[2023-06-16 22:13:53,035] [INFO] DFAST_QC pipeline started.
[2023-06-16 22:13:53,039] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 22:13:53,039] [INFO] DQC Reference Directory: /var/lib/cwl/stg7211e1ee-91fd-4eee-9fbd-5f1d7782b92f/dqc_reference
[2023-06-16 22:13:54,441] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 22:13:54,442] [INFO] Task started: Prodigal
[2023-06-16 22:13:54,442] [INFO] Running command: gunzip -c /var/lib/cwl/stg65a4f702-88fd-446a-8cff-4a6b1af5940f/GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna.gz | prodigal -d GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna/cds.fna -a GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 22:13:57,534] [INFO] Task succeeded: Prodigal
[2023-06-16 22:13:57,535] [INFO] Task started: HMMsearch
[2023-06-16 22:13:57,535] [INFO] Running command: hmmsearch --tblout GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7211e1ee-91fd-4eee-9fbd-5f1d7782b92f/dqc_reference/reference_markers.hmm GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna/protein.faa > /dev/null
[2023-06-16 22:13:57,745] [INFO] Task succeeded: HMMsearch
[2023-06-16 22:13:57,747] [INFO] Found 6/6 markers.
[2023-06-16 22:13:57,766] [INFO] Query marker FASTA was written to GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna/markers.fasta
[2023-06-16 22:13:57,766] [INFO] Task started: Blastn
[2023-06-16 22:13:57,766] [INFO] Running command: blastn -query GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna/markers.fasta -db /var/lib/cwl/stg7211e1ee-91fd-4eee-9fbd-5f1d7782b92f/dqc_reference/reference_markers.fasta -out GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:13:58,412] [INFO] Task succeeded: Blastn
[2023-06-16 22:13:58,417] [INFO] Selected 21 target genomes.
[2023-06-16 22:13:58,417] [INFO] Target genome list was writen to GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna/target_genomes.txt
[2023-06-16 22:13:58,429] [INFO] Task started: fastANI
[2023-06-16 22:13:58,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg65a4f702-88fd-446a-8cff-4a6b1af5940f/GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna.gz --refList GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna/target_genomes.txt --output GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 22:14:09,501] [INFO] Task succeeded: fastANI
[2023-06-16 22:14:09,501] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7211e1ee-91fd-4eee-9fbd-5f1d7782b92f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 22:14:09,501] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7211e1ee-91fd-4eee-9fbd-5f1d7782b92f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 22:14:09,503] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 22:14:09,503] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 22:14:09,503] [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
--------------------------------------------------------------------------------
[2023-06-16 22:14:09,505] [INFO] DFAST Taxonomy check result was written to GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna/tc_result.tsv
[2023-06-16 22:14:09,506] [INFO] ===== Taxonomy check completed =====
[2023-06-16 22:14:09,506] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 22:14:09,507] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7211e1ee-91fd-4eee-9fbd-5f1d7782b92f/dqc_reference/checkm_data
[2023-06-16 22:14:09,509] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 22:14:09,532] [INFO] Task started: CheckM
[2023-06-16 22:14:09,532] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna/checkm_input GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna/checkm_result
[2023-06-16 22:14:28,725] [INFO] Task succeeded: CheckM
[2023-06-16 22:14:28,726] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 5.09%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 22:14:28,747] [INFO] ===== Completeness check finished =====
[2023-06-16 22:14:28,748] [INFO] ===== Start GTDB Search =====
[2023-06-16 22:14:28,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna/markers.fasta)
[2023-06-16 22:14:28,748] [INFO] Task started: Blastn
[2023-06-16 22:14:28,749] [INFO] Running command: blastn -query GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna/markers.fasta -db /var/lib/cwl/stg7211e1ee-91fd-4eee-9fbd-5f1d7782b92f/dqc_reference/reference_markers_gtdb.fasta -out GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:14:29,556] [INFO] Task succeeded: Blastn
[2023-06-16 22:14:29,560] [INFO] Selected 12 target genomes.
[2023-06-16 22:14:29,560] [INFO] Target genome list was writen to GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 22:14:29,572] [INFO] Task started: fastANI
[2023-06-16 22:14:29,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg65a4f702-88fd-446a-8cff-4a6b1af5940f/GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna.gz --refList GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna/target_genomes_gtdb.txt --output GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 22:14:34,024] [INFO] Task succeeded: fastANI
[2023-06-16 22:14:34,040] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 22:14:34,040] [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_003258735.1	s__Zag111 sp003258735	98.3105	336	356	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	98.31	98.12	0.91	0.82	5	conclusive
GCA_002405805.1	s__Zag111 sp002405805	89.7999	319	356	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002438405.1	s__Zag111 sp002438405	79.6092	225	356	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	99.96	99.93	0.99	0.98	3	-
GCA_002102825.1	s__Zag111 sp002102825	79.5335	215	356	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	99.43	98.83	0.94	0.90	9	-
GCA_002103105.1	s__Zag111 sp002103105	79.512	208	356	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	97.50	95.26	0.92	0.84	7	-
GCA_017626055.1	s__Zag111 sp017626055	79.2811	181	356	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017536545.1	s__Zag111 sp017536545	79.1569	183	356	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551965.1	s__Zag111 sp900551965	79.1566	179	356	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584405.1	s__Zag111 sp910584405	79.0872	173	356	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905211505.1	s__Zag111 sp905211505	78.5406	78	356	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017472545.1	s__Zag111 sp017472545	78.3539	143	356	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004558955.1	s__Zag111 sp004558955	77.9793	147	356	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	98.49	98.49	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2023-06-16 22:14:34,042] [INFO] GTDB search result was written to GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna/result_gtdb.tsv
[2023-06-16 22:14:34,043] [INFO] ===== GTDB Search completed =====
[2023-06-16 22:14:34,046] [INFO] DFAST_QC result json was written to GCA_905207095.1_ERR321203-mag-bin.12_genomic.fna/dqc_result.json
[2023-06-16 22:14:34,046] [INFO] DFAST_QC completed!
[2023-06-16 22:14:34,046] [INFO] Total running time: 0h0m41s