[2024-01-24 13:13:12,368] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:12,371] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:12,371] [INFO] DQC Reference Directory: /var/lib/cwl/stgada8624a-46d5-4a93-9573-0be6b88344d3/dqc_reference
[2024-01-24 13:13:13,778] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:13,779] [INFO] Task started: Prodigal
[2024-01-24 13:13:13,779] [INFO] Running command: gunzip -c /var/lib/cwl/stgf19c991f-3843-406f-adab-72f685f2e352/GCF_003862475.1_ASM386247v1_genomic.fna.gz | prodigal -d GCF_003862475.1_ASM386247v1_genomic.fna/cds.fna -a GCF_003862475.1_ASM386247v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:20,161] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:20,161] [INFO] Task started: HMMsearch
[2024-01-24 13:13:20,161] [INFO] Running command: hmmsearch --tblout GCF_003862475.1_ASM386247v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgada8624a-46d5-4a93-9573-0be6b88344d3/dqc_reference/reference_markers.hmm GCF_003862475.1_ASM386247v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:20,433] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:20,435] [INFO] Found 6/6 markers.
[2024-01-24 13:13:20,462] [INFO] Query marker FASTA was written to GCF_003862475.1_ASM386247v1_genomic.fna/markers.fasta
[2024-01-24 13:13:20,462] [INFO] Task started: Blastn
[2024-01-24 13:13:20,462] [INFO] Running command: blastn -query GCF_003862475.1_ASM386247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgada8624a-46d5-4a93-9573-0be6b88344d3/dqc_reference/reference_markers.fasta -out GCF_003862475.1_ASM386247v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:21,094] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:21,097] [INFO] Selected 15 target genomes.
[2024-01-24 13:13:21,098] [INFO] Target genome list was writen to GCF_003862475.1_ASM386247v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:21,548] [INFO] Task started: fastANI
[2024-01-24 13:13:21,549] [INFO] Running command: fastANI --query /var/lib/cwl/stgf19c991f-3843-406f-adab-72f685f2e352/GCF_003862475.1_ASM386247v1_genomic.fna.gz --refList GCF_003862475.1_ASM386247v1_genomic.fna/target_genomes.txt --output GCF_003862475.1_ASM386247v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:30,002] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:30,002] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgada8624a-46d5-4a93-9573-0be6b88344d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:30,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgada8624a-46d5-4a93-9573-0be6b88344d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:30,009] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:30,009] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:30,009] [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
Lachnoanaerobaculum gingivalis	strain=KCOM 2030	GCA_003862475.1	2490855	2490855	type	True	100.0	1026	1026	95	conclusive
Lachnoanaerobaculum umeaense	strain=DSM 23576 = CCUG 58757	GCA_003589745.1	617123	617123	type	True	85.8047	646	1026	95	below_threshold
Lachnoanaerobaculum umeaense	strain=DSM 23576	GCA_003254255.1	617123	617123	type	True	85.6188	617	1026	95	below_threshold
Lachnoanaerobaculum orale	strain=DSM 24553	GCA_003862485.1	979627	979627	type	True	84.7858	655	1026	95	below_threshold
Lachnoanaerobaculum saburreum	strain=DSM 3986	GCA_000185385.1	467210	467210	type	True	83.1769	633	1026	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:30,011] [INFO] DFAST Taxonomy check result was written to GCF_003862475.1_ASM386247v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:30,012] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:30,012] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:30,012] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgada8624a-46d5-4a93-9573-0be6b88344d3/dqc_reference/checkm_data
[2024-01-24 13:13:30,013] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:30,050] [INFO] Task started: CheckM
[2024-01-24 13:13:30,050] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003862475.1_ASM386247v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003862475.1_ASM386247v1_genomic.fna/checkm_input GCF_003862475.1_ASM386247v1_genomic.fna/checkm_result
[2024-01-24 13:13:56,739] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:56,740] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:56,759] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:56,760] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:56,761] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003862475.1_ASM386247v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:56,761] [INFO] Task started: Blastn
[2024-01-24 13:13:56,761] [INFO] Running command: blastn -query GCF_003862475.1_ASM386247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgada8624a-46d5-4a93-9573-0be6b88344d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_003862475.1_ASM386247v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:57,714] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:57,717] [INFO] Selected 7 target genomes.
[2024-01-24 13:13:57,718] [INFO] Target genome list was writen to GCF_003862475.1_ASM386247v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:57,740] [INFO] Task started: fastANI
[2024-01-24 13:13:57,741] [INFO] Running command: fastANI --query /var/lib/cwl/stgf19c991f-3843-406f-adab-72f685f2e352/GCF_003862475.1_ASM386247v1_genomic.fna.gz --refList GCF_003862475.1_ASM386247v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003862475.1_ASM386247v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:03,443] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:03,450] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:03,450] [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_003862475.1	s__Lachnoanaerobaculum gingivalis	100.0	1026	1026	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000287675.1	s__Lachnoanaerobaculum sp000287675	93.5111	769	1026	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	96.71	96.71	0.86	0.86	2	-
GCF_000296385.1	s__Lachnoanaerobaculum sp000296385	93.4508	792	1026	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	96.95	96.95	0.89	0.89	2	-
GCA_000209465.1	s__Lachnoanaerobaculum sp000209465	85.9455	725	1026	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	98.01	98.01	0.91	0.91	2	-
GCF_003589745.1	s__Lachnoanaerobaculum umeaense	85.8194	648	1026	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003862485.1	s__Lachnoanaerobaculum orale	84.8397	657	1026	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	95.98	95.69	0.85	0.82	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:03,452] [INFO] GTDB search result was written to GCF_003862475.1_ASM386247v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:03,452] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:03,456] [INFO] DFAST_QC result json was written to GCF_003862475.1_ASM386247v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:03,456] [INFO] DFAST_QC completed!
[2024-01-24 13:14:03,456] [INFO] Total running time: 0h0m51s