[2023-06-28 04:20:01,761] [INFO] DFAST_QC pipeline started.
[2023-06-28 04:20:01,764] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 04:20:01,764] [INFO] DQC Reference Directory: /var/lib/cwl/stg22a61953-1c3d-4b09-93c2-e5f288e2b6fc/dqc_reference
[2023-06-28 04:20:03,009] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 04:20:03,010] [INFO] Task started: Prodigal
[2023-06-28 04:20:03,011] [INFO] Running command: gunzip -c /var/lib/cwl/stg14874b56-e8c6-42a7-8337-edb8f39deb5c/GCA_017455065.1_ASM1745506v1_genomic.fna.gz | prodigal -d GCA_017455065.1_ASM1745506v1_genomic.fna/cds.fna -a GCA_017455065.1_ASM1745506v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 04:20:14,930] [INFO] Task succeeded: Prodigal
[2023-06-28 04:20:14,930] [INFO] Task started: HMMsearch
[2023-06-28 04:20:14,930] [INFO] Running command: hmmsearch --tblout GCA_017455065.1_ASM1745506v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22a61953-1c3d-4b09-93c2-e5f288e2b6fc/dqc_reference/reference_markers.hmm GCA_017455065.1_ASM1745506v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 04:20:15,134] [INFO] Task succeeded: HMMsearch
[2023-06-28 04:20:15,135] [INFO] Found 6/6 markers.
[2023-06-28 04:20:15,156] [INFO] Query marker FASTA was written to GCA_017455065.1_ASM1745506v1_genomic.fna/markers.fasta
[2023-06-28 04:20:15,156] [INFO] Task started: Blastn
[2023-06-28 04:20:15,156] [INFO] Running command: blastn -query GCA_017455065.1_ASM1745506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22a61953-1c3d-4b09-93c2-e5f288e2b6fc/dqc_reference/reference_markers.fasta -out GCA_017455065.1_ASM1745506v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:20:15,743] [INFO] Task succeeded: Blastn
[2023-06-28 04:20:15,746] [INFO] Selected 25 target genomes.
[2023-06-28 04:20:15,747] [INFO] Target genome list was writen to GCA_017455065.1_ASM1745506v1_genomic.fna/target_genomes.txt
[2023-06-28 04:20:15,750] [INFO] Task started: fastANI
[2023-06-28 04:20:15,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg14874b56-e8c6-42a7-8337-edb8f39deb5c/GCA_017455065.1_ASM1745506v1_genomic.fna.gz --refList GCA_017455065.1_ASM1745506v1_genomic.fna/target_genomes.txt --output GCA_017455065.1_ASM1745506v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 04:20:30,274] [INFO] Task succeeded: fastANI
[2023-06-28 04:20:30,275] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22a61953-1c3d-4b09-93c2-e5f288e2b6fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 04:20:30,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22a61953-1c3d-4b09-93c2-e5f288e2b6fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 04:20:30,276] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 04:20:30,277] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 04:20:30,277] [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
--------------------------------------------------------------------------------
[2023-06-28 04:20:30,278] [INFO] DFAST Taxonomy check result was written to GCA_017455065.1_ASM1745506v1_genomic.fna/tc_result.tsv
[2023-06-28 04:20:30,279] [INFO] ===== Taxonomy check completed =====
[2023-06-28 04:20:30,279] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 04:20:30,279] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22a61953-1c3d-4b09-93c2-e5f288e2b6fc/dqc_reference/checkm_data
[2023-06-28 04:20:30,282] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 04:20:30,306] [INFO] Task started: CheckM
[2023-06-28 04:20:30,306] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017455065.1_ASM1745506v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017455065.1_ASM1745506v1_genomic.fna/checkm_input GCA_017455065.1_ASM1745506v1_genomic.fna/checkm_result
[2023-06-28 04:21:05,812] [INFO] Task succeeded: CheckM
[2023-06-28 04:21:05,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 04:21:05,828] [INFO] ===== Completeness check finished =====
[2023-06-28 04:21:05,828] [INFO] ===== Start GTDB Search =====
[2023-06-28 04:21:05,829] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017455065.1_ASM1745506v1_genomic.fna/markers.fasta)
[2023-06-28 04:21:05,829] [INFO] Task started: Blastn
[2023-06-28 04:21:05,829] [INFO] Running command: blastn -query GCA_017455065.1_ASM1745506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22a61953-1c3d-4b09-93c2-e5f288e2b6fc/dqc_reference/reference_markers_gtdb.fasta -out GCA_017455065.1_ASM1745506v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:21:06,686] [INFO] Task succeeded: Blastn
[2023-06-28 04:21:06,689] [INFO] Selected 20 target genomes.
[2023-06-28 04:21:06,689] [INFO] Target genome list was writen to GCA_017455065.1_ASM1745506v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 04:21:06,692] [INFO] Task started: fastANI
[2023-06-28 04:21:06,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg14874b56-e8c6-42a7-8337-edb8f39deb5c/GCA_017455065.1_ASM1745506v1_genomic.fna.gz --refList GCA_017455065.1_ASM1745506v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017455065.1_ASM1745506v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 04:21:14,196] [INFO] Task succeeded: fastANI
[2023-06-28 04:21:14,213] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 04:21:14,213] [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_017455065.1	s__Cryptobacteroides sp017455065	100.0	664	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017454335.1	s__Cryptobacteroides sp017454335	79.3431	282	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017477245.1	s__Cryptobacteroides sp017477245	78.9659	227	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.05	97.38	0.81	0.78	3	-
GCA_902787295.1	s__Cryptobacteroides sp902787295	78.7641	184	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.75	97.75	0.73	0.73	2	-
GCA_017428725.1	s__Cryptobacteroides sp017428725	78.5592	248	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.64	97.64	0.87	0.87	2	-
GCA_902768985.1	s__Cryptobacteroides sp902768985	78.5239	214	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.65	98.07	0.93	0.92	5	-
GCA_902789245.1	s__Cryptobacteroides sp902789245	78.3576	223	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.35	96.71	0.87	0.86	3	-
GCA_900319975.1	s__Cryptobacteroides sp900319975	78.3536	209	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.34	97.18	0.88	0.88	3	-
GCA_017651225.1	s__Cryptobacteroides sp017651225	78.2888	176	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017458145.1	s__Cryptobacteroides sp017458145	78.0569	212	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319185.1	s__Cryptobacteroides sp900319185	77.9935	150	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.95	98.63	0.93	0.89	6	-
GCA_900769905.1	s__Cryptobacteroides sp900769905	77.9235	134	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.32	98.32	0.78	0.78	2	-
GCA_017561865.1	s__Cryptobacteroides sp017561865	77.782	137	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016283985.1	s__Cryptobacteroides sp016283985	77.7759	127	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317065.1	s__Cryptobacteroides sp900317065	77.7684	117	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.61	96.75	0.82	0.75	6	-
GCA_001602885.1	s__Cryptobacteroides sp001602885	77.5915	94	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017453565.1	s__Cryptobacteroides sp017453565	77.4325	130	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017619675.1	s__Cryptobacteroides sp017619675	77.4293	131	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004555145.1	s__Cryptobacteroides sp004555145	77.212	104	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900767375.1	s__Cryptobacteroides sp900767375	77.1132	113	666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 04:21:14,215] [INFO] GTDB search result was written to GCA_017455065.1_ASM1745506v1_genomic.fna/result_gtdb.tsv
[2023-06-28 04:21:14,215] [INFO] ===== GTDB Search completed =====
[2023-06-28 04:21:14,219] [INFO] DFAST_QC result json was written to GCA_017455065.1_ASM1745506v1_genomic.fna/dqc_result.json
[2023-06-28 04:21:14,219] [INFO] DFAST_QC completed!
[2023-06-28 04:21:14,219] [INFO] Total running time: 0h1m12s