[2023-06-30 18:32:01,760] [INFO] DFAST_QC pipeline started.
[2023-06-30 18:32:01,768] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 18:32:01,768] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b3d35c1-adca-45b7-9f18-e44ffb91b543/dqc_reference
[2023-06-30 18:32:03,633] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 18:32:03,635] [INFO] Task started: Prodigal
[2023-06-30 18:32:03,635] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd5aca29-2e53-4561-a613-25e491d445de/GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna.gz | prodigal -d GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna/cds.fna -a GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 18:32:12,320] [INFO] Task succeeded: Prodigal
[2023-06-30 18:32:12,321] [INFO] Task started: HMMsearch
[2023-06-30 18:32:12,321] [INFO] Running command: hmmsearch --tblout GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b3d35c1-adca-45b7-9f18-e44ffb91b543/dqc_reference/reference_markers.hmm GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna/protein.faa > /dev/null
[2023-06-30 18:32:12,534] [INFO] Task succeeded: HMMsearch
[2023-06-30 18:32:12,536] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgfd5aca29-2e53-4561-a613-25e491d445de/GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna.gz]
[2023-06-30 18:32:12,559] [INFO] Query marker FASTA was written to GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna/markers.fasta
[2023-06-30 18:32:12,559] [INFO] Task started: Blastn
[2023-06-30 18:32:12,560] [INFO] Running command: blastn -query GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b3d35c1-adca-45b7-9f18-e44ffb91b543/dqc_reference/reference_markers.fasta -out GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:32:13,053] [INFO] Task succeeded: Blastn
[2023-06-30 18:32:13,057] [INFO] Selected 9 target genomes.
[2023-06-30 18:32:13,058] [INFO] Target genome list was writen to GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna/target_genomes.txt
[2023-06-30 18:32:13,059] [INFO] Task started: fastANI
[2023-06-30 18:32:13,059] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd5aca29-2e53-4561-a613-25e491d445de/GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna.gz --refList GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna/target_genomes.txt --output GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 18:32:17,752] [INFO] Task succeeded: fastANI
[2023-06-30 18:32:17,752] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b3d35c1-adca-45b7-9f18-e44ffb91b543/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 18:32:17,753] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b3d35c1-adca-45b7-9f18-e44ffb91b543/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 18:32:17,760] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 18:32:17,760] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 18:32:17,760] [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	80.0577	248	447	95	below_threshold
Chlorobium ferrooxidans	strain=DSM 13031	GCA_000168715.1	84205	84205	type	True	78.2388	162	447	95	below_threshold
Chlorobium limicola	strain=DSM 245	GCA_000020465.1	1092	1092	type	True	77.2848	72	447	95	below_threshold
Pelodictyon luteolum	strain=DSM 273	GCA_000012485.1	1100	1100	type	True	77.2226	56	447	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 18:32:17,763] [INFO] DFAST Taxonomy check result was written to GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna/tc_result.tsv
[2023-06-30 18:32:17,764] [INFO] ===== Taxonomy check completed =====
[2023-06-30 18:32:17,764] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 18:32:17,764] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b3d35c1-adca-45b7-9f18-e44ffb91b543/dqc_reference/checkm_data
[2023-06-30 18:32:17,767] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 18:32:17,789] [INFO] Task started: CheckM
[2023-06-30 18:32:17,790] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna/checkm_input GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna/checkm_result
[2023-06-30 18:32:49,613] [INFO] Task succeeded: CheckM
[2023-06-30 18:32:49,615] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 18:32:49,651] [INFO] ===== Completeness check finished =====
[2023-06-30 18:32:49,651] [INFO] ===== Start GTDB Search =====
[2023-06-30 18:32:49,651] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna/markers.fasta)
[2023-06-30 18:32:49,652] [INFO] Task started: Blastn
[2023-06-30 18:32:49,652] [INFO] Running command: blastn -query GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b3d35c1-adca-45b7-9f18-e44ffb91b543/dqc_reference/reference_markers_gtdb.fasta -out GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:32:50,099] [INFO] Task succeeded: Blastn
[2023-06-30 18:32:50,103] [INFO] Selected 7 target genomes.
[2023-06-30 18:32:50,103] [INFO] Target genome list was writen to GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 18:32:50,104] [INFO] Task started: fastANI
[2023-06-30 18:32:50,105] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd5aca29-2e53-4561-a613-25e491d445de/GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna.gz --refList GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna/target_genomes_gtdb.txt --output GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 18:32:53,592] [INFO] Task succeeded: fastANI
[2023-06-30 18:32:53,599] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 18:32:53,600] [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_903836465.1	s__Chlorobium sp903836465	97.699	409	447	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.30	97.63	0.95	0.90	12	conclusive
GCA_903887845.1	s__Chlorobium sp903887845	92.9887	377	447	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.96	99.96	0.95	0.95	2	-
GCA_903937835.1	s__Chlorobium sp903937835	89.2782	342	447	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.77	99.60	0.93	0.86	6	-
GCA_903929845.1	s__Chlorobium sp903929845	88.711	286	447	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.53	99.40	0.83	0.81	5	-
GCA_903994455.1	s__Chlorobium sp903994455	87.2552	338	447	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.65	99.40	0.86	0.85	13	-
GCA_903843305.1	s__Chlorobium sp903843305	84.2887	338	447	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	98.98	96.88	0.93	0.82	17	-
GCA_903865705.1	s__Chlorobium sp903865705	79.5733	221	447	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.47	99.06	0.91	0.87	5	-
--------------------------------------------------------------------------------
[2023-06-30 18:32:53,602] [INFO] GTDB search result was written to GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna/result_gtdb.tsv
[2023-06-30 18:32:53,602] [INFO] ===== GTDB Search completed =====
[2023-06-30 18:32:53,606] [INFO] DFAST_QC result json was written to GCA_903845435.1_freshwater_MAG_---_Ki2-D4_bin-0437_genomic.fna/dqc_result.json
[2023-06-30 18:32:53,606] [INFO] DFAST_QC completed!
[2023-06-30 18:32:53,606] [INFO] Total running time: 0h0m52s