[2024-01-24 13:32:25,936] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:25,938] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:25,938] [INFO] DQC Reference Directory: /var/lib/cwl/stg19d1175e-0a62-4d72-8810-14f360c448ac/dqc_reference
[2024-01-24 13:32:27,180] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:27,181] [INFO] Task started: Prodigal
[2024-01-24 13:32:27,182] [INFO] Running command: gunzip -c /var/lib/cwl/stg9769ded7-dda3-439a-9ae3-333536acc514/GCF_000521465.1_ASM52146v1_genomic.fna.gz | prodigal -d GCF_000521465.1_ASM52146v1_genomic.fna/cds.fna -a GCF_000521465.1_ASM52146v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:35,452] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:35,453] [INFO] Task started: HMMsearch
[2024-01-24 13:32:35,453] [INFO] Running command: hmmsearch --tblout GCF_000521465.1_ASM52146v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19d1175e-0a62-4d72-8810-14f360c448ac/dqc_reference/reference_markers.hmm GCF_000521465.1_ASM52146v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:35,719] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:35,721] [INFO] Found 6/6 markers.
[2024-01-24 13:32:35,761] [INFO] Query marker FASTA was written to GCF_000521465.1_ASM52146v1_genomic.fna/markers.fasta
[2024-01-24 13:32:35,762] [INFO] Task started: Blastn
[2024-01-24 13:32:35,762] [INFO] Running command: blastn -query GCF_000521465.1_ASM52146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19d1175e-0a62-4d72-8810-14f360c448ac/dqc_reference/reference_markers.fasta -out GCF_000521465.1_ASM52146v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:36,361] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:36,408] [INFO] Selected 13 target genomes.
[2024-01-24 13:32:36,408] [INFO] Target genome list was writen to GCF_000521465.1_ASM52146v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:36,523] [INFO] Task started: fastANI
[2024-01-24 13:32:36,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg9769ded7-dda3-439a-9ae3-333536acc514/GCF_000521465.1_ASM52146v1_genomic.fna.gz --refList GCF_000521465.1_ASM52146v1_genomic.fna/target_genomes.txt --output GCF_000521465.1_ASM52146v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:44,674] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:44,675] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19d1175e-0a62-4d72-8810-14f360c448ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:44,675] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19d1175e-0a62-4d72-8810-14f360c448ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:44,685] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:44,685] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:44,685] [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
Acetivibrio straminisolvens	strain=JCM 21531	GCA_000521465.1	253314	253314	type	True	100.0	1208	1214	95	conclusive
Acetivibrio mesophilus	strain=N2K1	GCA_004102745.1	2487273	2487273	type	True	85.4191	945	1214	95	below_threshold
Acetivibrio thermocellus	strain=ATCC 27405	GCA_000015865.1	1515	1515	type	True	84.3425	913	1214	95	below_threshold
Acetivibrio saccincola	strain=GGR1	GCA_002844395.1	1677857	1677857	type	True	79.1524	124	1214	95	below_threshold
Ruminiclostridium sufflavum	strain=DSM 19573	GCA_003208175.1	396504	396504	type	True	75.7196	52	1214	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:44,688] [INFO] DFAST Taxonomy check result was written to GCF_000521465.1_ASM52146v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:44,689] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:44,689] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:44,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19d1175e-0a62-4d72-8810-14f360c448ac/dqc_reference/checkm_data
[2024-01-24 13:32:44,691] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:44,730] [INFO] Task started: CheckM
[2024-01-24 13:32:44,730] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000521465.1_ASM52146v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000521465.1_ASM52146v1_genomic.fna/checkm_input GCF_000521465.1_ASM52146v1_genomic.fna/checkm_result
[2024-01-24 13:33:14,847] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:14,848] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:14,872] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:14,872] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:14,873] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000521465.1_ASM52146v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:14,873] [INFO] Task started: Blastn
[2024-01-24 13:33:14,873] [INFO] Running command: blastn -query GCF_000521465.1_ASM52146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19d1175e-0a62-4d72-8810-14f360c448ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_000521465.1_ASM52146v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:15,778] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:15,782] [INFO] Selected 18 target genomes.
[2024-01-24 13:33:15,782] [INFO] Target genome list was writen to GCF_000521465.1_ASM52146v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:15,940] [INFO] Task started: fastANI
[2024-01-24 13:33:15,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg9769ded7-dda3-439a-9ae3-333536acc514/GCF_000521465.1_ASM52146v1_genomic.fna.gz --refList GCF_000521465.1_ASM52146v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000521465.1_ASM52146v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:27,452] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:27,464] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:27,465] [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_000521465.1	s__Hungateiclostridium straminisolvens	100.0	1208	1214	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Hungateiclostridium	95.0	99.73	99.73	0.92	0.92	2	conclusive
GCF_004102745.1	s__Hungateiclostridium mesophilum	85.4166	945	1214	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Hungateiclostridium	95.0	99.61	99.52	0.93	0.90	4	-
GCF_000015865.1	s__Hungateiclostridium thermocellum	84.3534	912	1214	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Hungateiclostridium	95.0	99.61	99.46	0.95	0.92	14	-
GCF_002844395.1	s__Herbivorax saccincola	79.2286	122	1214	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Herbivorax	95.0	99.55	99.29	0.94	0.85	5	-
GCA_001512505.1	s__Hungateiclostridium sp001512505	78.8409	321	1214	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Hungateiclostridium	95.0	99.73	99.73	0.91	0.91	2	-
GCA_012523755.1	s__Hungateiclostridium sp012523755	78.0229	249	1214	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Hungateiclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012517995.1	s__Herbivorax sp012517995	77.5235	101	1214	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Herbivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000179595.2	s__Acetivibrio cellulolyticus	77.1474	133	1214	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Acetivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003208175.1	s__Ruminiclostridium sufflavum	75.7227	52	1214	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-27016;g__Ruminiclostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:27,466] [INFO] GTDB search result was written to GCF_000521465.1_ASM52146v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:27,467] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:27,470] [INFO] DFAST_QC result json was written to GCF_000521465.1_ASM52146v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:27,470] [INFO] DFAST_QC completed!
[2024-01-24 13:33:27,470] [INFO] Total running time: 0h1m2s