[2023-06-17 13:43:51,265] [INFO] DFAST_QC pipeline started.
[2023-06-17 13:43:51,268] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 13:43:51,269] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5fb0404-435c-4af1-9c7c-64a33a821106/dqc_reference
[2023-06-17 13:43:52,511] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 13:43:52,512] [INFO] Task started: Prodigal
[2023-06-17 13:43:52,512] [INFO] Running command: gunzip -c /var/lib/cwl/stg0cb83ac7-596e-4244-b486-a231ea32478f/GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna.gz | prodigal -d GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna/cds.fna -a GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 13:43:57,339] [INFO] Task succeeded: Prodigal
[2023-06-17 13:43:57,340] [INFO] Task started: HMMsearch
[2023-06-17 13:43:57,340] [INFO] Running command: hmmsearch --tblout GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5fb0404-435c-4af1-9c7c-64a33a821106/dqc_reference/reference_markers.hmm GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna/protein.faa > /dev/null
[2023-06-17 13:43:57,548] [INFO] Task succeeded: HMMsearch
[2023-06-17 13:43:57,550] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg0cb83ac7-596e-4244-b486-a231ea32478f/GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna.gz]
[2023-06-17 13:43:57,574] [INFO] Query marker FASTA was written to GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna/markers.fasta
[2023-06-17 13:43:57,575] [INFO] Task started: Blastn
[2023-06-17 13:43:57,575] [INFO] Running command: blastn -query GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5fb0404-435c-4af1-9c7c-64a33a821106/dqc_reference/reference_markers.fasta -out GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 13:43:58,117] [INFO] Task succeeded: Blastn
[2023-06-17 13:43:58,121] [INFO] Selected 10 target genomes.
[2023-06-17 13:43:58,122] [INFO] Target genome list was writen to GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna/target_genomes.txt
[2023-06-17 13:43:58,123] [INFO] Task started: fastANI
[2023-06-17 13:43:58,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cb83ac7-596e-4244-b486-a231ea32478f/GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna.gz --refList GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna/target_genomes.txt --output GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 13:44:02,517] [INFO] Task succeeded: fastANI
[2023-06-17 13:44:02,518] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5fb0404-435c-4af1-9c7c-64a33a821106/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 13:44:02,519] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5fb0404-435c-4af1-9c7c-64a33a821106/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 13:44:02,530] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2023-06-17 13:44:02,531] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-17 13:44:02,531] [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
Adlercreutzia equolifaciens subsp. equolifaciens	strain=DSM 19450	GCA_000478885.1	2864143	446660	type	True	96.2985	223	252	95	conclusive
Adlercreutzia equolifaciens subsp. celatus	strain=DSM 18785	GCA_003726015.1	394340	446660	type	True	96.1924	214	252	95	conclusive
Adlercreutzia equolifaciens subsp. celatus	strain=DSM 18785	GCA_024171685.1	394340	446660	type	True	96.0968	215	252	95	conclusive
Adlercreutzia equolifaciens subsp. celatus	strain=JCM 14811	GCA_003428485.1	394340	446660	type	True	96.092	213	252	95	conclusive
Adlercreutzia equolifaciens subsp. celatus	strain=JCM 14811	GCA_016865385.1	394340	446660	type	True	96.0157	218	252	95	conclusive
--------------------------------------------------------------------------------
[2023-06-17 13:44:02,533] [INFO] DFAST Taxonomy check result was written to GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna/tc_result.tsv
[2023-06-17 13:44:02,533] [INFO] ===== Taxonomy check completed =====
[2023-06-17 13:44:02,533] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 13:44:02,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5fb0404-435c-4af1-9c7c-64a33a821106/dqc_reference/checkm_data
[2023-06-17 13:44:02,535] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 13:44:02,562] [INFO] Task started: CheckM
[2023-06-17 13:44:02,563] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna/checkm_input GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna/checkm_result
[2023-06-17 13:44:23,254] [INFO] Task succeeded: CheckM
[2023-06-17 13:44:23,255] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.05%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 13:44:23,284] [INFO] ===== Completeness check finished =====
[2023-06-17 13:44:23,284] [INFO] ===== Start GTDB Search =====
[2023-06-17 13:44:23,285] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna/markers.fasta)
[2023-06-17 13:44:23,285] [INFO] Task started: Blastn
[2023-06-17 13:44:23,285] [INFO] Running command: blastn -query GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5fb0404-435c-4af1-9c7c-64a33a821106/dqc_reference/reference_markers_gtdb.fasta -out GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 13:44:23,914] [INFO] Task succeeded: Blastn
[2023-06-17 13:44:23,919] [INFO] Selected 12 target genomes.
[2023-06-17 13:44:23,919] [INFO] Target genome list was writen to GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 13:44:23,921] [INFO] Task started: fastANI
[2023-06-17 13:44:23,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cb83ac7-596e-4244-b486-a231ea32478f/GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna.gz --refList GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna/target_genomes_gtdb.txt --output GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 13:44:29,420] [INFO] Task succeeded: fastANI
[2023-06-17 13:44:29,432] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 13:44:29,432] [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_000478885.1	s__Adlercreutzia equolifaciens	96.2985	223	252	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.05	95.56	0.84	0.79	7	conclusive
GCF_011405655.1	s__Adlercreutzia celatus_A	92.6068	208	252	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	96.32	95.52	0.87	0.80	16	-
GCF_008831045.1	s__Adlercreutzia muris	83.584	177	252	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.80	97.69	0.87	0.84	7	-
GCF_000403355.2	s__Adlercreutzia caecimuris	83.5044	174	252	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.41	97.35	0.86	0.85	5	-
GCA_910589165.1	s__Adlercreutzia sp910589165	83.4152	164	252	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422625.1	s__Adlercreutzia mucosicola	83.2121	165	252	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.91	97.91	0.87	0.87	2	-
GCF_013185065.1	s__CAAEEV01 sp013185065	80.9237	90	252	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	97.04	97.04	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2023-06-17 13:44:29,434] [INFO] GTDB search result was written to GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna/result_gtdb.tsv
[2023-06-17 13:44:29,435] [INFO] ===== GTDB Search completed =====
[2023-06-17 13:44:29,438] [INFO] DFAST_QC result json was written to GCA_905193435.1_ERR1190671-mag-bin.15_genomic.fna/dqc_result.json
[2023-06-17 13:44:29,438] [INFO] DFAST_QC completed!
[2023-06-17 13:44:29,438] [INFO] Total running time: 0h0m38s