[2023-06-17 12:24:50,835] [INFO] DFAST_QC pipeline started.
[2023-06-17 12:24:50,842] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 12:24:50,842] [INFO] DQC Reference Directory: /var/lib/cwl/stg56ca8839-dfa8-4f26-9108-a70a4d8056ac/dqc_reference
[2023-06-17 12:24:52,604] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 12:24:52,605] [INFO] Task started: Prodigal
[2023-06-17 12:24:52,605] [INFO] Running command: gunzip -c /var/lib/cwl/stg37082a77-bf9a-417c-ab0e-a9594af3836e/GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna.gz | prodigal -d GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna/cds.fna -a GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 12:24:55,629] [INFO] Task succeeded: Prodigal
[2023-06-17 12:24:55,629] [INFO] Task started: HMMsearch
[2023-06-17 12:24:55,629] [INFO] Running command: hmmsearch --tblout GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56ca8839-dfa8-4f26-9108-a70a4d8056ac/dqc_reference/reference_markers.hmm GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna/protein.faa > /dev/null
[2023-06-17 12:24:55,882] [INFO] Task succeeded: HMMsearch
[2023-06-17 12:24:55,884] [INFO] Found 6/6 markers.
[2023-06-17 12:24:55,914] [INFO] Query marker FASTA was written to GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna/markers.fasta
[2023-06-17 12:24:55,914] [INFO] Task started: Blastn
[2023-06-17 12:24:55,914] [INFO] Running command: blastn -query GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna/markers.fasta -db /var/lib/cwl/stg56ca8839-dfa8-4f26-9108-a70a4d8056ac/dqc_reference/reference_markers.fasta -out GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:24:56,644] [INFO] Task succeeded: Blastn
[2023-06-17 12:24:56,655] [INFO] Selected 26 target genomes.
[2023-06-17 12:24:56,656] [INFO] Target genome list was writen to GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna/target_genomes.txt
[2023-06-17 12:24:56,667] [INFO] Task started: fastANI
[2023-06-17 12:24:56,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg37082a77-bf9a-417c-ab0e-a9594af3836e/GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna.gz --refList GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna/target_genomes.txt --output GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 12:25:17,225] [INFO] Task succeeded: fastANI
[2023-06-17 12:25:17,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56ca8839-dfa8-4f26-9108-a70a4d8056ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 12:25:17,226] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56ca8839-dfa8-4f26-9108-a70a4d8056ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 12:25:17,229] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 12:25:17,229] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 12:25:17,229] [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
Succinatimonas hippei	strain=YIT 12066	GCA_000188195.1	626938	626938	type	True	77.384	50	502	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 12:25:17,231] [INFO] DFAST Taxonomy check result was written to GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna/tc_result.tsv
[2023-06-17 12:25:17,232] [INFO] ===== Taxonomy check completed =====
[2023-06-17 12:25:17,232] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 12:25:17,232] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56ca8839-dfa8-4f26-9108-a70a4d8056ac/dqc_reference/checkm_data
[2023-06-17 12:25:17,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 12:25:17,259] [INFO] Task started: CheckM
[2023-06-17 12:25:17,260] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna/checkm_input GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna/checkm_result
[2023-06-17 12:25:35,008] [INFO] Task succeeded: CheckM
[2023-06-17 12:25:35,010] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 14.58%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 12:25:35,035] [INFO] ===== Completeness check finished =====
[2023-06-17 12:25:35,035] [INFO] ===== Start GTDB Search =====
[2023-06-17 12:25:35,036] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna/markers.fasta)
[2023-06-17 12:25:35,036] [INFO] Task started: Blastn
[2023-06-17 12:25:35,036] [INFO] Running command: blastn -query GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna/markers.fasta -db /var/lib/cwl/stg56ca8839-dfa8-4f26-9108-a70a4d8056ac/dqc_reference/reference_markers_gtdb.fasta -out GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:25:36,089] [INFO] Task succeeded: Blastn
[2023-06-17 12:25:36,094] [INFO] Selected 17 target genomes.
[2023-06-17 12:25:36,094] [INFO] Target genome list was writen to GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 12:25:36,109] [INFO] Task started: fastANI
[2023-06-17 12:25:36,109] [INFO] Running command: fastANI --query /var/lib/cwl/stg37082a77-bf9a-417c-ab0e-a9594af3836e/GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna.gz --refList GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna/target_genomes_gtdb.txt --output GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 12:25:43,429] [INFO] Task succeeded: fastANI
[2023-06-17 12:25:43,442] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 12:25:43,442] [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_905201175.1	s__Succinivibrio sp905201175	100.0	499	502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900548485.1	s__Succinivibrio sp900548485	83.1162	317	502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	99.05	99.05	0.77	0.77	2	-
GCA_900552905.1	s__Succinivibrio sp900552905	79.8279	150	502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	98.96	98.95	0.94	0.94	3	-
GCA_905186145.1	s__Succinivibrio sp905186145	79.4946	200	502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315395.1	s__Succinivibrio sp900315395	77.5069	77	502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	99.82	99.64	0.93	0.87	3	-
GCF_000188195.1	s__Succinatimonas hippei	77.384	50	502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinatimonas	95.0	98.70	97.40	0.92	0.85	3	-
GCA_902785325.1	s__Succinivibrio sp003456415	77.3456	64	502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	98.60	98.18	0.90	0.86	5	-
GCA_900316175.1	s__Succinivibrio sp900316175	77.0719	54	502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	99.29	98.66	0.86	0.80	9	-
GCA_002449335.1	s__Succinivibrio sp002449335	77.0502	69	502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	97.89	95.86	0.90	0.86	3	-
--------------------------------------------------------------------------------
[2023-06-17 12:25:43,445] [INFO] GTDB search result was written to GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna/result_gtdb.tsv
[2023-06-17 12:25:43,446] [INFO] ===== GTDB Search completed =====
[2023-06-17 12:25:43,450] [INFO] DFAST_QC result json was written to GCA_905201175.1_ERR321598-mag-bin.14_genomic.fna/dqc_result.json
[2023-06-17 12:25:43,450] [INFO] DFAST_QC completed!
[2023-06-17 12:25:43,451] [INFO] Total running time: 0h0m53s