[2024-01-24 13:28:25,952] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:25,960] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:25,960] [INFO] DQC Reference Directory: /var/lib/cwl/stg98a1fa08-7b41-4952-b206-79485006d7bc/dqc_reference
[2024-01-24 13:28:27,341] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:27,345] [INFO] Task started: Prodigal
[2024-01-24 13:28:27,346] [INFO] Running command: gunzip -c /var/lib/cwl/stgb36129f6-5eeb-44cc-b120-6808e536cdae/GCF_009697385.1_ASM969738v1_genomic.fna.gz | prodigal -d GCF_009697385.1_ASM969738v1_genomic.fna/cds.fna -a GCF_009697385.1_ASM969738v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:35,090] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:35,090] [INFO] Task started: HMMsearch
[2024-01-24 13:28:35,090] [INFO] Running command: hmmsearch --tblout GCF_009697385.1_ASM969738v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98a1fa08-7b41-4952-b206-79485006d7bc/dqc_reference/reference_markers.hmm GCF_009697385.1_ASM969738v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:35,387] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:35,389] [INFO] Found 6/6 markers.
[2024-01-24 13:28:35,415] [INFO] Query marker FASTA was written to GCF_009697385.1_ASM969738v1_genomic.fna/markers.fasta
[2024-01-24 13:28:35,415] [INFO] Task started: Blastn
[2024-01-24 13:28:35,416] [INFO] Running command: blastn -query GCF_009697385.1_ASM969738v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98a1fa08-7b41-4952-b206-79485006d7bc/dqc_reference/reference_markers.fasta -out GCF_009697385.1_ASM969738v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:36,043] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:36,047] [INFO] Selected 15 target genomes.
[2024-01-24 13:28:36,048] [INFO] Target genome list was writen to GCF_009697385.1_ASM969738v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:36,070] [INFO] Task started: fastANI
[2024-01-24 13:28:36,070] [INFO] Running command: fastANI --query /var/lib/cwl/stgb36129f6-5eeb-44cc-b120-6808e536cdae/GCF_009697385.1_ASM969738v1_genomic.fna.gz --refList GCF_009697385.1_ASM969738v1_genomic.fna/target_genomes.txt --output GCF_009697385.1_ASM969738v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:43,310] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:43,311] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98a1fa08-7b41-4952-b206-79485006d7bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:43,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98a1fa08-7b41-4952-b206-79485006d7bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:43,323] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:43,323] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:43,323] [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 montiformis	strain=WCA-380-WT-3B3	GCA_009697385.1	2652285	2652285	type	True	100.0	864	867	95	conclusive
Mitsuokella jalaludinii	strain=DSM 13811	GCA_000702905.1	187979	187979	type	True	80.2831	203	867	95	below_threshold
Mitsuokella multacida	strain=DSM 20544	GCA_000155955.1	52226	52226	type	True	79.7558	222	867	95	below_threshold
Selenomonas ruminantium subsp. ruminantium	strain=ATCC 12561	GCA_000424065.1	114196	971	type	True	78.3083	185	867	95	below_threshold
Selenomonas sputigena	strain=ATCC 35185	GCA_000160495.1	69823	69823	neotype	True	76.8754	79	867	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:43,325] [INFO] DFAST Taxonomy check result was written to GCF_009697385.1_ASM969738v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:43,325] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:43,325] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:43,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98a1fa08-7b41-4952-b206-79485006d7bc/dqc_reference/checkm_data
[2024-01-24 13:28:43,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:43,357] [INFO] Task started: CheckM
[2024-01-24 13:28:43,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009697385.1_ASM969738v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009697385.1_ASM969738v1_genomic.fna/checkm_input GCF_009697385.1_ASM969738v1_genomic.fna/checkm_result
[2024-01-24 13:29:10,926] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:10,928] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:10,948] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:10,949] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:10,949] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009697385.1_ASM969738v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:10,950] [INFO] Task started: Blastn
[2024-01-24 13:29:10,950] [INFO] Running command: blastn -query GCF_009697385.1_ASM969738v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98a1fa08-7b41-4952-b206-79485006d7bc/dqc_reference/reference_markers_gtdb.fasta -out GCF_009697385.1_ASM969738v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:11,889] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:11,892] [INFO] Selected 18 target genomes.
[2024-01-24 13:29:11,892] [INFO] Target genome list was writen to GCF_009697385.1_ASM969738v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:11,936] [INFO] Task started: fastANI
[2024-01-24 13:29:11,936] [INFO] Running command: fastANI --query /var/lib/cwl/stgb36129f6-5eeb-44cc-b120-6808e536cdae/GCF_009697385.1_ASM969738v1_genomic.fna.gz --refList GCF_009697385.1_ASM969738v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009697385.1_ASM969738v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:21,108] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:21,131] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:21,132] [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_009697385.1	s__Selenomonas_A montiformis	100.0	864	867	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A	95.0	98.83	98.83	0.79	0.79	2	conclusive
GCF_000155955.1	s__Mitsuokella multacida	79.7336	223	867	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella	95.0	97.52	96.22	0.92	0.87	5	-
GCA_900769615.1	s__Selenomonas_A sp900769615	79.6614	115	867	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_015058575.1	s__Selenomonas_A ruminantium_O	79.2432	269	867	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_000702005.1	s__Selenomonas_A sp000702005	79.1836	245	867	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A	95.0	98.34	98.34	0.89	0.89	2	-
GCA_902364065.1	s__Mitsuokella sp003458855	79.1542	215	867	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella	95.0	97.62	95.79	0.87	0.62	6	-
GCF_900113715.1	s__Selenomonas_A ruminantium_F	79.0516	298	867	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A	95.0	97.92	97.43	0.89	0.84	3	-
GCF_008271295.1	s__Selenomonas_A sp008271295	79.0391	269	867	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A	95.0	98.50	98.50	0.96	0.96	2	-
GCF_900116485.1	s__Selenomonas_A ruminantium_G	78.9156	278	867	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_000424065.1	s__Selenomonas_A ruminantium	78.3295	184	867	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_018052705.1	s__Selenomonas_A sp018052705	78.1232	200	867	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_902766015.1	s__RUG11126 sp902766015	77.0169	111	867	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__RUG11126	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000286455.1	s__Centipeda sp000286455	76.7522	68	867	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Centipeda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902777615.1	s__RUG12372 sp902777615	76.2329	50	867	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__RUG12372	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:21,133] [INFO] GTDB search result was written to GCF_009697385.1_ASM969738v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:21,134] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:21,137] [INFO] DFAST_QC result json was written to GCF_009697385.1_ASM969738v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:21,137] [INFO] DFAST_QC completed!
[2024-01-24 13:29:21,137] [INFO] Total running time: 0h0m55s