[2023-06-29 06:24:07,904] [INFO] DFAST_QC pipeline started.
[2023-06-29 06:24:07,909] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 06:24:07,909] [INFO] DQC Reference Directory: /var/lib/cwl/stg0392edc2-2880-4f14-9496-3b454d09a249/dqc_reference
[2023-06-29 06:24:10,160] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 06:24:10,161] [INFO] Task started: Prodigal
[2023-06-29 06:24:10,161] [INFO] Running command: gunzip -c /var/lib/cwl/stgf6bac41b-6b81-4021-b5f1-5c98f91d3fb4/GCA_020025035.1_ASM2002503v1_genomic.fna.gz | prodigal -d GCA_020025035.1_ASM2002503v1_genomic.fna/cds.fna -a GCA_020025035.1_ASM2002503v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 06:24:11,853] [INFO] Task succeeded: Prodigal
[2023-06-29 06:24:11,853] [INFO] Task started: HMMsearch
[2023-06-29 06:24:11,853] [INFO] Running command: hmmsearch --tblout GCA_020025035.1_ASM2002503v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0392edc2-2880-4f14-9496-3b454d09a249/dqc_reference/reference_markers.hmm GCA_020025035.1_ASM2002503v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 06:24:12,092] [INFO] Task succeeded: HMMsearch
[2023-06-29 06:24:12,094] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf6bac41b-6b81-4021-b5f1-5c98f91d3fb4/GCA_020025035.1_ASM2002503v1_genomic.fna.gz]
[2023-06-29 06:24:12,113] [INFO] Query marker FASTA was written to GCA_020025035.1_ASM2002503v1_genomic.fna/markers.fasta
[2023-06-29 06:24:12,114] [INFO] Task started: Blastn
[2023-06-29 06:24:12,114] [INFO] Running command: blastn -query GCA_020025035.1_ASM2002503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0392edc2-2880-4f14-9496-3b454d09a249/dqc_reference/reference_markers.fasta -out GCA_020025035.1_ASM2002503v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 06:24:13,962] [INFO] Task succeeded: Blastn
[2023-06-29 06:24:13,966] [INFO] Selected 23 target genomes.
[2023-06-29 06:24:13,967] [INFO] Target genome list was writen to GCA_020025035.1_ASM2002503v1_genomic.fna/target_genomes.txt
[2023-06-29 06:24:13,988] [INFO] Task started: fastANI
[2023-06-29 06:24:13,988] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6bac41b-6b81-4021-b5f1-5c98f91d3fb4/GCA_020025035.1_ASM2002503v1_genomic.fna.gz --refList GCA_020025035.1_ASM2002503v1_genomic.fna/target_genomes.txt --output GCA_020025035.1_ASM2002503v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 06:24:22,700] [INFO] Task succeeded: fastANI
[2023-06-29 06:24:22,701] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0392edc2-2880-4f14-9496-3b454d09a249/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 06:24:22,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0392edc2-2880-4f14-9496-3b454d09a249/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 06:24:22,713] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 06:24:22,714] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 06:24:22,714] [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
Longibaculum muris	strain=DSM 29487	GCA_024622235.1	1796628	1796628	type	True	77.4276	50	349	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_004343035.1	1796628	1796628	type	True	77.4276	50	349	95	below_threshold
Faecalibacillus faecis	strain=SNUG30370	GCA_003024675.1	1982628	1982628	type	True	77.2078	57	349	95	below_threshold
[Clostridium] cocleatum	strain=I50	GCA_010206155.1	69824	69824	type	True	77.1666	62	349	95	below_threshold
[Clostridium] cocleatum	strain=ATCC 29902	GCA_002803405.1	69824	69824	type	True	77.1184	63	349	95	below_threshold
Tannockella kyphosi	strain=BP52G	GCA_021054785.1	2899121	2899121	type	True	77.0229	67	349	95	below_threshold
[Clostridium] cocleatum	strain=DSM 1551	GCA_900102365.1	69824	69824	type	True	77.0003	63	349	95	below_threshold
[Clostridium] saccharogumia	strain=DSM 17460	GCA_000686665.1	341225	341225	type	True	76.9229	57	349	95	below_threshold
[Clostridium] cocleatum	strain=DSM 1551	GCA_024622895.1	69824	69824	type	True	76.9215	64	349	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_025149465.1	29348	29348	type	True	76.824	74	349	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 06:24:22,716] [INFO] DFAST Taxonomy check result was written to GCA_020025035.1_ASM2002503v1_genomic.fna/tc_result.tsv
[2023-06-29 06:24:22,717] [INFO] ===== Taxonomy check completed =====
[2023-06-29 06:24:22,717] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 06:24:22,717] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0392edc2-2880-4f14-9496-3b454d09a249/dqc_reference/checkm_data
[2023-06-29 06:24:22,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 06:24:22,739] [INFO] Task started: CheckM
[2023-06-29 06:24:22,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020025035.1_ASM2002503v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020025035.1_ASM2002503v1_genomic.fna/checkm_input GCA_020025035.1_ASM2002503v1_genomic.fna/checkm_result
[2023-06-29 06:24:36,431] [INFO] Task succeeded: CheckM
[2023-06-29 06:24:36,433] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 06:24:36,452] [INFO] ===== Completeness check finished =====
[2023-06-29 06:24:36,453] [INFO] ===== Start GTDB Search =====
[2023-06-29 06:24:36,453] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020025035.1_ASM2002503v1_genomic.fna/markers.fasta)
[2023-06-29 06:24:36,454] [INFO] Task started: Blastn
[2023-06-29 06:24:36,454] [INFO] Running command: blastn -query GCA_020025035.1_ASM2002503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0392edc2-2880-4f14-9496-3b454d09a249/dqc_reference/reference_markers_gtdb.fasta -out GCA_020025035.1_ASM2002503v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 06:24:37,268] [INFO] Task succeeded: Blastn
[2023-06-29 06:24:37,273] [INFO] Selected 21 target genomes.
[2023-06-29 06:24:37,273] [INFO] Target genome list was writen to GCA_020025035.1_ASM2002503v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 06:24:37,279] [INFO] Task started: fastANI
[2023-06-29 06:24:37,279] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6bac41b-6b81-4021-b5f1-5c98f91d3fb4/GCA_020025035.1_ASM2002503v1_genomic.fna.gz --refList GCA_020025035.1_ASM2002503v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020025035.1_ASM2002503v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 06:24:44,700] [INFO] Task succeeded: fastANI
[2023-06-29 06:24:44,727] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 06:24:44,728] [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_018365815.1	s__Beduini sp018365815	78.5459	142	349	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Beduini	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588075.1	s__MGBC163490 sp910588075	77.4824	63	349	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__MGBC163490	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001244545.1	s__Stoquefichus sp001244545	77.2898	64	349	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Stoquefichus	95.0	98.22	98.22	0.87	0.87	2	-
GCF_003024675.1	s__Faecalibacillus faecis	77.2134	56	349	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	97.99	96.95	0.86	0.80	14	-
GCA_000508865.1	s__Erysipelatoclostridium sp000508865	77.0042	57	349	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102365.1	s__Erysipelatoclostridium cocleatum	77.0003	63	349	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	99.07	98.04	0.92	0.85	5	-
GCA_900550005.1	s__Beduini sp900550005	76.9709	59	349	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Beduini	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686665.1	s__Erysipelatoclostridium saccharogumia	76.8787	58	349	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003024685.1	s__Faecalibacillus intestinalis	76.8495	70	349	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	97.94	96.13	0.85	0.76	51	-
GCA_018369555.1	s__Erysipelatoclostridium spiroforme_A	76.7946	67	349	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 06:24:44,730] [INFO] GTDB search result was written to GCA_020025035.1_ASM2002503v1_genomic.fna/result_gtdb.tsv
[2023-06-29 06:24:44,730] [INFO] ===== GTDB Search completed =====
[2023-06-29 06:24:44,734] [INFO] DFAST_QC result json was written to GCA_020025035.1_ASM2002503v1_genomic.fna/dqc_result.json
[2023-06-29 06:24:44,735] [INFO] DFAST_QC completed!
[2023-06-29 06:24:44,735] [INFO] Total running time: 0h0m37s