[2024-01-25 20:22:05,722] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:22:05,724] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:22:05,724] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ad3bc62-6b82-4148-8188-54a264a4d1e4/dqc_reference
[2024-01-25 20:22:06,940] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:22:06,941] [INFO] Task started: Prodigal
[2024-01-25 20:22:06,941] [INFO] Running command: gunzip -c /var/lib/cwl/stg393818fc-250a-4bc2-9fb3-6e435f3ca462/GCF_000424065.1_ASM42406v1_genomic.fna.gz | prodigal -d GCF_000424065.1_ASM42406v1_genomic.fna/cds.fna -a GCF_000424065.1_ASM42406v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:22:14,844] [INFO] Task succeeded: Prodigal
[2024-01-25 20:22:14,845] [INFO] Task started: HMMsearch
[2024-01-25 20:22:14,845] [INFO] Running command: hmmsearch --tblout GCF_000424065.1_ASM42406v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ad3bc62-6b82-4148-8188-54a264a4d1e4/dqc_reference/reference_markers.hmm GCF_000424065.1_ASM42406v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:22:15,066] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:22:15,067] [INFO] Found 6/6 markers.
[2024-01-25 20:22:15,128] [INFO] Query marker FASTA was written to GCF_000424065.1_ASM42406v1_genomic.fna/markers.fasta
[2024-01-25 20:22:15,128] [INFO] Task started: Blastn
[2024-01-25 20:22:15,128] [INFO] Running command: blastn -query GCF_000424065.1_ASM42406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ad3bc62-6b82-4148-8188-54a264a4d1e4/dqc_reference/reference_markers.fasta -out GCF_000424065.1_ASM42406v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:15,715] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:15,718] [INFO] Selected 19 target genomes.
[2024-01-25 20:22:15,719] [INFO] Target genome list was writen to GCF_000424065.1_ASM42406v1_genomic.fna/target_genomes.txt
[2024-01-25 20:22:15,728] [INFO] Task started: fastANI
[2024-01-25 20:22:15,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg393818fc-250a-4bc2-9fb3-6e435f3ca462/GCF_000424065.1_ASM42406v1_genomic.fna.gz --refList GCF_000424065.1_ASM42406v1_genomic.fna/target_genomes.txt --output GCF_000424065.1_ASM42406v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:22:25,316] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:25,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ad3bc62-6b82-4148-8188-54a264a4d1e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:22:25,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ad3bc62-6b82-4148-8188-54a264a4d1e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:22:25,322] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:22:25,323] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:22:25,323] [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
Selenomonas ruminantium subsp. ruminantium	strain=ATCC 12561	GCA_000424065.1	114196	971	type	True	100.0	1093	1095	95	conclusive
Selenomonas montiformis	strain=WCA-380-WT-3B3	GCA_009697385.1	2652285	2652285	type	True	78.0764	195	1095	95	below_threshold
Mitsuokella jalaludinii	strain=DSM 13811	GCA_000702905.1	187979	187979	type	True	77.9635	123	1095	95	below_threshold
Mitsuokella multacida	strain=DSM 20544	GCA_000155955.1	52226	52226	type	True	77.7102	138	1095	95	below_threshold
Anaerovibrio lipolyticus	strain=DSM 3074	GCA_900141865.1	82374	82374	type	True	77.5336	67	1095	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:22:25,324] [INFO] DFAST Taxonomy check result was written to GCF_000424065.1_ASM42406v1_genomic.fna/tc_result.tsv
[2024-01-25 20:22:25,325] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:22:25,325] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:22:25,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ad3bc62-6b82-4148-8188-54a264a4d1e4/dqc_reference/checkm_data
[2024-01-25 20:22:25,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:22:25,365] [INFO] Task started: CheckM
[2024-01-25 20:22:25,365] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000424065.1_ASM42406v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000424065.1_ASM42406v1_genomic.fna/checkm_input GCF_000424065.1_ASM42406v1_genomic.fna/checkm_result
[2024-01-25 20:22:52,441] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:52,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:52,463] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:52,463] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:52,463] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000424065.1_ASM42406v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:52,463] [INFO] Task started: Blastn
[2024-01-25 20:22:52,463] [INFO] Running command: blastn -query GCF_000424065.1_ASM42406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ad3bc62-6b82-4148-8188-54a264a4d1e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000424065.1_ASM42406v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:53,333] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:53,337] [INFO] Selected 7 target genomes.
[2024-01-25 20:22:53,337] [INFO] Target genome list was writen to GCF_000424065.1_ASM42406v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:53,346] [INFO] Task started: fastANI
[2024-01-25 20:22:53,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg393818fc-250a-4bc2-9fb3-6e435f3ca462/GCF_000424065.1_ASM42406v1_genomic.fna.gz --refList GCF_000424065.1_ASM42406v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000424065.1_ASM42406v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:58,627] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:58,633] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:22:58,633] [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_000424065.1	s__Selenomonas_A ruminantium	100.0	1092	1095	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902781305.1	s__Selenomonas_A ruminantium_K	91.5995	689	1095	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A	95.0	96.19	96.12	0.81	0.81	3	-
GCA_902798865.1	s__Selenomonas_A ruminantium_L	91.5853	576	1095	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785885.1	s__Selenomonas_A ruminantium_M	91.0618	604	1095	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002373045.1	s__Selenomonas_A ruminantium_J	90.8982	616	1095	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A	95.0	95.67	95.67	0.66	0.66	2	-
GCA_002448495.1	s__Selenomonas_A ruminantium_I	87.6079	454	1095	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687995.1	s__Selenomonas_A ruminantium_B	86.396	621	1095	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A	95.0	96.25	95.94	0.82	0.80	5	-
--------------------------------------------------------------------------------
[2024-01-25 20:22:58,634] [INFO] GTDB search result was written to GCF_000424065.1_ASM42406v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:58,635] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:58,637] [INFO] DFAST_QC result json was written to GCF_000424065.1_ASM42406v1_genomic.fna/dqc_result.json
[2024-01-25 20:22:58,637] [INFO] DFAST_QC completed!
[2024-01-25 20:22:58,637] [INFO] Total running time: 0h0m53s