[2023-06-05 02:23:19,541] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:23:19,549] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:23:19,549] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f916bdd-fb9e-4cd0-af1a-7ff5e20f7c73/dqc_reference
[2023-06-05 02:23:21,070] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:23:21,071] [INFO] Task started: Prodigal
[2023-06-05 02:23:21,072] [INFO] Running command: gunzip -c /var/lib/cwl/stg20a863e0-5225-46ff-be56-9ae1235d59a4/GCA_934630965.1_ERR7745411_bin.69_genomic.fna.gz | prodigal -d GCA_934630965.1_ERR7745411_bin.69_genomic.fna/cds.fna -a GCA_934630965.1_ERR7745411_bin.69_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:23:27,158] [INFO] Task succeeded: Prodigal
[2023-06-05 02:23:27,158] [INFO] Task started: HMMsearch
[2023-06-05 02:23:27,158] [INFO] Running command: hmmsearch --tblout GCA_934630965.1_ERR7745411_bin.69_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f916bdd-fb9e-4cd0-af1a-7ff5e20f7c73/dqc_reference/reference_markers.hmm GCA_934630965.1_ERR7745411_bin.69_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:23:27,430] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:23:27,431] [INFO] Found 6/6 markers.
[2023-06-05 02:23:27,468] [INFO] Query marker FASTA was written to GCA_934630965.1_ERR7745411_bin.69_genomic.fna/markers.fasta
[2023-06-05 02:23:27,469] [INFO] Task started: Blastn
[2023-06-05 02:23:27,469] [INFO] Running command: blastn -query GCA_934630965.1_ERR7745411_bin.69_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f916bdd-fb9e-4cd0-af1a-7ff5e20f7c73/dqc_reference/reference_markers.fasta -out GCA_934630965.1_ERR7745411_bin.69_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:23:28,222] [INFO] Task succeeded: Blastn
[2023-06-05 02:23:28,256] [INFO] Selected 25 target genomes.
[2023-06-05 02:23:28,257] [INFO] Target genome list was writen to GCA_934630965.1_ERR7745411_bin.69_genomic.fna/target_genomes.txt
[2023-06-05 02:23:28,273] [INFO] Task started: fastANI
[2023-06-05 02:23:28,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg20a863e0-5225-46ff-be56-9ae1235d59a4/GCA_934630965.1_ERR7745411_bin.69_genomic.fna.gz --refList GCA_934630965.1_ERR7745411_bin.69_genomic.fna/target_genomes.txt --output GCA_934630965.1_ERR7745411_bin.69_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:23:45,943] [INFO] Task succeeded: fastANI
[2023-06-05 02:23:45,944] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f916bdd-fb9e-4cd0-af1a-7ff5e20f7c73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:23:45,944] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f916bdd-fb9e-4cd0-af1a-7ff5e20f7c73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:23:45,948] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:23:45,948] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 02:23:45,949] [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
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	76.0652	59	707	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 02:23:45,951] [INFO] DFAST Taxonomy check result was written to GCA_934630965.1_ERR7745411_bin.69_genomic.fna/tc_result.tsv
[2023-06-05 02:23:45,952] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:23:45,952] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:23:45,952] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f916bdd-fb9e-4cd0-af1a-7ff5e20f7c73/dqc_reference/checkm_data
[2023-06-05 02:23:45,954] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:23:45,981] [INFO] Task started: CheckM
[2023-06-05 02:23:45,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934630965.1_ERR7745411_bin.69_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934630965.1_ERR7745411_bin.69_genomic.fna/checkm_input GCA_934630965.1_ERR7745411_bin.69_genomic.fna/checkm_result
[2023-06-05 02:24:09,610] [INFO] Task succeeded: CheckM
[2023-06-05 02:24:09,611] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:24:09,632] [INFO] ===== Completeness check finished =====
[2023-06-05 02:24:09,633] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:24:09,633] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934630965.1_ERR7745411_bin.69_genomic.fna/markers.fasta)
[2023-06-05 02:24:09,634] [INFO] Task started: Blastn
[2023-06-05 02:24:09,634] [INFO] Running command: blastn -query GCA_934630965.1_ERR7745411_bin.69_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f916bdd-fb9e-4cd0-af1a-7ff5e20f7c73/dqc_reference/reference_markers_gtdb.fasta -out GCA_934630965.1_ERR7745411_bin.69_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:24:10,866] [INFO] Task succeeded: Blastn
[2023-06-05 02:24:10,870] [INFO] Selected 20 target genomes.
[2023-06-05 02:24:10,871] [INFO] Target genome list was writen to GCA_934630965.1_ERR7745411_bin.69_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:24:10,877] [INFO] Task started: fastANI
[2023-06-05 02:24:10,877] [INFO] Running command: fastANI --query /var/lib/cwl/stg20a863e0-5225-46ff-be56-9ae1235d59a4/GCA_934630965.1_ERR7745411_bin.69_genomic.fna.gz --refList GCA_934630965.1_ERR7745411_bin.69_genomic.fna/target_genomes_gtdb.txt --output GCA_934630965.1_ERR7745411_bin.69_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:24:19,261] [INFO] Task succeeded: fastANI
[2023-06-05 02:24:19,292] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:24:19,292] [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_003150355.1	s__Limivicinus sp003150355	95.8381	466	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.34	96.94	0.74	0.68	6	conclusive
GCA_900547315.1	s__Limivicinus sp900547315	80.1584	261	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.47	98.42	0.88	0.83	3	-
GCA_900549645.1	s__Limivicinus sp900549645	79.9243	259	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.52	99.05	0.92	0.86	3	-
GCA_900549865.1	s__Limivicinus sp900549865	79.7277	269	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.13	98.09	0.79	0.79	3	-
GCA_902778115.1	s__Limivicinus sp902778115	79.0322	192	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.60	97.29	0.87	0.83	3	-
GCA_017458085.1	s__Limivicinus sp017458085	78.9982	206	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902802215.1	s__Limivicinus sp902802215	78.9118	209	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.44	98.44	0.76	0.76	2	-
GCA_902786615.1	s__Limivicinus sp902786615	78.8947	210	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785905.1	s__Limivicinus sp902785905	78.8239	186	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902778285.1	s__Limivicinus sp902778285	78.7253	188	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.33	98.33	0.79	0.79	2	-
GCA_902793285.1	s__Limivicinus sp902793285	78.717	189	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.34	97.34	0.78	0.78	2	-
GCA_902791215.1	s__Limivicinus sp902791215	78.7076	223	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779945.1	s__Limivicinus sp902779945	78.6135	210	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900321275.1	s__Limivicinus sp900321275	78.5851	198	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.70	95.66	0.85	0.80	7	-
GCA_900319465.1	s__Limivicinus sp900319465	78.5833	206	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.77	99.67	0.93	0.92	4	-
GCA_900319275.1	s__Limivicinus sp900319275	78.3723	139	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.07	95.72	0.86	0.73	4	-
GCA_902789745.1	s__Limivicinus sp902789745	78.1051	196	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543625.1	s__CAG-103 sp900543625	77.7122	151	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	96.93	95.23	0.89	0.87	12	-
--------------------------------------------------------------------------------
[2023-06-05 02:24:19,295] [INFO] GTDB search result was written to GCA_934630965.1_ERR7745411_bin.69_genomic.fna/result_gtdb.tsv
[2023-06-05 02:24:19,295] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:24:19,300] [INFO] DFAST_QC result json was written to GCA_934630965.1_ERR7745411_bin.69_genomic.fna/dqc_result.json
[2023-06-05 02:24:19,300] [INFO] DFAST_QC completed!
[2023-06-05 02:24:19,301] [INFO] Total running time: 0h0m60s