[2023-06-27 17:41:05,491] [INFO] DFAST_QC pipeline started.
[2023-06-27 17:41:05,497] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 17:41:05,497] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb2fdbb4-4c2e-464f-814f-a5c64580a3fa/dqc_reference
[2023-06-27 17:41:08,724] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 17:41:08,728] [INFO] Task started: Prodigal
[2023-06-27 17:41:08,730] [INFO] Running command: gunzip -c /var/lib/cwl/stg8fb575e3-5141-4689-9613-01d048d9b79c/GCA_002103035.1_ASM210303v1_genomic.fna.gz | prodigal -d GCA_002103035.1_ASM210303v1_genomic.fna/cds.fna -a GCA_002103035.1_ASM210303v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 17:41:12,243] [INFO] Task succeeded: Prodigal
[2023-06-27 17:41:12,244] [INFO] Task started: HMMsearch
[2023-06-27 17:41:12,244] [INFO] Running command: hmmsearch --tblout GCA_002103035.1_ASM210303v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb2fdbb4-4c2e-464f-814f-a5c64580a3fa/dqc_reference/reference_markers.hmm GCA_002103035.1_ASM210303v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 17:41:12,590] [INFO] Task succeeded: HMMsearch
[2023-06-27 17:41:12,593] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8fb575e3-5141-4689-9613-01d048d9b79c/GCA_002103035.1_ASM210303v1_genomic.fna.gz]
[2023-06-27 17:41:12,641] [INFO] Query marker FASTA was written to GCA_002103035.1_ASM210303v1_genomic.fna/markers.fasta
[2023-06-27 17:41:12,642] [INFO] Task started: Blastn
[2023-06-27 17:41:12,642] [INFO] Running command: blastn -query GCA_002103035.1_ASM210303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb2fdbb4-4c2e-464f-814f-a5c64580a3fa/dqc_reference/reference_markers.fasta -out GCA_002103035.1_ASM210303v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 17:41:13,357] [INFO] Task succeeded: Blastn
[2023-06-27 17:41:13,363] [INFO] Selected 10 target genomes.
[2023-06-27 17:41:13,364] [INFO] Target genome list was writen to GCA_002103035.1_ASM210303v1_genomic.fna/target_genomes.txt
[2023-06-27 17:41:13,368] [INFO] Task started: fastANI
[2023-06-27 17:41:13,368] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fb575e3-5141-4689-9613-01d048d9b79c/GCA_002103035.1_ASM210303v1_genomic.fna.gz --refList GCA_002103035.1_ASM210303v1_genomic.fna/target_genomes.txt --output GCA_002103035.1_ASM210303v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 17:41:19,287] [INFO] Task succeeded: fastANI
[2023-06-27 17:41:19,288] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb2fdbb4-4c2e-464f-814f-a5c64580a3fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 17:41:19,288] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb2fdbb4-4c2e-464f-814f-a5c64580a3fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 17:41:19,290] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 17:41:19,290] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 17:41:19,290] [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
--------------------------------------------------------------------------------
[2023-06-27 17:41:19,292] [INFO] DFAST Taxonomy check result was written to GCA_002103035.1_ASM210303v1_genomic.fna/tc_result.tsv
[2023-06-27 17:41:19,292] [INFO] ===== Taxonomy check completed =====
[2023-06-27 17:41:19,293] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 17:41:19,293] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb2fdbb4-4c2e-464f-814f-a5c64580a3fa/dqc_reference/checkm_data
[2023-06-27 17:41:19,295] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 17:41:19,322] [INFO] Task started: CheckM
[2023-06-27 17:41:19,322] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002103035.1_ASM210303v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002103035.1_ASM210303v1_genomic.fna/checkm_input GCA_002103035.1_ASM210303v1_genomic.fna/checkm_result
[2023-06-27 17:41:37,311] [INFO] Task succeeded: CheckM
[2023-06-27 17:41:37,312] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 17:41:37,344] [INFO] ===== Completeness check finished =====
[2023-06-27 17:41:37,344] [INFO] ===== Start GTDB Search =====
[2023-06-27 17:41:37,345] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002103035.1_ASM210303v1_genomic.fna/markers.fasta)
[2023-06-27 17:41:37,345] [INFO] Task started: Blastn
[2023-06-27 17:41:37,345] [INFO] Running command: blastn -query GCA_002103035.1_ASM210303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb2fdbb4-4c2e-464f-814f-a5c64580a3fa/dqc_reference/reference_markers_gtdb.fasta -out GCA_002103035.1_ASM210303v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 17:41:38,104] [INFO] Task succeeded: Blastn
[2023-06-27 17:41:38,108] [INFO] Selected 18 target genomes.
[2023-06-27 17:41:38,109] [INFO] Target genome list was writen to GCA_002103035.1_ASM210303v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 17:41:38,142] [INFO] Task started: fastANI
[2023-06-27 17:41:38,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fb575e3-5141-4689-9613-01d048d9b79c/GCA_002103035.1_ASM210303v1_genomic.fna.gz --refList GCA_002103035.1_ASM210303v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002103035.1_ASM210303v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 17:41:45,391] [INFO] Task succeeded: fastANI
[2023-06-27 17:41:45,416] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 17:41:45,416] [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_900552525.1	s__CAG-196 sp002102975	98.6052	515	572	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	98.29	97.43	0.85	0.68	20	conclusive
GCA_900549855.1	s__CAG-196 sp900549855	78.7355	245	572	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	99.91	99.91	0.89	0.89	2	-
GCA_910579975.1	s__CAG-196 sp910579975	77.8892	145	572	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553895.1	s__CAG-196 sp900553895	77.8455	194	572	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	99.90	99.90	0.94	0.94	2	-
GCA_900321205.1	s__CAG-196 sp900321205	77.6676	127	572	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	98.88	98.15	0.93	0.87	4	-
GCA_902788575.1	s__CAG-196 sp902788575	77.602	139	572	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902777605.1	s__CAG-196 sp902777605	77.4566	156	572	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015152525.1	s__CAG-196 sp015152525	77.3951	125	572	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797965.1	s__CAG-196 sp902797965	77.3687	151	572	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761225.1	s__Stercorousia sp900761225	77.3404	70	572	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779645.1	s__CAG-196 sp902779645	77.3194	150	572	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902760905.1	s__CAG-196 sp902760905	77.094	120	572	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017629215.1	s__CAG-196 sp017629215	77.0853	112	572	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003150395.1	s__Scatenecus sp003150395	76.8434	71	572	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Scatenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017541565.1	s__CAG-196 sp017541565	76.8341	76	572	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014803505.1	s__Zag111 sp014803505	76.743	64	572	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902794035.1	s__UBA2813 sp902794035	76.407	59	572	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902796585.1	s__CAG-196 sp902796585	76.1319	115	572	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__CAG-196	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 17:41:45,419] [INFO] GTDB search result was written to GCA_002103035.1_ASM210303v1_genomic.fna/result_gtdb.tsv
[2023-06-27 17:41:45,419] [INFO] ===== GTDB Search completed =====
[2023-06-27 17:41:45,423] [INFO] DFAST_QC result json was written to GCA_002103035.1_ASM210303v1_genomic.fna/dqc_result.json
[2023-06-27 17:41:45,423] [INFO] DFAST_QC completed!
[2023-06-27 17:41:45,423] [INFO] Total running time: 0h0m40s