[2023-06-05 23:46:11,507] [INFO] DFAST_QC pipeline started.
[2023-06-05 23:46:11,509] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 23:46:11,509] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe0e2d56-df80-43a9-a8fb-9a9a3ff13d31/dqc_reference
[2023-06-05 23:46:13,116] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 23:46:13,116] [INFO] Task started: Prodigal
[2023-06-05 23:46:13,117] [INFO] Running command: gunzip -c /var/lib/cwl/stga886e9ba-9c1b-449d-9a38-c0bc16e13b85/GCA_934693025.1_ERR7738209_bin.83_genomic.fna.gz | prodigal -d GCA_934693025.1_ERR7738209_bin.83_genomic.fna/cds.fna -a GCA_934693025.1_ERR7738209_bin.83_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 23:46:28,146] [INFO] Task succeeded: Prodigal
[2023-06-05 23:46:28,146] [INFO] Task started: HMMsearch
[2023-06-05 23:46:28,146] [INFO] Running command: hmmsearch --tblout GCA_934693025.1_ERR7738209_bin.83_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe0e2d56-df80-43a9-a8fb-9a9a3ff13d31/dqc_reference/reference_markers.hmm GCA_934693025.1_ERR7738209_bin.83_genomic.fna/protein.faa > /dev/null
[2023-06-05 23:46:28,351] [INFO] Task succeeded: HMMsearch
[2023-06-05 23:46:28,352] [INFO] Found 6/6 markers.
[2023-06-05 23:46:28,378] [INFO] Query marker FASTA was written to GCA_934693025.1_ERR7738209_bin.83_genomic.fna/markers.fasta
[2023-06-05 23:46:28,378] [INFO] Task started: Blastn
[2023-06-05 23:46:28,378] [INFO] Running command: blastn -query GCA_934693025.1_ERR7738209_bin.83_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe0e2d56-df80-43a9-a8fb-9a9a3ff13d31/dqc_reference/reference_markers.fasta -out GCA_934693025.1_ERR7738209_bin.83_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:46:28,895] [INFO] Task succeeded: Blastn
[2023-06-05 23:46:28,898] [INFO] Selected 25 target genomes.
[2023-06-05 23:46:28,899] [INFO] Target genome list was writen to GCA_934693025.1_ERR7738209_bin.83_genomic.fna/target_genomes.txt
[2023-06-05 23:46:28,902] [INFO] Task started: fastANI
[2023-06-05 23:46:28,902] [INFO] Running command: fastANI --query /var/lib/cwl/stga886e9ba-9c1b-449d-9a38-c0bc16e13b85/GCA_934693025.1_ERR7738209_bin.83_genomic.fna.gz --refList GCA_934693025.1_ERR7738209_bin.83_genomic.fna/target_genomes.txt --output GCA_934693025.1_ERR7738209_bin.83_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 23:46:42,235] [INFO] Task succeeded: fastANI
[2023-06-05 23:46:42,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe0e2d56-df80-43a9-a8fb-9a9a3ff13d31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 23:46:42,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe0e2d56-df80-43a9-a8fb-9a9a3ff13d31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 23:46:42,237] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 23:46:42,237] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 23:46:42,237] [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
--------------------------------------------------------------------------------
[2023-06-05 23:46:42,239] [INFO] DFAST Taxonomy check result was written to GCA_934693025.1_ERR7738209_bin.83_genomic.fna/tc_result.tsv
[2023-06-05 23:46:42,239] [INFO] ===== Taxonomy check completed =====
[2023-06-05 23:46:42,239] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 23:46:42,240] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe0e2d56-df80-43a9-a8fb-9a9a3ff13d31/dqc_reference/checkm_data
[2023-06-05 23:46:42,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 23:46:42,276] [INFO] Task started: CheckM
[2023-06-05 23:46:42,276] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934693025.1_ERR7738209_bin.83_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934693025.1_ERR7738209_bin.83_genomic.fna/checkm_input GCA_934693025.1_ERR7738209_bin.83_genomic.fna/checkm_result
[2023-06-05 23:47:26,281] [INFO] Task succeeded: CheckM
[2023-06-05 23:47:26,282] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 23:47:26,296] [INFO] ===== Completeness check finished =====
[2023-06-05 23:47:26,296] [INFO] ===== Start GTDB Search =====
[2023-06-05 23:47:26,296] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934693025.1_ERR7738209_bin.83_genomic.fna/markers.fasta)
[2023-06-05 23:47:26,297] [INFO] Task started: Blastn
[2023-06-05 23:47:26,297] [INFO] Running command: blastn -query GCA_934693025.1_ERR7738209_bin.83_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe0e2d56-df80-43a9-a8fb-9a9a3ff13d31/dqc_reference/reference_markers_gtdb.fasta -out GCA_934693025.1_ERR7738209_bin.83_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:47:27,086] [INFO] Task succeeded: Blastn
[2023-06-05 23:47:27,090] [INFO] Selected 10 target genomes.
[2023-06-05 23:47:27,090] [INFO] Target genome list was writen to GCA_934693025.1_ERR7738209_bin.83_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 23:47:27,095] [INFO] Task started: fastANI
[2023-06-05 23:47:27,095] [INFO] Running command: fastANI --query /var/lib/cwl/stga886e9ba-9c1b-449d-9a38-c0bc16e13b85/GCA_934693025.1_ERR7738209_bin.83_genomic.fna.gz --refList GCA_934693025.1_ERR7738209_bin.83_genomic.fna/target_genomes_gtdb.txt --output GCA_934693025.1_ERR7738209_bin.83_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 23:47:34,671] [INFO] Task succeeded: fastANI
[2023-06-05 23:47:34,678] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 23:47:34,678] [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_900544195.1	s__Cryptobacteroides sp900544195	97.0994	770	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.99	97.97	0.92	0.84	3	conclusive
GCA_000433355.1	s__Cryptobacteroides sp000433355	91.6327	685	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.66	97.93	0.86	0.80	6	-
GCA_000431015.1	s__Cryptobacteroides sp000431015	88.1555	556	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.39	98.13	0.87	0.74	9	-
GCA_002438845.1	s__Cryptobacteroides sp002438845	84.7183	568	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.65	99.58	0.89	0.89	3	-
GCA_002314195.1	s__Cryptobacteroides sp002314195	83.9889	515	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.70	98.15	0.81	0.75	7	-
GCA_002439875.1	s__Cryptobacteroides sp002439875	83.9067	577	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002321335.1	s__Cryptobacteroides sp002321335	83.8919	542	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.53	99.38	0.88	0.86	3	-
GCA_002437305.1	s__Cryptobacteroides sp002437305	82.8078	492	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.56	99.17	0.93	0.89	9	-
GCA_002297815.1	s__Cryptobacteroides sp002297815	82.6178	528	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.51	97.81	0.90	0.86	6	-
GCA_002438905.1	s__Cryptobacteroides sp002438905	76.6976	58	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 23:47:34,705] [INFO] GTDB search result was written to GCA_934693025.1_ERR7738209_bin.83_genomic.fna/result_gtdb.tsv
[2023-06-05 23:47:34,706] [INFO] ===== GTDB Search completed =====
[2023-06-05 23:47:34,708] [INFO] DFAST_QC result json was written to GCA_934693025.1_ERR7738209_bin.83_genomic.fna/dqc_result.json
[2023-06-05 23:47:34,708] [INFO] DFAST_QC completed!
[2023-06-05 23:47:34,708] [INFO] Total running time: 0h1m23s