[2023-06-18 22:25:10,939] [INFO] DFAST_QC pipeline started.
[2023-06-18 22:25:10,942] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 22:25:10,942] [INFO] DQC Reference Directory: /var/lib/cwl/stg0baf0134-1ba2-4112-a87b-7ab58b0a3a95/dqc_reference
[2023-06-18 22:25:14,799] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 22:25:14,803] [INFO] Task started: Prodigal
[2023-06-18 22:25:14,804] [INFO] Running command: gunzip -c /var/lib/cwl/stg01ff4b73-1ada-42a3-b59c-73e467ce30de/GCA_014846375.1_ASM1484637v1_genomic.fna.gz | prodigal -d GCA_014846375.1_ASM1484637v1_genomic.fna/cds.fna -a GCA_014846375.1_ASM1484637v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 22:25:17,148] [INFO] Task succeeded: Prodigal
[2023-06-18 22:25:17,149] [INFO] Task started: HMMsearch
[2023-06-18 22:25:17,149] [INFO] Running command: hmmsearch --tblout GCA_014846375.1_ASM1484637v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0baf0134-1ba2-4112-a87b-7ab58b0a3a95/dqc_reference/reference_markers.hmm GCA_014846375.1_ASM1484637v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 22:25:17,356] [INFO] Task succeeded: HMMsearch
[2023-06-18 22:25:17,357] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg01ff4b73-1ada-42a3-b59c-73e467ce30de/GCA_014846375.1_ASM1484637v1_genomic.fna.gz]
[2023-06-18 22:25:17,380] [INFO] Query marker FASTA was written to GCA_014846375.1_ASM1484637v1_genomic.fna/markers.fasta
[2023-06-18 22:25:17,381] [INFO] Task started: Blastn
[2023-06-18 22:25:17,381] [INFO] Running command: blastn -query GCA_014846375.1_ASM1484637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0baf0134-1ba2-4112-a87b-7ab58b0a3a95/dqc_reference/reference_markers.fasta -out GCA_014846375.1_ASM1484637v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:25:18,820] [INFO] Task succeeded: Blastn
[2023-06-18 22:25:18,825] [INFO] Selected 14 target genomes.
[2023-06-18 22:25:18,826] [INFO] Target genome list was writen to GCA_014846375.1_ASM1484637v1_genomic.fna/target_genomes.txt
[2023-06-18 22:25:18,827] [INFO] Task started: fastANI
[2023-06-18 22:25:18,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg01ff4b73-1ada-42a3-b59c-73e467ce30de/GCA_014846375.1_ASM1484637v1_genomic.fna.gz --refList GCA_014846375.1_ASM1484637v1_genomic.fna/target_genomes.txt --output GCA_014846375.1_ASM1484637v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 22:25:26,296] [INFO] Task succeeded: fastANI
[2023-06-18 22:25:26,297] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0baf0134-1ba2-4112-a87b-7ab58b0a3a95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 22:25:26,297] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0baf0134-1ba2-4112-a87b-7ab58b0a3a95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 22:25:26,305] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 22:25:26,305] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 22:25:26,305] [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
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	85.2327	188	240	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	79.139	116	240	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.5661	68	240	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.4189	60	240	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 22:25:26,307] [INFO] DFAST Taxonomy check result was written to GCA_014846375.1_ASM1484637v1_genomic.fna/tc_result.tsv
[2023-06-18 22:25:26,318] [INFO] ===== Taxonomy check completed =====
[2023-06-18 22:25:26,318] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 22:25:26,319] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0baf0134-1ba2-4112-a87b-7ab58b0a3a95/dqc_reference/checkm_data
[2023-06-18 22:25:26,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 22:25:26,341] [INFO] Task started: CheckM
[2023-06-18 22:25:26,341] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014846375.1_ASM1484637v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014846375.1_ASM1484637v1_genomic.fna/checkm_input GCA_014846375.1_ASM1484637v1_genomic.fna/checkm_result
[2023-06-18 22:25:41,381] [INFO] Task succeeded: CheckM
[2023-06-18 22:25:41,382] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 22:25:41,416] [INFO] ===== Completeness check finished =====
[2023-06-18 22:25:41,416] [INFO] ===== Start GTDB Search =====
[2023-06-18 22:25:41,417] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014846375.1_ASM1484637v1_genomic.fna/markers.fasta)
[2023-06-18 22:25:41,417] [INFO] Task started: Blastn
[2023-06-18 22:25:41,418] [INFO] Running command: blastn -query GCA_014846375.1_ASM1484637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0baf0134-1ba2-4112-a87b-7ab58b0a3a95/dqc_reference/reference_markers_gtdb.fasta -out GCA_014846375.1_ASM1484637v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:25:42,252] [INFO] Task succeeded: Blastn
[2023-06-18 22:25:42,260] [INFO] Selected 9 target genomes.
[2023-06-18 22:25:42,260] [INFO] Target genome list was writen to GCA_014846375.1_ASM1484637v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 22:25:42,262] [INFO] Task started: fastANI
[2023-06-18 22:25:42,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg01ff4b73-1ada-42a3-b59c-73e467ce30de/GCA_014846375.1_ASM1484637v1_genomic.fna.gz --refList GCA_014846375.1_ASM1484637v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014846375.1_ASM1484637v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 22:25:45,588] [INFO] Task succeeded: fastANI
[2023-06-18 22:25:45,597] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 22:25:45,598] [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_003539495.1	s__CAG-83 sp003539495	98.2864	236	240	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.87	97.47	0.86	0.82	8	conclusive
GCA_902388735.1	s__CAG-83 sp902388735	89.6864	193	240	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.86	98.86	0.87	0.87	2	-
GCF_018326305.1	s__CAG-83 sp900549395	85.2327	188	240	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.26	97.06	0.85	0.74	6	-
GCA_900550615.1	s__CAG-83 sp900550615	85.1022	166	240	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.53	97.53	0.77	0.77	2	-
GCA_900313295.1	s__CAG-83 sp900313295	83.0132	151	240	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.79	96.38	0.88	0.79	5	-
GCA_004557655.1	s__CAG-83 sp004557655	82.5385	162	240	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018228685.1	s__CAG-83 sp001916855	80.0782	133	240	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	96.79	95.43	0.86	0.74	11	-
GCA_900554275.1	s__CAG-83 sp900554275	79.2615	98	240	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.46	96.91	0.80	0.75	4	-
--------------------------------------------------------------------------------
[2023-06-18 22:25:45,600] [INFO] GTDB search result was written to GCA_014846375.1_ASM1484637v1_genomic.fna/result_gtdb.tsv
[2023-06-18 22:25:45,600] [INFO] ===== GTDB Search completed =====
[2023-06-18 22:25:45,604] [INFO] DFAST_QC result json was written to GCA_014846375.1_ASM1484637v1_genomic.fna/dqc_result.json
[2023-06-18 22:25:45,604] [INFO] DFAST_QC completed!
[2023-06-18 22:25:45,605] [INFO] Total running time: 0h0m35s