[2024-01-24 13:32:11,687] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:11,688] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:11,689] [INFO] DQC Reference Directory: /var/lib/cwl/stg5024b2aa-d8cf-4f21-9b86-e7addae5b3e2/dqc_reference
[2024-01-24 13:32:12,907] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:12,908] [INFO] Task started: Prodigal
[2024-01-24 13:32:12,908] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ee4c789-f43e-4845-894f-0c447788cfea/GCF_000467875.1_ASM46787v1_genomic.fna.gz | prodigal -d GCF_000467875.1_ASM46787v1_genomic.fna/cds.fna -a GCF_000467875.1_ASM46787v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:25,753] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:25,753] [INFO] Task started: HMMsearch
[2024-01-24 13:32:25,754] [INFO] Running command: hmmsearch --tblout GCF_000467875.1_ASM46787v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5024b2aa-d8cf-4f21-9b86-e7addae5b3e2/dqc_reference/reference_markers.hmm GCF_000467875.1_ASM46787v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:26,000] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:26,001] [INFO] Found 6/6 markers.
[2024-01-24 13:32:26,031] [INFO] Query marker FASTA was written to GCF_000467875.1_ASM46787v1_genomic.fna/markers.fasta
[2024-01-24 13:32:26,032] [INFO] Task started: Blastn
[2024-01-24 13:32:26,032] [INFO] Running command: blastn -query GCF_000467875.1_ASM46787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5024b2aa-d8cf-4f21-9b86-e7addae5b3e2/dqc_reference/reference_markers.fasta -out GCF_000467875.1_ASM46787v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:26,621] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:26,624] [INFO] Selected 13 target genomes.
[2024-01-24 13:32:26,625] [INFO] Target genome list was writen to GCF_000467875.1_ASM46787v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:26,632] [INFO] Task started: fastANI
[2024-01-24 13:32:26,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ee4c789-f43e-4845-894f-0c447788cfea/GCF_000467875.1_ASM46787v1_genomic.fna.gz --refList GCF_000467875.1_ASM46787v1_genomic.fna/target_genomes.txt --output GCF_000467875.1_ASM46787v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:34,150] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:34,150] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5024b2aa-d8cf-4f21-9b86-e7addae5b3e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:34,151] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5024b2aa-d8cf-4f21-9b86-e7addae5b3e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:34,168] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:32:34,169] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:34,169] [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
Prevotella disiens	strain=ATCC 29426	GCA_000467875.1	28130	28130	type	True	100.0	767	777	95	conclusive
Prevotella disiens	strain=NCTC11157	GCA_900454955.1	28130	28130	type	True	99.9081	773	777	95	conclusive
Prevotella disiens	strain=JCM 6334	GCA_000613345.1	28130	28130	type	True	99.825	745	777	95	conclusive
Prevotella ihumii	strain=Marseille-P3385	GCA_900155655.1	1917878	1917878	type	True	82.6368	310	777	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	80.6554	79	777	95	below_threshold
Prevotella intermedia	strain=ATCC 25611	GCA_001953955.1	28131	28131	type	True	80.2662	341	777	95	below_threshold
Prevotella intermedia	strain=DSM 20706	GCA_000439065.1	28131	28131	type	True	80.2272	329	777	95	below_threshold
Prevotella intermedia	strain=ATCC 25611	GCA_000519165.1	28131	28131	type	True	80.1515	331	777	95	below_threshold
Prevotella falsenii	strain=JCM 15124	GCA_000613945.1	515414	515414	type	True	79.9813	327	777	95	below_threshold
Prevotella aurantiaca	strain=JCM 15754	GCA_000614025.1	596085	596085	type	True	79.7877	311	777	95	below_threshold
Prevotella scopos	strain=W2052	GCA_001683355.1	589437	589437	type	True	78.9793	152	777	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:34,171] [INFO] DFAST Taxonomy check result was written to GCF_000467875.1_ASM46787v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:34,172] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:34,172] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:34,172] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5024b2aa-d8cf-4f21-9b86-e7addae5b3e2/dqc_reference/checkm_data
[2024-01-24 13:32:34,174] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:34,201] [INFO] Task started: CheckM
[2024-01-24 13:32:34,201] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000467875.1_ASM46787v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000467875.1_ASM46787v1_genomic.fna/checkm_input GCF_000467875.1_ASM46787v1_genomic.fna/checkm_result
[2024-01-24 13:33:16,552] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:16,553] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:16,571] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:16,571] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:16,571] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000467875.1_ASM46787v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:16,572] [INFO] Task started: Blastn
[2024-01-24 13:33:16,572] [INFO] Running command: blastn -query GCF_000467875.1_ASM46787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5024b2aa-d8cf-4f21-9b86-e7addae5b3e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000467875.1_ASM46787v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:17,500] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:17,503] [INFO] Selected 16 target genomes.
[2024-01-24 13:33:17,503] [INFO] Target genome list was writen to GCF_000467875.1_ASM46787v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:17,515] [INFO] Task started: fastANI
[2024-01-24 13:33:17,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ee4c789-f43e-4845-894f-0c447788cfea/GCF_000467875.1_ASM46787v1_genomic.fna.gz --refList GCF_000467875.1_ASM46787v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000467875.1_ASM46787v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:25,842] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:25,853] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:25,854] [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_000613345.1	s__Prevotella disiens	99.825	745	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.74	97.99	0.90	0.82	7	conclusive
GCF_900155655.1	s__Prevotella ihumii	82.6932	308	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378745.1	s__Prevotella amnii	81.9003	110	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.70	98.21	0.90	0.86	5	-
GCF_001953955.1	s__Prevotella intermedia	80.2662	341	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.61	96.13	0.88	0.83	34	-
GCF_000613945.1	s__Prevotella falsenii	79.9813	327	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000614025.1	s__Prevotella aurantiaca	79.7873	311	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.47	98.39	0.93	0.91	4	-
GCF_018127925.1	s__Prevotella melaninogenica_C	79.7725	127	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000144405.1	s__Prevotella melaninogenica	79.3434	120	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.46	95.36	0.87	0.78	36	-
GCF_000220255.1	s__Prevotella pallens	79.2059	285	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.33	96.89	0.94	0.88	40	-
GCF_000220235.1	s__Prevotella nigrescens	78.9544	262	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.14	97.70	0.92	0.78	13	-
GCF_018127785.1	s__Prevotella scopos	78.8435	144	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.97	1.00	1.00	4	-
GCF_018127965.1	s__Prevotella melaninogenica_B	77.4284	111	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.77	95.72	0.91	0.89	4	-
GCA_013333285.2	s__Prevotella sp013333285	77.3724	57	777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.46	97.41	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:25,855] [INFO] GTDB search result was written to GCF_000467875.1_ASM46787v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:25,856] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:25,859] [INFO] DFAST_QC result json was written to GCF_000467875.1_ASM46787v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:25,859] [INFO] DFAST_QC completed!
[2024-01-24 13:33:25,859] [INFO] Total running time: 0h1m14s