[2023-06-05 18:37:30,242] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:37:30,245] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:37:30,245] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ddb17ed-c6fb-4beb-aca7-6857ddd8e1cb/dqc_reference
[2023-06-05 18:37:32,070] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:37:32,071] [INFO] Task started: Prodigal
[2023-06-05 18:37:32,071] [INFO] Running command: gunzip -c /var/lib/cwl/stg1cc0335b-a8d5-4186-bd37-c9808910998b/GCA_934699035.1_ERR7746465_bin.138_genomic.fna.gz | prodigal -d GCA_934699035.1_ERR7746465_bin.138_genomic.fna/cds.fna -a GCA_934699035.1_ERR7746465_bin.138_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:37:46,700] [INFO] Task succeeded: Prodigal
[2023-06-05 18:37:46,700] [INFO] Task started: HMMsearch
[2023-06-05 18:37:46,700] [INFO] Running command: hmmsearch --tblout GCA_934699035.1_ERR7746465_bin.138_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ddb17ed-c6fb-4beb-aca7-6857ddd8e1cb/dqc_reference/reference_markers.hmm GCA_934699035.1_ERR7746465_bin.138_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:37:46,909] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:37:46,911] [INFO] Found 6/6 markers.
[2023-06-05 18:37:46,963] [INFO] Query marker FASTA was written to GCA_934699035.1_ERR7746465_bin.138_genomic.fna/markers.fasta
[2023-06-05 18:37:46,963] [INFO] Task started: Blastn
[2023-06-05 18:37:46,963] [INFO] Running command: blastn -query GCA_934699035.1_ERR7746465_bin.138_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ddb17ed-c6fb-4beb-aca7-6857ddd8e1cb/dqc_reference/reference_markers.fasta -out GCA_934699035.1_ERR7746465_bin.138_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:37:47,569] [INFO] Task succeeded: Blastn
[2023-06-05 18:37:47,573] [INFO] Selected 24 target genomes.
[2023-06-05 18:37:47,574] [INFO] Target genome list was writen to GCA_934699035.1_ERR7746465_bin.138_genomic.fna/target_genomes.txt
[2023-06-05 18:37:47,577] [INFO] Task started: fastANI
[2023-06-05 18:37:47,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cc0335b-a8d5-4186-bd37-c9808910998b/GCA_934699035.1_ERR7746465_bin.138_genomic.fna.gz --refList GCA_934699035.1_ERR7746465_bin.138_genomic.fna/target_genomes.txt --output GCA_934699035.1_ERR7746465_bin.138_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:38:11,817] [INFO] Task succeeded: fastANI
[2023-06-05 18:38:11,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ddb17ed-c6fb-4beb-aca7-6857ddd8e1cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:38:11,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ddb17ed-c6fb-4beb-aca7-6857ddd8e1cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:38:11,821] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:38:11,821] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:38:11,821] [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 18:38:11,824] [INFO] DFAST Taxonomy check result was written to GCA_934699035.1_ERR7746465_bin.138_genomic.fna/tc_result.tsv
[2023-06-05 18:38:11,825] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:38:11,825] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:38:11,825] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ddb17ed-c6fb-4beb-aca7-6857ddd8e1cb/dqc_reference/checkm_data
[2023-06-05 18:38:11,828] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:38:11,852] [INFO] Task started: CheckM
[2023-06-05 18:38:11,853] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934699035.1_ERR7746465_bin.138_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934699035.1_ERR7746465_bin.138_genomic.fna/checkm_input GCA_934699035.1_ERR7746465_bin.138_genomic.fna/checkm_result
[2023-06-05 18:38:55,750] [INFO] Task succeeded: CheckM
[2023-06-05 18:38:55,751] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:38:55,769] [INFO] ===== Completeness check finished =====
[2023-06-05 18:38:55,769] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:38:55,769] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934699035.1_ERR7746465_bin.138_genomic.fna/markers.fasta)
[2023-06-05 18:38:55,769] [INFO] Task started: Blastn
[2023-06-05 18:38:55,769] [INFO] Running command: blastn -query GCA_934699035.1_ERR7746465_bin.138_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ddb17ed-c6fb-4beb-aca7-6857ddd8e1cb/dqc_reference/reference_markers_gtdb.fasta -out GCA_934699035.1_ERR7746465_bin.138_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:38:56,487] [INFO] Task succeeded: Blastn
[2023-06-05 18:38:56,491] [INFO] Selected 19 target genomes.
[2023-06-05 18:38:56,491] [INFO] Target genome list was writen to GCA_934699035.1_ERR7746465_bin.138_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:38:56,495] [INFO] Task started: fastANI
[2023-06-05 18:38:56,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cc0335b-a8d5-4186-bd37-c9808910998b/GCA_934699035.1_ERR7746465_bin.138_genomic.fna.gz --refList GCA_934699035.1_ERR7746465_bin.138_genomic.fna/target_genomes_gtdb.txt --output GCA_934699035.1_ERR7746465_bin.138_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:39:03,299] [INFO] Task succeeded: fastANI
[2023-06-05 18:39:03,307] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:39:03,307] [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_900546465.1	s__Onthomorpha sp900546465	97.804	479	712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__Onthomorpha	95.0	98.11	98.11	0.81	0.81	2	conclusive
GCA_900545215.1	s__Onthomorpha sp900545215	88.6652	549	712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__Onthomorpha	95.0	98.29	98.29	0.90	0.90	2	-
GCA_016296345.1	s__Onthomorpha sp016296345	77.7695	192	712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__Onthomorpha	95.0	97.30	97.30	0.84	0.84	2	-
GCA_004551865.1	s__Onthomorpha sp004551865	77.5989	212	712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__Onthomorpha	95.0	98.58	98.00	0.85	0.80	9	-
GCA_002358835.1	s__Onthomorpha sp002358835	77.183	100	712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__Onthomorpha	95.0	97.28	97.00	0.78	0.66	8	-
GCA_019114015.1	s__Onthomorpha intestinigallinarum	76.4715	52	712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__Onthomorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002358855.1	s__Onthomorpha sp002358855	76.4601	57	712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__Onthomorpha	95.0	96.75	96.51	0.86	0.83	6	-
--------------------------------------------------------------------------------
[2023-06-05 18:39:03,309] [INFO] GTDB search result was written to GCA_934699035.1_ERR7746465_bin.138_genomic.fna/result_gtdb.tsv
[2023-06-05 18:39:03,309] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:39:03,312] [INFO] DFAST_QC result json was written to GCA_934699035.1_ERR7746465_bin.138_genomic.fna/dqc_result.json
[2023-06-05 18:39:03,312] [INFO] DFAST_QC completed!
[2023-06-05 18:39:03,312] [INFO] Total running time: 0h1m33s