[2024-01-24 14:55:51,316] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:51,319] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:51,319] [INFO] DQC Reference Directory: /var/lib/cwl/stg84efd2ac-0f38-4d0e-a953-a76da4edd01e/dqc_reference
[2024-01-24 14:55:52,601] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:52,602] [INFO] Task started: Prodigal
[2024-01-24 14:55:52,602] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d0dbf71-cc59-42b4-9eff-6afd25ab866c/GCF_000585335.1_ASM58533v1_genomic.fna.gz | prodigal -d GCF_000585335.1_ASM58533v1_genomic.fna/cds.fna -a GCF_000585335.1_ASM58533v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:01,625] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:01,625] [INFO] Task started: HMMsearch
[2024-01-24 14:56:01,626] [INFO] Running command: hmmsearch --tblout GCF_000585335.1_ASM58533v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84efd2ac-0f38-4d0e-a953-a76da4edd01e/dqc_reference/reference_markers.hmm GCF_000585335.1_ASM58533v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:01,896] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:01,925] [INFO] Found 6/6 markers.
[2024-01-24 14:56:01,958] [INFO] Query marker FASTA was written to GCF_000585335.1_ASM58533v1_genomic.fna/markers.fasta
[2024-01-24 14:56:01,958] [INFO] Task started: Blastn
[2024-01-24 14:56:01,958] [INFO] Running command: blastn -query GCF_000585335.1_ASM58533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84efd2ac-0f38-4d0e-a953-a76da4edd01e/dqc_reference/reference_markers.fasta -out GCF_000585335.1_ASM58533v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:02,592] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:02,595] [INFO] Selected 5 target genomes.
[2024-01-24 14:56:02,596] [INFO] Target genome list was writen to GCF_000585335.1_ASM58533v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:02,600] [INFO] Task started: fastANI
[2024-01-24 14:56:02,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d0dbf71-cc59-42b4-9eff-6afd25ab866c/GCF_000585335.1_ASM58533v1_genomic.fna.gz --refList GCF_000585335.1_ASM58533v1_genomic.fna/target_genomes.txt --output GCF_000585335.1_ASM58533v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:06,716] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:06,717] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84efd2ac-0f38-4d0e-a953-a76da4edd01e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:06,717] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84efd2ac-0f38-4d0e-a953-a76da4edd01e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:06,723] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:56:06,723] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:06,723] [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
Cloacibacillus evryensis	strain=DSM 19522	GCA_000585335.1	508460	508460	type	True	100.0	1161	1162	95	conclusive
Cloacibacillus porcorum	strain=CL-84	GCA_001701045.1	1197717	1197717	type	True	84.323	758	1162	95	below_threshold
Synergistes jonesii	strain=ATCC 49833	GCA_001757485.1	2754	2754	type	True	78.8298	322	1162	95	below_threshold
Synergistes jonesii	strain=78-1	GCA_000712295.1	2754	2754	type	True	78.7984	335	1162	95	below_threshold
Synergistes jonesii	strain=78-1	GCA_001757465.1	2754	2754	type	True	78.7671	318	1162	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:06,724] [INFO] DFAST Taxonomy check result was written to GCF_000585335.1_ASM58533v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:06,725] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:06,725] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:06,725] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84efd2ac-0f38-4d0e-a953-a76da4edd01e/dqc_reference/checkm_data
[2024-01-24 14:56:06,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:06,765] [INFO] Task started: CheckM
[2024-01-24 14:56:06,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000585335.1_ASM58533v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000585335.1_ASM58533v1_genomic.fna/checkm_input GCF_000585335.1_ASM58533v1_genomic.fna/checkm_result
[2024-01-24 14:56:37,620] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:37,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:37,643] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:37,644] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:37,644] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000585335.1_ASM58533v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:37,644] [INFO] Task started: Blastn
[2024-01-24 14:56:37,645] [INFO] Running command: blastn -query GCF_000585335.1_ASM58533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84efd2ac-0f38-4d0e-a953-a76da4edd01e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000585335.1_ASM58533v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:38,678] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:38,681] [INFO] Selected 6 target genomes.
[2024-01-24 14:56:38,682] [INFO] Target genome list was writen to GCF_000585335.1_ASM58533v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:38,688] [INFO] Task started: fastANI
[2024-01-24 14:56:38,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d0dbf71-cc59-42b4-9eff-6afd25ab866c/GCF_000585335.1_ASM58533v1_genomic.fna.gz --refList GCF_000585335.1_ASM58533v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000585335.1_ASM58533v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:43,587] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:43,594] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:43,594] [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_000585335.1	s__Cloacibacillus evryensis	100.0	1161	1162	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Cloacibacillus	95.0	98.47	98.41	0.85	0.85	4	conclusive
GCF_001701045.1	s__Cloacibacillus porcorum	84.311	760	1162	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Cloacibacillus	95.0	98.00	97.94	0.91	0.91	4	-
GCA_900544635.1	s__Caccocola faecigallinarum	79.4104	262	1162	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Caccocola	95.0	96.54	96.25	0.92	0.91	3	-
GCF_000712295.1	s__Synergistes jonesii	78.8147	333	1162	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Synergistes	95.0	99.99	99.98	1.00	1.00	6	-
GCA_018716365.1	s__Caccocola faecipullorum	78.6347	261	1162	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Caccocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159945.1	s__Caccocola sp002159945	78.5763	342	1162	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Caccocola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:43,596] [INFO] GTDB search result was written to GCF_000585335.1_ASM58533v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:43,596] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:43,600] [INFO] DFAST_QC result json was written to GCF_000585335.1_ASM58533v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:43,600] [INFO] DFAST_QC completed!
[2024-01-24 14:56:43,600] [INFO] Total running time: 0h0m52s