[2024-01-25 20:14:50,468] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:50,470] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:50,470] [INFO] DQC Reference Directory: /var/lib/cwl/stge394bae6-1baa-4b10-8fa7-2e80716b9186/dqc_reference
[2024-01-25 20:14:51,737] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:51,738] [INFO] Task started: Prodigal
[2024-01-25 20:14:51,738] [INFO] Running command: gunzip -c /var/lib/cwl/stg1402d48a-7818-44e1-9a4c-b6fe12c0bc46/GCF_002896855.1_ASM289685v1_genomic.fna.gz | prodigal -d GCF_002896855.1_ASM289685v1_genomic.fna/cds.fna -a GCF_002896855.1_ASM289685v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:15:01,867] [INFO] Task succeeded: Prodigal
[2024-01-25 20:15:01,867] [INFO] Task started: HMMsearch
[2024-01-25 20:15:01,867] [INFO] Running command: hmmsearch --tblout GCF_002896855.1_ASM289685v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge394bae6-1baa-4b10-8fa7-2e80716b9186/dqc_reference/reference_markers.hmm GCF_002896855.1_ASM289685v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:15:02,117] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:15:02,118] [INFO] Found 6/6 markers.
[2024-01-25 20:15:02,153] [INFO] Query marker FASTA was written to GCF_002896855.1_ASM289685v1_genomic.fna/markers.fasta
[2024-01-25 20:15:02,153] [INFO] Task started: Blastn
[2024-01-25 20:15:02,153] [INFO] Running command: blastn -query GCF_002896855.1_ASM289685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge394bae6-1baa-4b10-8fa7-2e80716b9186/dqc_reference/reference_markers.fasta -out GCF_002896855.1_ASM289685v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:02,726] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:02,730] [INFO] Selected 16 target genomes.
[2024-01-25 20:15:02,730] [INFO] Target genome list was writen to GCF_002896855.1_ASM289685v1_genomic.fna/target_genomes.txt
[2024-01-25 20:15:02,741] [INFO] Task started: fastANI
[2024-01-25 20:15:02,742] [INFO] Running command: fastANI --query /var/lib/cwl/stg1402d48a-7818-44e1-9a4c-b6fe12c0bc46/GCF_002896855.1_ASM289685v1_genomic.fna.gz --refList GCF_002896855.1_ASM289685v1_genomic.fna/target_genomes.txt --output GCF_002896855.1_ASM289685v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:15:13,070] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:13,071] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge394bae6-1baa-4b10-8fa7-2e80716b9186/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:15:13,071] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge394bae6-1baa-4b10-8fa7-2e80716b9186/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:15:13,076] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:15:13,076] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:15:13,076] [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
Pseudoclostridium thermosuccinogenes	strain=DSM 5807	GCA_002896855.1	84032	84032	type	True	100.0	1576	1577	95	conclusive
Acetivibrio thermocellus	strain=ATCC 27405	GCA_000015865.1	1515	1515	type	True	81.9984	87	1577	95	below_threshold
Acetivibrio clariflavus	strain=DSM 19732	GCA_000237085.1	288965	288965	type	True	81.5793	127	1577	95	below_threshold
Acetivibrio mesophilus	strain=N2K1	GCA_004102745.1	2487273	2487273	type	True	81.1437	82	1577	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:15:13,078] [INFO] DFAST Taxonomy check result was written to GCF_002896855.1_ASM289685v1_genomic.fna/tc_result.tsv
[2024-01-25 20:15:13,079] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:15:13,079] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:15:13,079] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge394bae6-1baa-4b10-8fa7-2e80716b9186/dqc_reference/checkm_data
[2024-01-25 20:15:13,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:15:13,129] [INFO] Task started: CheckM
[2024-01-25 20:15:13,129] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002896855.1_ASM289685v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002896855.1_ASM289685v1_genomic.fna/checkm_input GCF_002896855.1_ASM289685v1_genomic.fna/checkm_result
[2024-01-25 20:15:45,549] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:45,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:45,569] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:45,569] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:45,569] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002896855.1_ASM289685v1_genomic.fna/markers.fasta)
[2024-01-25 20:15:45,569] [INFO] Task started: Blastn
[2024-01-25 20:15:45,569] [INFO] Running command: blastn -query GCF_002896855.1_ASM289685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge394bae6-1baa-4b10-8fa7-2e80716b9186/dqc_reference/reference_markers_gtdb.fasta -out GCF_002896855.1_ASM289685v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:46,507] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:46,510] [INFO] Selected 26 target genomes.
[2024-01-25 20:15:46,510] [INFO] Target genome list was writen to GCF_002896855.1_ASM289685v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:46,545] [INFO] Task started: fastANI
[2024-01-25 20:15:46,545] [INFO] Running command: fastANI --query /var/lib/cwl/stg1402d48a-7818-44e1-9a4c-b6fe12c0bc46/GCF_002896855.1_ASM289685v1_genomic.fna.gz --refList GCF_002896855.1_ASM289685v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002896855.1_ASM289685v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:16:01,226] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:01,231] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:16:01,231] [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_002896855.1	s__Pseudoclostridium thermosuccinogenes	100.0	1575	1577	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-27016;g__Pseudoclostridium	95.0	99.44	98.87	0.95	0.88	5	conclusive
GCF_000015865.1	s__Hungateiclostridium thermocellum	81.872	87	1577	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_000237085.1	s__Acetivibrio clariflavus	81.3939	125	1577	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Acetivibrio	95.0	98.23	96.28	0.88	0.88	4	-
GCF_004102745.1	s__Hungateiclostridium mesophilum	81.2245	81	1577	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Hungateiclostridium	95.0	99.61	99.52	0.93	0.90	4	-
GCA_001512505.1	s__Hungateiclostridium sp001512505	76.5286	65	1577	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Hungateiclostridium	95.0	99.73	99.73	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:16:01,233] [INFO] GTDB search result was written to GCF_002896855.1_ASM289685v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:16:01,233] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:16:01,235] [INFO] DFAST_QC result json was written to GCF_002896855.1_ASM289685v1_genomic.fna/dqc_result.json
[2024-01-25 20:16:01,236] [INFO] DFAST_QC completed!
[2024-01-25 20:16:01,236] [INFO] Total running time: 0h1m11s