[2024-01-24 13:01:39,198] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:39,201] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:39,201] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d9a488c-e0d6-445b-a5fe-5c2ab02d9c02/dqc_reference
[2024-01-24 13:01:41,090] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:41,091] [INFO] Task started: Prodigal
[2024-01-24 13:01:41,091] [INFO] Running command: gunzip -c /var/lib/cwl/stgd334416c-dd56-4b7a-bc75-8b4f40f4ca34/GCF_003265305.2_ASM326530v2_genomic.fna.gz | prodigal -d GCF_003265305.2_ASM326530v2_genomic.fna/cds.fna -a GCF_003265305.2_ASM326530v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:58,045] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:58,046] [INFO] Task started: HMMsearch
[2024-01-24 13:01:58,046] [INFO] Running command: hmmsearch --tblout GCF_003265305.2_ASM326530v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d9a488c-e0d6-445b-a5fe-5c2ab02d9c02/dqc_reference/reference_markers.hmm GCF_003265305.2_ASM326530v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:58,297] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:58,298] [INFO] Found 6/6 markers.
[2024-01-24 13:01:58,334] [INFO] Query marker FASTA was written to GCF_003265305.2_ASM326530v2_genomic.fna/markers.fasta
[2024-01-24 13:01:58,335] [INFO] Task started: Blastn
[2024-01-24 13:01:58,335] [INFO] Running command: blastn -query GCF_003265305.2_ASM326530v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d9a488c-e0d6-445b-a5fe-5c2ab02d9c02/dqc_reference/reference_markers.fasta -out GCF_003265305.2_ASM326530v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:58,944] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:58,948] [INFO] Selected 17 target genomes.
[2024-01-24 13:01:58,948] [INFO] Target genome list was writen to GCF_003265305.2_ASM326530v2_genomic.fna/target_genomes.txt
[2024-01-24 13:01:58,956] [INFO] Task started: fastANI
[2024-01-24 13:01:58,956] [INFO] Running command: fastANI --query /var/lib/cwl/stgd334416c-dd56-4b7a-bc75-8b4f40f4ca34/GCF_003265305.2_ASM326530v2_genomic.fna.gz --refList GCF_003265305.2_ASM326530v2_genomic.fna/target_genomes.txt --output GCF_003265305.2_ASM326530v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:11,266] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:11,267] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d9a488c-e0d6-445b-a5fe-5c2ab02d9c02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:11,267] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d9a488c-e0d6-445b-a5fe-5c2ab02d9c02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:11,272] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:11,272] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:11,272] [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
Pseudoprevotella muciniphila	strain=E39	GCA_003265305.2	2133944	2133944	type	True	100.0	973	973	95	conclusive
Prevotellamassilia timonensis	strain=Marseille-P2831	GCA_900106785.1	1852370	1852370	type	True	77.2589	64	973	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:11,274] [INFO] DFAST Taxonomy check result was written to GCF_003265305.2_ASM326530v2_genomic.fna/tc_result.tsv
[2024-01-24 13:02:11,274] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:11,274] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:11,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d9a488c-e0d6-445b-a5fe-5c2ab02d9c02/dqc_reference/checkm_data
[2024-01-24 13:02:11,276] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:11,314] [INFO] Task started: CheckM
[2024-01-24 13:02:11,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003265305.2_ASM326530v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003265305.2_ASM326530v2_genomic.fna/checkm_input GCF_003265305.2_ASM326530v2_genomic.fna/checkm_result
[2024-01-24 13:03:02,558] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:02,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:02,583] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:02,583] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:02,584] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003265305.2_ASM326530v2_genomic.fna/markers.fasta)
[2024-01-24 13:03:02,584] [INFO] Task started: Blastn
[2024-01-24 13:03:02,584] [INFO] Running command: blastn -query GCF_003265305.2_ASM326530v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d9a488c-e0d6-445b-a5fe-5c2ab02d9c02/dqc_reference/reference_markers_gtdb.fasta -out GCF_003265305.2_ASM326530v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:03,418] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:03,423] [INFO] Selected 23 target genomes.
[2024-01-24 13:03:03,423] [INFO] Target genome list was writen to GCF_003265305.2_ASM326530v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:03,460] [INFO] Task started: fastANI
[2024-01-24 13:03:03,461] [INFO] Running command: fastANI --query /var/lib/cwl/stgd334416c-dd56-4b7a-bc75-8b4f40f4ca34/GCF_003265305.2_ASM326530v2_genomic.fna.gz --refList GCF_003265305.2_ASM326530v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003265305.2_ASM326530v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:13,778] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:13,790] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:13,791] [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_003265305.2	s__Alloprevotella sp003265305	100.0	972	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	98.73	98.61	0.95	0.95	3	conclusive
GCA_900539625.1	s__Alloprevotella sp900539625	76.898	55	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	98.08	97.36	0.88	0.77	5	-
GCA_017461605.1	s__Alloprevotella sp017461605	76.7773	52	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004557185.1	s__Alloprevotella sp004557185	76.7161	72	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	98.58	98.39	0.90	0.87	3	-
GCA_017933995.1	s__Alloprevotella sp017933995	76.6404	91	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004557035.1	s__Alloprevotella sp004557035	76.2914	66	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	96.70	96.46	0.93	0.92	3	-
GCA_004556745.1	s__Alloprevotella sp004556745	76.1535	61	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	96.07	96.01	0.90	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:13,792] [INFO] GTDB search result was written to GCF_003265305.2_ASM326530v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:13,793] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:13,796] [INFO] DFAST_QC result json was written to GCF_003265305.2_ASM326530v2_genomic.fna/dqc_result.json
[2024-01-24 13:03:13,797] [INFO] DFAST_QC completed!
[2024-01-24 13:03:13,797] [INFO] Total running time: 0h1m35s