[2023-06-13 22:21:32,318] [INFO] DFAST_QC pipeline started.
[2023-06-13 22:21:32,324] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 22:21:32,324] [INFO] DQC Reference Directory: /var/lib/cwl/stg534f9232-1506-4816-a135-9b17258754ca/dqc_reference
[2023-06-13 22:21:34,136] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 22:21:34,136] [INFO] Task started: Prodigal
[2023-06-13 22:21:34,137] [INFO] Running command: gunzip -c /var/lib/cwl/stg72ac1cfc-2a6f-4c2a-a36f-71daec2c500d/GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 22:21:39,464] [INFO] Task succeeded: Prodigal
[2023-06-13 22:21:39,464] [INFO] Task started: HMMsearch
[2023-06-13 22:21:39,464] [INFO] Running command: hmmsearch --tblout GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg534f9232-1506-4816-a135-9b17258754ca/dqc_reference/reference_markers.hmm GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 22:21:39,657] [INFO] Task succeeded: HMMsearch
[2023-06-13 22:21:39,658] [INFO] Found 6/6 markers.
[2023-06-13 22:21:39,680] [INFO] Query marker FASTA was written to GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 22:21:39,680] [INFO] Task started: Blastn
[2023-06-13 22:21:39,680] [INFO] Running command: blastn -query GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg534f9232-1506-4816-a135-9b17258754ca/dqc_reference/reference_markers.fasta -out GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:21:40,310] [INFO] Task succeeded: Blastn
[2023-06-13 22:21:40,313] [INFO] Selected 26 target genomes.
[2023-06-13 22:21:40,313] [INFO] Target genome list was writen to GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 22:21:40,316] [INFO] Task started: fastANI
[2023-06-13 22:21:40,317] [INFO] Running command: fastANI --query /var/lib/cwl/stg72ac1cfc-2a6f-4c2a-a36f-71daec2c500d/GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 22:21:53,196] [INFO] Task succeeded: fastANI
[2023-06-13 22:21:53,197] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg534f9232-1506-4816-a135-9b17258754ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 22:21:53,197] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg534f9232-1506-4816-a135-9b17258754ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 22:21:53,205] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 22:21:53,205] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 22:21:53,205] [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
Schaalia vaccimaxillae	strain=DSM 15804	GCA_000420425.1	183916	183916	type	True	77.6802	81	650	95	below_threshold
Schaalia hyovaginalis	strain=DSM 10695	GCA_014208035.1	29316	29316	type	True	77.4781	90	650	95	below_threshold
Schaalia meyeri	strain=FDAARGOS_985	GCA_016127995.1	52773	52773	type	True	77.3345	98	650	95	below_threshold
Schaalia meyeri	strain=DSM 20733	GCA_900105015.1	52773	52773	type	True	77.172	95	650	95	below_threshold
Actinomyces polynesiensis	strain=MS2	GCA_000820725.1	1325934	1325934	type	True	77.1201	64	650	95	below_threshold
Schaalia suimastitidis	strain=DSM 15538	GCA_000429105.1	121163	121163	type	True	77.0083	52	650	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 22:21:53,207] [INFO] DFAST Taxonomy check result was written to GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 22:21:53,207] [INFO] ===== Taxonomy check completed =====
[2023-06-13 22:21:53,207] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 22:21:53,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg534f9232-1506-4816-a135-9b17258754ca/dqc_reference/checkm_data
[2023-06-13 22:21:53,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 22:21:53,232] [INFO] Task started: CheckM
[2023-06-13 22:21:53,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 22:22:13,548] [INFO] Task succeeded: CheckM
[2023-06-13 22:22:13,549] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.60%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 22:22:13,569] [INFO] ===== Completeness check finished =====
[2023-06-13 22:22:13,570] [INFO] ===== Start GTDB Search =====
[2023-06-13 22:22:13,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 22:22:13,572] [INFO] Task started: Blastn
[2023-06-13 22:22:13,572] [INFO] Running command: blastn -query GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg534f9232-1506-4816-a135-9b17258754ca/dqc_reference/reference_markers_gtdb.fasta -out GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:22:14,421] [INFO] Task succeeded: Blastn
[2023-06-13 22:22:14,424] [INFO] Selected 11 target genomes.
[2023-06-13 22:22:14,425] [INFO] Target genome list was writen to GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 22:22:14,430] [INFO] Task started: fastANI
[2023-06-13 22:22:14,430] [INFO] Running command: fastANI --query /var/lib/cwl/stg72ac1cfc-2a6f-4c2a-a36f-71daec2c500d/GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 22:22:19,452] [INFO] Task succeeded: fastANI
[2023-06-13 22:22:19,460] [INFO] Found 9 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-13 22:22:19,460] [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
GCF_000758755.1	s__Pauljensenia sp000758755	95.2555	578	650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.30	97.11	0.96	0.96	3	inconclusive
GCF_900155605.1	s__Pauljensenia marseillensis	95.2034	573	650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	99.98	99.98	1.00	1.00	2	inconclusive
GCA_900554605.1	s__Pauljensenia sp900554605	93.9721	291	650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001070855.1	s__Pauljensenia pyogenes_A	84.2718	397	650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.06	97.06	0.98	0.98	2	-
GCF_000308055.1	s__Pauljensenia sp000308055	83.8179	410	650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.51	95.51	0.96	0.95	7	-
GCA_900541895.1	s__Pauljensenia sp900541895	83.6996	368	650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.30	95.78	0.91	0.83	4	-
GCF_001838165.1	s__Pauljensenia sp001838165	78.6516	140	650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.43	95.77	0.94	0.90	5	-
GCF_900445025.1	s__Pauljensenia odontolytica	78.0338	121	650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556405.1	s__Pauljensenia sp900556405	77.7685	79	650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 22:22:19,462] [INFO] GTDB search result was written to GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 22:22:19,462] [INFO] ===== GTDB Search completed =====
[2023-06-13 22:22:19,466] [INFO] DFAST_QC result json was written to GCA_938014245.1_SRR8114034_bin.62_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 22:22:19,466] [INFO] DFAST_QC completed!
[2023-06-13 22:22:19,467] [INFO] Total running time: 0h0m47s