[2023-06-08 00:35:09,265] [INFO] DFAST_QC pipeline started.
[2023-06-08 00:35:09,271] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 00:35:09,271] [INFO] DQC Reference Directory: /var/lib/cwl/stg0296fa1c-e07d-4eb0-886d-17bcbc18b08a/dqc_reference
[2023-06-08 00:35:10,758] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 00:35:10,759] [INFO] Task started: Prodigal
[2023-06-08 00:35:10,759] [INFO] Running command: gunzip -c /var/lib/cwl/stg47c52f77-fcba-4fdb-afc5-58172d89b1cc/GCA_945861045.1_AE-03may19-191_genomic.fna.gz | prodigal -d GCA_945861045.1_AE-03may19-191_genomic.fna/cds.fna -a GCA_945861045.1_AE-03may19-191_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 00:35:22,242] [INFO] Task succeeded: Prodigal
[2023-06-08 00:35:22,242] [INFO] Task started: HMMsearch
[2023-06-08 00:35:22,243] [INFO] Running command: hmmsearch --tblout GCA_945861045.1_AE-03may19-191_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0296fa1c-e07d-4eb0-886d-17bcbc18b08a/dqc_reference/reference_markers.hmm GCA_945861045.1_AE-03may19-191_genomic.fna/protein.faa > /dev/null
[2023-06-08 00:35:22,480] [INFO] Task succeeded: HMMsearch
[2023-06-08 00:35:22,481] [INFO] Found 6/6 markers.
[2023-06-08 00:35:22,503] [INFO] Query marker FASTA was written to GCA_945861045.1_AE-03may19-191_genomic.fna/markers.fasta
[2023-06-08 00:35:22,503] [INFO] Task started: Blastn
[2023-06-08 00:35:22,503] [INFO] Running command: blastn -query GCA_945861045.1_AE-03may19-191_genomic.fna/markers.fasta -db /var/lib/cwl/stg0296fa1c-e07d-4eb0-886d-17bcbc18b08a/dqc_reference/reference_markers.fasta -out GCA_945861045.1_AE-03may19-191_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:35:23,119] [INFO] Task succeeded: Blastn
[2023-06-08 00:35:23,122] [INFO] Selected 25 target genomes.
[2023-06-08 00:35:23,123] [INFO] Target genome list was writen to GCA_945861045.1_AE-03may19-191_genomic.fna/target_genomes.txt
[2023-06-08 00:35:23,127] [INFO] Task started: fastANI
[2023-06-08 00:35:23,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg47c52f77-fcba-4fdb-afc5-58172d89b1cc/GCA_945861045.1_AE-03may19-191_genomic.fna.gz --refList GCA_945861045.1_AE-03may19-191_genomic.fna/target_genomes.txt --output GCA_945861045.1_AE-03may19-191_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 00:35:39,292] [INFO] Task succeeded: fastANI
[2023-06-08 00:35:39,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0296fa1c-e07d-4eb0-886d-17bcbc18b08a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 00:35:39,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0296fa1c-e07d-4eb0-886d-17bcbc18b08a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 00:35:39,295] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 00:35:39,295] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 00:35:39,295] [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
--------------------------------------------------------------------------------
[2023-06-08 00:35:39,297] [INFO] DFAST Taxonomy check result was written to GCA_945861045.1_AE-03may19-191_genomic.fna/tc_result.tsv
[2023-06-08 00:35:39,298] [INFO] ===== Taxonomy check completed =====
[2023-06-08 00:35:39,299] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 00:35:39,299] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0296fa1c-e07d-4eb0-886d-17bcbc18b08a/dqc_reference/checkm_data
[2023-06-08 00:35:39,302] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 00:35:39,326] [INFO] Task started: CheckM
[2023-06-08 00:35:39,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945861045.1_AE-03may19-191_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945861045.1_AE-03may19-191_genomic.fna/checkm_input GCA_945861045.1_AE-03may19-191_genomic.fna/checkm_result
[2023-06-08 00:36:15,356] [INFO] Task succeeded: CheckM
[2023-06-08 00:36:15,357] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.90%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2023-06-08 00:36:15,381] [INFO] ===== Completeness check finished =====
[2023-06-08 00:36:15,381] [INFO] ===== Start GTDB Search =====
[2023-06-08 00:36:15,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945861045.1_AE-03may19-191_genomic.fna/markers.fasta)
[2023-06-08 00:36:15,382] [INFO] Task started: Blastn
[2023-06-08 00:36:15,382] [INFO] Running command: blastn -query GCA_945861045.1_AE-03may19-191_genomic.fna/markers.fasta -db /var/lib/cwl/stg0296fa1c-e07d-4eb0-886d-17bcbc18b08a/dqc_reference/reference_markers_gtdb.fasta -out GCA_945861045.1_AE-03may19-191_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:36:16,259] [INFO] Task succeeded: Blastn
[2023-06-08 00:36:16,270] [INFO] Selected 9 target genomes.
[2023-06-08 00:36:16,271] [INFO] Target genome list was writen to GCA_945861045.1_AE-03may19-191_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 00:36:16,277] [INFO] Task started: fastANI
[2023-06-08 00:36:16,277] [INFO] Running command: fastANI --query /var/lib/cwl/stg47c52f77-fcba-4fdb-afc5-58172d89b1cc/GCA_945861045.1_AE-03may19-191_genomic.fna.gz --refList GCA_945861045.1_AE-03may19-191_genomic.fna/target_genomes_gtdb.txt --output GCA_945861045.1_AE-03may19-191_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 00:36:20,577] [INFO] Task succeeded: fastANI
[2023-06-08 00:36:20,589] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 00:36:20,590] [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_903895475.1	s__UBA953 sp903895475	94.9731	455	632	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	97.79	97.63	0.79	0.78	5	-
GCA_903924185.1	s__UBA953 sp903924185	93.1041	359	632	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.29	99.29	0.85	0.85	2	-
GCA_003569205.1	s__UBA953 sp003569205	92.891	556	632	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919185.1	s__UBA953 sp903919185	91.9878	496	632	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.87	99.74	0.94	0.93	4	-
GCA_002293065.1	s__UBA953 sp002293065	85.7003	493	632	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	97.98	96.04	0.82	0.76	4	-
GCA_903925205.1	s__UBA953 sp903925205	85.3856	473	632	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009924965.1	s__UBA953 sp009924965	82.7707	294	632	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003569245.1	s__UBA953 sp003569245	79.9918	324	632	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903853185.1	s__UBA953 sp903853185	79.7091	181	632	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	98.54	98.54	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2023-06-08 00:36:20,591] [INFO] GTDB search result was written to GCA_945861045.1_AE-03may19-191_genomic.fna/result_gtdb.tsv
[2023-06-08 00:36:20,592] [INFO] ===== GTDB Search completed =====
[2023-06-08 00:36:20,594] [INFO] DFAST_QC result json was written to GCA_945861045.1_AE-03may19-191_genomic.fna/dqc_result.json
[2023-06-08 00:36:20,595] [INFO] DFAST_QC completed!
[2023-06-08 00:36:20,595] [INFO] Total running time: 0h1m11s