm GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:59:26,114] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:59:26,116] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb2e66a37-3777-462b-bebd-4b0f77f6bf01/GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna.gz]
[2023-06-29 22:59:26,144] [INFO] Query marker FASTA was written to GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna/markers.fasta
[2023-06-29 22:59:26,145] [INFO] Task started: Blastn
[2023-06-29 22:59:26,145] [INFO] Running command: blastn -query GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna/markers.fasta -db /var/lib/cwl/stg311b9925-e66b-4205-8f8d-e641cb9cafec/dqc_reference/reference_markers.fasta -out GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:59:26,819] [INFO] Task succeeded: Blastn
[2023-06-29 22:59:26,823] [INFO] Selected 10 target genomes.
[2023-06-29 22:59:26,823] [INFO] Target genome list was writen to GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna/target_genomes.txt
[2023-06-29 22:59:26,824] [INFO] Task started: fastANI
[2023-06-29 22:59:26,824] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2e66a37-3777-462b-bebd-4b0f77f6bf01/GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna.gz --refList GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna/target_genomes.txt --output GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:59:31,383] [INFO] Task succeeded: fastANI
[2023-06-29 22:59:31,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg311b9925-e66b-4205-8f8d-e641cb9cafec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:59:31,383] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg311b9925-e66b-4205-8f8d-e641cb9cafec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:59:31,390] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:59:31,391] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 22:59:31,391] [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	78.9534	316	747	95	below_threshold
Chlorobium ferrooxidans	strain=DSM 13031	GCA_000168715.1	84205	84205	type	True	77.8607	183	747	95	below_threshold
Chlorobium phaeobacteroides	strain=DSM 266	GCA_000015125.1	1096	1096	type	True	77.7596	117	747	95	below_threshold
Chlorobium limicola	strain=DSM 245	GCA_000020465.1	1092	1092	type	True	76.906	84	747	95	below_threshold
Chlorobaculum thiosulfatiphilum	strain=DSM 249	GCA_006265165.1	115852	115852	type	True	76.2911	52	747	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 22:59:31,393] [INFO] DFAST Taxonomy check result was written to GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna/tc_result.tsv
[2023-06-29 22:59:31,394] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:59:31,394] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:59:31,394] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg311b9925-e66b-4205-8f8d-e641cb9cafec/dqc_reference/checkm_data
[2023-06-29 22:59:31,396] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:59:31,426] [INFO] Task started: CheckM
[2023-06-29 22:59:31,426] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna/checkm_input GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna/checkm_result
[2023-06-29 22:59:57,752] [INFO] Task succeeded: CheckM
[2023-06-29 22:59:57,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 22:59:57,773] [INFO] ===== Completeness check finished =====
[2023-06-29 22:59:57,774] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:59:57,774] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna/markers.fasta)
[2023-06-29 22:59:57,775] [INFO] Task started: Blastn
[2023-06-29 22:59:57,775] [INFO] Running command: blastn -query GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna/markers.fasta -db /var/lib/cwl/stg311b9925-e66b-4205-8f8d-e641cb9cafec/dqc_reference/reference_markers_gtdb.fasta -out GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:59:58,547] [INFO] Task succeeded: Blastn
[2023-06-29 22:59:58,551] [INFO] Selected 9 target genomes.
[2023-06-29 22:59:58,551] [INFO] Target genome list was writen to GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:59:58,557] [INFO] Task started: fastANI
[2023-06-29 22:59:58,557] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2e66a37-3777-462b-bebd-4b0f77f6bf01/GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna.gz --refList GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna/target_genomes_gtdb.txt --output GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:00:03,042] [INFO] Task succeeded: fastANI
[2023-06-29 23:00:03,059] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 23:00:03,059] [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	99.85	686	747	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	88.926	531	747	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	85.1641	486	747	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.98	99.98	0.95	0.93	3	-
GCA_005843815.1	s__Chlorobium sp005843815	82.2465	368	747	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	81.9488	353	747	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	81.9158	422	747	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	98.74	96.45	0.88	0.78	5	-
GCA_903994635.1	s__Chlorobium sp903994635	81.8392	376	747	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.09	98.12	0.80	0.68	12	-
GCA_903838095.1	s__Chlorobium sp903838095	78.8117	213	747	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	77.9086	223	747	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.60	99.60	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-06-29 23:00:03,061] [INFO] GTDB search result was written to GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna/result_gtdb.tsv
[2023-06-29 23:00:03,062] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:00:03,065] [INFO] DFAST_QC result json was written to GCA_903852185.1_freshwater_MAG_---_Day6-6_bin-415_genomic.fna/dqc_result.json
[2023-06-29 23:00:03,065] [INFO] DFAST_QC completed!
[2023-06-29 23:00:03,066] [INFO] Total running time: 0h0m45s