[2023-06-05 03:59:52,364] [INFO] DFAST_QC pipeline started.
[2023-06-05 03:59:52,366] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 03:59:52,366] [INFO] DQC Reference Directory: /var/lib/cwl/stg132733ce-0b8f-4d1a-964a-4d05948a39af/dqc_reference
[2023-06-05 03:59:54,226] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 03:59:54,227] [INFO] Task started: Prodigal
[2023-06-05 03:59:54,227] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8e7608f-38d9-4438-98f6-f48cec121506/GCA_934660855.1_ERR7738582_bin.159_genomic.fna.gz | prodigal -d GCA_934660855.1_ERR7738582_bin.159_genomic.fna/cds.fna -a GCA_934660855.1_ERR7738582_bin.159_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 04:00:00,782] [INFO] Task succeeded: Prodigal
[2023-06-05 04:00:00,783] [INFO] Task started: HMMsearch
[2023-06-05 04:00:00,783] [INFO] Running command: hmmsearch --tblout GCA_934660855.1_ERR7738582_bin.159_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg132733ce-0b8f-4d1a-964a-4d05948a39af/dqc_reference/reference_markers.hmm GCA_934660855.1_ERR7738582_bin.159_genomic.fna/protein.faa > /dev/null
[2023-06-05 04:00:01,009] [INFO] Task succeeded: HMMsearch
[2023-06-05 04:00:01,010] [INFO] Found 6/6 markers.
[2023-06-05 04:00:01,033] [INFO] Query marker FASTA was written to GCA_934660855.1_ERR7738582_bin.159_genomic.fna/markers.fasta
[2023-06-05 04:00:01,034] [INFO] Task started: Blastn
[2023-06-05 04:00:01,034] [INFO] Running command: blastn -query GCA_934660855.1_ERR7738582_bin.159_genomic.fna/markers.fasta -db /var/lib/cwl/stg132733ce-0b8f-4d1a-964a-4d05948a39af/dqc_reference/reference_markers.fasta -out GCA_934660855.1_ERR7738582_bin.159_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:00:01,655] [INFO] Task succeeded: Blastn
[2023-06-05 04:00:01,659] [INFO] Selected 18 target genomes.
[2023-06-05 04:00:01,659] [INFO] Target genome list was writen to GCA_934660855.1_ERR7738582_bin.159_genomic.fna/target_genomes.txt
[2023-06-05 04:00:01,695] [INFO] Task started: fastANI
[2023-06-05 04:00:01,695] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8e7608f-38d9-4438-98f6-f48cec121506/GCA_934660855.1_ERR7738582_bin.159_genomic.fna.gz --refList GCA_934660855.1_ERR7738582_bin.159_genomic.fna/target_genomes.txt --output GCA_934660855.1_ERR7738582_bin.159_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 04:00:13,823] [INFO] Task succeeded: fastANI
[2023-06-05 04:00:13,824] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg132733ce-0b8f-4d1a-964a-4d05948a39af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 04:00:13,824] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg132733ce-0b8f-4d1a-964a-4d05948a39af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 04:00:13,826] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 04:00:13,826] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 04:00:13,827] [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 04:00:13,829] [INFO] DFAST Taxonomy check result was written to GCA_934660855.1_ERR7738582_bin.159_genomic.fna/tc_result.tsv
[2023-06-05 04:00:13,829] [INFO] ===== Taxonomy check completed =====
[2023-06-05 04:00:13,830] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 04:00:13,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg132733ce-0b8f-4d1a-964a-4d05948a39af/dqc_reference/checkm_data
[2023-06-05 04:00:13,834] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 04:00:13,861] [INFO] Task started: CheckM
[2023-06-05 04:00:13,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934660855.1_ERR7738582_bin.159_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934660855.1_ERR7738582_bin.159_genomic.fna/checkm_input GCA_934660855.1_ERR7738582_bin.159_genomic.fna/checkm_result
[2023-06-05 04:00:38,387] [INFO] Task succeeded: CheckM
[2023-06-05 04:00:38,389] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 04:00:38,409] [INFO] ===== Completeness check finished =====
[2023-06-05 04:00:38,409] [INFO] ===== Start GTDB Search =====
[2023-06-05 04:00:38,410] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934660855.1_ERR7738582_bin.159_genomic.fna/markers.fasta)
[2023-06-05 04:00:38,410] [INFO] Task started: Blastn
[2023-06-05 04:00:38,410] [INFO] Running command: blastn -query GCA_934660855.1_ERR7738582_bin.159_genomic.fna/markers.fasta -db /var/lib/cwl/stg132733ce-0b8f-4d1a-964a-4d05948a39af/dqc_reference/reference_markers_gtdb.fasta -out GCA_934660855.1_ERR7738582_bin.159_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:00:39,293] [INFO] Task succeeded: Blastn
[2023-06-05 04:00:39,298] [INFO] Selected 12 target genomes.
[2023-06-05 04:00:39,298] [INFO] Target genome list was writen to GCA_934660855.1_ERR7738582_bin.159_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 04:00:39,307] [INFO] Task started: fastANI
[2023-06-05 04:00:39,307] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8e7608f-38d9-4438-98f6-f48cec121506/GCA_934660855.1_ERR7738582_bin.159_genomic.fna.gz --refList GCA_934660855.1_ERR7738582_bin.159_genomic.fna/target_genomes_gtdb.txt --output GCA_934660855.1_ERR7738582_bin.159_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 04:00:44,425] [INFO] Task succeeded: fastANI
[2023-06-05 04:00:44,439] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 04:00:44,439] [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_002405555.1	s__Merdousia sp002405555	95.2452	527	761	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__CAG-312;g__Merdousia	95.0	95.22	95.22	0.80	0.80	2	conclusive
GCA_900548275.1	s__Merdousia sp900548275	82.5219	502	761	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__CAG-312;g__Merdousia	95.0	98.47	98.47	0.89	0.89	2	-
GCA_002437405.1	s__Merdousia sp002437405	78.9366	252	761	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__CAG-312;g__Merdousia	95.0	98.41	95.60	0.92	0.87	4	-
GCA_900760055.1	s__Merdousia sp900760055	78.8201	332	761	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__CAG-312;g__Merdousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546565.1	s__Merdousia sp900546565	78.1837	202	761	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__CAG-312;g__Merdousia	95.0	98.09	98.09	0.92	0.92	2	-
GCA_904424815.1	s__Merdousia sp001917305	77.7133	224	761	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__CAG-312;g__Merdousia	95.0	98.91	98.75	0.96	0.93	5	-
GCA_905214995.1	s__Merdousia sp905214995	77.4317	176	761	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__CAG-312;g__Merdousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760665.1	s__Merdousia sp900760665	77.4228	204	761	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__CAG-312;g__Merdousia	95.0	97.95	97.87	0.94	0.93	3	-
GCA_015061945.1	s__Merdousia sp015061945	76.9503	59	761	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__CAG-312;g__Merdousia	95.0	98.70	98.70	0.95	0.95	2	-
GCA_003343565.1	s__QALA01 sp003343565	76.4425	116	761	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__CAG-312;g__QALA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 04:00:44,441] [INFO] GTDB search result was written to GCA_934660855.1_ERR7738582_bin.159_genomic.fna/result_gtdb.tsv
[2023-06-05 04:00:44,442] [INFO] ===== GTDB Search completed =====
[2023-06-05 04:00:44,444] [INFO] DFAST_QC result json was written to GCA_934660855.1_ERR7738582_bin.159_genomic.fna/dqc_result.json
[2023-06-05 04:00:44,445] [INFO] DFAST_QC completed!
[2023-06-05 04:00:44,445] [INFO] Total running time: 0h0m52s