[2024-01-24 13:31:12,131] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:12,132] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:12,133] [INFO] DQC Reference Directory: /var/lib/cwl/stga1de0107-544b-4862-9717-b82995eecf9b/dqc_reference
[2024-01-24 13:31:13,293] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:13,294] [INFO] Task started: Prodigal
[2024-01-24 13:31:13,294] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ed61bf5-afa3-4b43-9024-14617c11c7e6/GCF_001050195.2_ASM105019v2_genomic.fna.gz | prodigal -d GCF_001050195.2_ASM105019v2_genomic.fna/cds.fna -a GCF_001050195.2_ASM105019v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:24,806] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:24,806] [INFO] Task started: HMMsearch
[2024-01-24 13:31:24,806] [INFO] Running command: hmmsearch --tblout GCF_001050195.2_ASM105019v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1de0107-544b-4862-9717-b82995eecf9b/dqc_reference/reference_markers.hmm GCF_001050195.2_ASM105019v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:25,048] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:25,049] [INFO] Found 6/6 markers.
[2024-01-24 13:31:25,084] [INFO] Query marker FASTA was written to GCF_001050195.2_ASM105019v2_genomic.fna/markers.fasta
[2024-01-24 13:31:25,084] [INFO] Task started: Blastn
[2024-01-24 13:31:25,084] [INFO] Running command: blastn -query GCF_001050195.2_ASM105019v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga1de0107-544b-4862-9717-b82995eecf9b/dqc_reference/reference_markers.fasta -out GCF_001050195.2_ASM105019v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:25,627] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:25,631] [INFO] Selected 24 target genomes.
[2024-01-24 13:31:25,631] [INFO] Target genome list was writen to GCF_001050195.2_ASM105019v2_genomic.fna/target_genomes.txt
[2024-01-24 13:31:25,646] [INFO] Task started: fastANI
[2024-01-24 13:31:25,646] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ed61bf5-afa3-4b43-9024-14617c11c7e6/GCF_001050195.2_ASM105019v2_genomic.fna.gz --refList GCF_001050195.2_ASM105019v2_genomic.fna/target_genomes.txt --output GCF_001050195.2_ASM105019v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:39,841] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:39,841] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1de0107-544b-4862-9717-b82995eecf9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:39,842] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1de0107-544b-4862-9717-b82995eecf9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:39,849] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:31:39,849] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:39,849] [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
Anaerolinea thermolimosa	strain=IMO-1	GCA_001050195.2	229919	229919	type	True	99.9999	1363	1388	95	conclusive
Anaerolinea thermophila	strain=UNI-1	GCA_000199675.1	167964	167964	type	True	80.1746	146	1388	95	below_threshold
Thermanaerothrix daxensis	strain=GNS-1	GCA_001306145.1	869279	869279	type	True	76.8521	56	1388	95	below_threshold
Levilinea saccharolytica	strain=KIBI-1	GCA_001050255.2	229921	229921	type	True	76.5551	67	1388	95	below_threshold
Levilinea saccharolytica	strain=KIBI-1	GCA_001306035.1	229921	229921	type	True	76.3453	60	1388	95	below_threshold
Ornatilinea apprima	strain=P3M-1	GCA_001306115.1	1134406	1134406	type	True	75.7221	53	1388	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:39,851] [INFO] DFAST Taxonomy check result was written to GCF_001050195.2_ASM105019v2_genomic.fna/tc_result.tsv
[2024-01-24 13:31:39,851] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:39,851] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:39,851] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1de0107-544b-4862-9717-b82995eecf9b/dqc_reference/checkm_data
[2024-01-24 13:31:39,852] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:39,890] [INFO] Task started: CheckM
[2024-01-24 13:31:39,890] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001050195.2_ASM105019v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001050195.2_ASM105019v2_genomic.fna/checkm_input GCF_001050195.2_ASM105019v2_genomic.fna/checkm_result
[2024-01-24 13:32:17,261] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:17,262] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:17,298] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:17,299] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:17,299] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001050195.2_ASM105019v2_genomic.fna/markers.fasta)
[2024-01-24 13:32:17,299] [INFO] Task started: Blastn
[2024-01-24 13:32:17,299] [INFO] Running command: blastn -query GCF_001050195.2_ASM105019v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga1de0107-544b-4862-9717-b82995eecf9b/dqc_reference/reference_markers_gtdb.fasta -out GCF_001050195.2_ASM105019v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:18,069] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:18,072] [INFO] Selected 24 target genomes.
[2024-01-24 13:32:18,072] [INFO] Target genome list was writen to GCF_001050195.2_ASM105019v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:18,091] [INFO] Task started: fastANI
[2024-01-24 13:32:18,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ed61bf5-afa3-4b43-9024-14617c11c7e6/GCF_001050195.2_ASM105019v2_genomic.fna.gz --refList GCF_001050195.2_ASM105019v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001050195.2_ASM105019v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:31,827] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:31,834] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:31,834] [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_001050195.2	s__Anaerolinea thermolimosa	99.9999	1356	1388	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Anaerolinea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000199675.1	s__Anaerolinea thermophila	80.2702	148	1388	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Anaerolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001306145.1	s__Thermanaerothrix daxensis	76.8521	56	1388	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Thermanaerothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001306035.1	s__Levilinea saccharolytica	76.277	61	1388	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Levilinea	95.0	99.90	99.90	0.95	0.95	2	-
GCA_016927865.1	s__Anaerolinea sp016927865	76.2135	88	1388	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Anaerolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213455.1	s__Anaerolinea sp016213455	76.1234	72	1388	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Anaerolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002385985.1	s__UBA3924 sp002385985	75.475	52	1388	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA3924	95.0	99.86	99.86	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:31,836] [INFO] GTDB search result was written to GCF_001050195.2_ASM105019v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:31,837] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:31,839] [INFO] DFAST_QC result json was written to GCF_001050195.2_ASM105019v2_genomic.fna/dqc_result.json
[2024-01-24 13:32:31,840] [INFO] DFAST_QC completed!
[2024-01-24 13:32:31,840] [INFO] Total running time: 0h1m20s