[2023-06-05 00:30:29,298] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:30:29,324] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:30:29,324] [INFO] DQC Reference Directory: /var/lib/cwl/stg86c8df58-5876-476d-9c95-44793eeab71e/dqc_reference
[2023-06-05 00:30:30,573] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:30:30,574] [INFO] Task started: Prodigal
[2023-06-05 00:30:30,574] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6490a86-f7a4-4c0c-a23a-2c50f590fde6/GCA_934643645.1_ERR7745963_bin.163_genomic.fna.gz | prodigal -d GCA_934643645.1_ERR7745963_bin.163_genomic.fna/cds.fna -a GCA_934643645.1_ERR7745963_bin.163_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:30:38,084] [INFO] Task succeeded: Prodigal
[2023-06-05 00:30:38,084] [INFO] Task started: HMMsearch
[2023-06-05 00:30:38,084] [INFO] Running command: hmmsearch --tblout GCA_934643645.1_ERR7745963_bin.163_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86c8df58-5876-476d-9c95-44793eeab71e/dqc_reference/reference_markers.hmm GCA_934643645.1_ERR7745963_bin.163_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:30:38,357] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:30:38,358] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc6490a86-f7a4-4c0c-a23a-2c50f590fde6/GCA_934643645.1_ERR7745963_bin.163_genomic.fna.gz]
[2023-06-05 00:30:38,384] [INFO] Query marker FASTA was written to GCA_934643645.1_ERR7745963_bin.163_genomic.fna/markers.fasta
[2023-06-05 00:30:38,385] [INFO] Task started: Blastn
[2023-06-05 00:30:38,385] [INFO] Running command: blastn -query GCA_934643645.1_ERR7745963_bin.163_genomic.fna/markers.fasta -db /var/lib/cwl/stg86c8df58-5876-476d-9c95-44793eeab71e/dqc_reference/reference_markers.fasta -out GCA_934643645.1_ERR7745963_bin.163_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:30:39,026] [INFO] Task succeeded: Blastn
[2023-06-05 00:30:39,030] [INFO] Selected 23 target genomes.
[2023-06-05 00:30:39,030] [INFO] Target genome list was writen to GCA_934643645.1_ERR7745963_bin.163_genomic.fna/target_genomes.txt
[2023-06-05 00:30:39,034] [INFO] Task started: fastANI
[2023-06-05 00:30:39,034] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6490a86-f7a4-4c0c-a23a-2c50f590fde6/GCA_934643645.1_ERR7745963_bin.163_genomic.fna.gz --refList GCA_934643645.1_ERR7745963_bin.163_genomic.fna/target_genomes.txt --output GCA_934643645.1_ERR7745963_bin.163_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:30:53,883] [INFO] Task succeeded: fastANI
[2023-06-05 00:30:53,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86c8df58-5876-476d-9c95-44793eeab71e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:30:53,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86c8df58-5876-476d-9c95-44793eeab71e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:30:53,889] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:30:53,889] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 00:30:53,889] [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 coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.4409	82	870	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	76.6692	76	870	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	75.6536	64	870	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 00:30:53,896] [INFO] DFAST Taxonomy check result was written to GCA_934643645.1_ERR7745963_bin.163_genomic.fna/tc_result.tsv
[2023-06-05 00:30:53,898] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:30:53,898] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:30:53,899] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86c8df58-5876-476d-9c95-44793eeab71e/dqc_reference/checkm_data
[2023-06-05 00:30:53,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:30:53,940] [INFO] Task started: CheckM
[2023-06-05 00:30:53,940] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934643645.1_ERR7745963_bin.163_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934643645.1_ERR7745963_bin.163_genomic.fna/checkm_input GCA_934643645.1_ERR7745963_bin.163_genomic.fna/checkm_result
[2023-06-05 00:31:21,583] [INFO] Task succeeded: CheckM
[2023-06-05 00:31:21,584] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:31:21,606] [INFO] ===== Completeness check finished =====
[2023-06-05 00:31:21,606] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:31:21,607] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934643645.1_ERR7745963_bin.163_genomic.fna/markers.fasta)
[2023-06-05 00:31:21,607] [INFO] Task started: Blastn
[2023-06-05 00:31:21,607] [INFO] Running command: blastn -query GCA_934643645.1_ERR7745963_bin.163_genomic.fna/markers.fasta -db /var/lib/cwl/stg86c8df58-5876-476d-9c95-44793eeab71e/dqc_reference/reference_markers_gtdb.fasta -out GCA_934643645.1_ERR7745963_bin.163_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:31:22,705] [INFO] Task succeeded: Blastn
[2023-06-05 00:31:22,709] [INFO] Selected 9 target genomes.
[2023-06-05 00:31:22,710] [INFO] Target genome list was writen to GCA_934643645.1_ERR7745963_bin.163_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:31:22,712] [INFO] Task started: fastANI
[2023-06-05 00:31:22,712] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6490a86-f7a4-4c0c-a23a-2c50f590fde6/GCA_934643645.1_ERR7745963_bin.163_genomic.fna.gz --refList GCA_934643645.1_ERR7745963_bin.163_genomic.fna/target_genomes_gtdb.txt --output GCA_934643645.1_ERR7745963_bin.163_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:31:27,908] [INFO] Task succeeded: fastANI
[2023-06-05 00:31:27,917] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 00:31:27,918] [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_900751035.1	s__CAG-170 sp900751035	97.5509	472	870	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000432135.1	s__CAG-170 sp000432135	91.844	563	870	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	98.47	98.15	0.85	0.82	4	-
GCA_902796245.1	s__CAG-170 sp902796245	89.123	411	870	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545925.1	s__CAG-170 sp900545925	88.4898	608	870	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	98.27	97.70	0.79	0.64	4	-
GCA_002404795.1	s__CAG-170 sp002404795	84.8446	406	870	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	95.77	95.28	0.76	0.71	13	-
GCA_900548625.1	s__CAG-170 sp900548625	80.4563	285	870	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	99.06	98.12	0.91	0.84	3	-
GCA_002437575.1	s__CAG-170 sp002437575	79.8483	242	870	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549635.1	s__CAG-170 sp900549635	79.4698	235	870	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	97.02	95.99	0.80	0.73	4	-
GCA_902803075.1	s__CAG-170 sp902803075	79.0237	208	870	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 00:31:27,920] [INFO] GTDB search result was written to GCA_934643645.1_ERR7745963_bin.163_genomic.fna/result_gtdb.tsv
[2023-06-05 00:31:27,920] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:31:27,923] [INFO] DFAST_QC result json was written to GCA_934643645.1_ERR7745963_bin.163_genomic.fna/dqc_result.json
[2023-06-05 00:31:27,924] [INFO] DFAST_QC completed!
[2023-06-05 00:31:27,924] [INFO] Total running time: 0h0m59s