[2024-01-24 12:06:50,745] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:50,747] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:50,747] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5c5c292-be09-43bb-b350-9c74c73d6f00/dqc_reference
[2024-01-24 12:06:51,961] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:51,962] [INFO] Task started: Prodigal
[2024-01-24 12:06:51,962] [INFO] Running command: gunzip -c /var/lib/cwl/stgd02e3035-e21d-4daa-947b-7b26cfa7c6e5/GCF_003149165.1_ASM314916v1_genomic.fna.gz | prodigal -d GCF_003149165.1_ASM314916v1_genomic.fna/cds.fna -a GCF_003149165.1_ASM314916v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:02,153] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:02,154] [INFO] Task started: HMMsearch
[2024-01-24 12:07:02,154] [INFO] Running command: hmmsearch --tblout GCF_003149165.1_ASM314916v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5c5c292-be09-43bb-b350-9c74c73d6f00/dqc_reference/reference_markers.hmm GCF_003149165.1_ASM314916v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:02,424] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:02,426] [INFO] Found 6/6 markers.
[2024-01-24 12:07:02,461] [INFO] Query marker FASTA was written to GCF_003149165.1_ASM314916v1_genomic.fna/markers.fasta
[2024-01-24 12:07:02,461] [INFO] Task started: Blastn
[2024-01-24 12:07:02,461] [INFO] Running command: blastn -query GCF_003149165.1_ASM314916v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5c5c292-be09-43bb-b350-9c74c73d6f00/dqc_reference/reference_markers.fasta -out GCF_003149165.1_ASM314916v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:03,056] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:03,059] [INFO] Selected 13 target genomes.
[2024-01-24 12:07:03,060] [INFO] Target genome list was writen to GCF_003149165.1_ASM314916v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:03,068] [INFO] Task started: fastANI
[2024-01-24 12:07:03,068] [INFO] Running command: fastANI --query /var/lib/cwl/stgd02e3035-e21d-4daa-947b-7b26cfa7c6e5/GCF_003149165.1_ASM314916v1_genomic.fna.gz --refList GCF_003149165.1_ASM314916v1_genomic.fna/target_genomes.txt --output GCF_003149165.1_ASM314916v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:10,246] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:10,247] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5c5c292-be09-43bb-b350-9c74c73d6f00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:10,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5c5c292-be09-43bb-b350-9c74c73d6f00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:10,255] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:07:10,255] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:07:10,256] [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
Fibrobacter succinogenes subsp. succinogenes	strain=S85	GCA_000146505.1	834	833	type	True	93.4765	993	1167	95	below_threshold
Fibrobacter succinogenes subsp. succinogenes	strain=S85	GCA_000024665.1	834	833	type	True	93.4632	995	1167	95	below_threshold
Hallerella succinigenes	strain=UWS3	GCA_002797675.1	1896222	1896222	type	True	79.5449	193	1167	95	below_threshold
Hallerella porci	strain=UWS4	GCA_003148885.1	1945871	1945871	type	True	78.1526	99	1167	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:10,257] [INFO] DFAST Taxonomy check result was written to GCF_003149165.1_ASM314916v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:10,258] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:10,258] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:10,258] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5c5c292-be09-43bb-b350-9c74c73d6f00/dqc_reference/checkm_data
[2024-01-24 12:07:10,259] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:10,299] [INFO] Task started: CheckM
[2024-01-24 12:07:10,300] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003149165.1_ASM314916v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003149165.1_ASM314916v1_genomic.fna/checkm_input GCF_003149165.1_ASM314916v1_genomic.fna/checkm_result
[2024-01-24 12:07:44,472] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:44,473] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:44,497] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:44,497] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:44,498] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003149165.1_ASM314916v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:44,498] [INFO] Task started: Blastn
[2024-01-24 12:07:44,498] [INFO] Running command: blastn -query GCF_003149165.1_ASM314916v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5c5c292-be09-43bb-b350-9c74c73d6f00/dqc_reference/reference_markers_gtdb.fasta -out GCF_003149165.1_ASM314916v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:45,278] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:45,281] [INFO] Selected 7 target genomes.
[2024-01-24 12:07:45,282] [INFO] Target genome list was writen to GCF_003149165.1_ASM314916v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:45,287] [INFO] Task started: fastANI
[2024-01-24 12:07:45,288] [INFO] Running command: fastANI --query /var/lib/cwl/stgd02e3035-e21d-4daa-947b-7b26cfa7c6e5/GCF_003149165.1_ASM314916v1_genomic.fna.gz --refList GCF_003149165.1_ASM314916v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003149165.1_ASM314916v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:52,161] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:52,174] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:52,174] [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_002210425.1	s__Fibrobacter elongatus	97.1286	1035	1167	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.37	97.19	0.91	0.89	4	conclusive
GCF_000146505.1	s__Fibrobacter succinogenes	93.4765	993	1167	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900177805.1	s__Fibrobacter sp900177805	91.9702	955	1167	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.22	97.22	0.89	0.89	2	-
GCF_900215325.1	s__Fibrobacter sp900215325	91.7392	942	1167	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.50	97.09	0.94	0.94	6	-
GCA_002394865.1	s__Fibrobacter sp002394865	91.4613	937	1167	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCA_902791475.1	s__Fibrobacter succinogenes_J	91.2368	910	1167	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	95.39	95.39	0.76	0.76	2	-
GCF_002210345.1	s__Fibrobacter sp002210345	89.4524	897	1167	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.16	96.29	0.89	0.80	6	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:52,177] [INFO] GTDB search result was written to GCF_003149165.1_ASM314916v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:52,177] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:52,181] [INFO] DFAST_QC result json was written to GCF_003149165.1_ASM314916v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:52,181] [INFO] DFAST_QC completed!
[2024-01-24 12:07:52,181] [INFO] Total running time: 0h1m1s