[2024-01-24 13:28:25,950] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:25,953] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:25,953] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1903438-0f60-4f48-b864-e1231dce8f1c/dqc_reference
[2024-01-24 13:28:27,431] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:27,433] [INFO] Task started: Prodigal
[2024-01-24 13:28:27,433] [INFO] Running command: gunzip -c /var/lib/cwl/stga54c5200-3de5-4bd2-a0b2-2da52bbf8e83/GCF_000421205.1_ASM42120v1_genomic.fna.gz | prodigal -d GCF_000421205.1_ASM42120v1_genomic.fna/cds.fna -a GCF_000421205.1_ASM42120v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:44,129] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:44,130] [INFO] Task started: HMMsearch
[2024-01-24 13:28:44,130] [INFO] Running command: hmmsearch --tblout GCF_000421205.1_ASM42120v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1903438-0f60-4f48-b864-e1231dce8f1c/dqc_reference/reference_markers.hmm GCF_000421205.1_ASM42120v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:44,425] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:44,427] [INFO] Found 6/6 markers.
[2024-01-24 13:28:44,458] [INFO] Query marker FASTA was written to GCF_000421205.1_ASM42120v1_genomic.fna/markers.fasta
[2024-01-24 13:28:44,459] [INFO] Task started: Blastn
[2024-01-24 13:28:44,459] [INFO] Running command: blastn -query GCF_000421205.1_ASM42120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1903438-0f60-4f48-b864-e1231dce8f1c/dqc_reference/reference_markers.fasta -out GCF_000421205.1_ASM42120v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:45,083] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:45,087] [INFO] Selected 12 target genomes.
[2024-01-24 13:28:45,088] [INFO] Target genome list was writen to GCF_000421205.1_ASM42120v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:45,106] [INFO] Task started: fastANI
[2024-01-24 13:28:45,106] [INFO] Running command: fastANI --query /var/lib/cwl/stga54c5200-3de5-4bd2-a0b2-2da52bbf8e83/GCF_000421205.1_ASM42120v1_genomic.fna.gz --refList GCF_000421205.1_ASM42120v1_genomic.fna/target_genomes.txt --output GCF_000421205.1_ASM42120v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:53,543] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:53,544] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1903438-0f60-4f48-b864-e1231dce8f1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:53,544] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1903438-0f60-4f48-b864-e1231dce8f1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:53,552] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:53,553] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:53,553] [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 denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	100.0	985	988	95	conclusive
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	99.995	985	988	95	conclusive
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	89.6764	721	988	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	81.0408	526	988	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	81.0163	525	988	95	below_threshold
Prevotella fusca	strain=JCM 17724	GCA_000614245.1	589436	589436	type	True	80.9566	521	988	95	below_threshold
Palleniella intestinalis	strain=PINT	GCA_013166595.1	2736291	2736291	type	True	76.9591	50	988	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.8013	110	988	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.6915	104	988	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:53,555] [INFO] DFAST Taxonomy check result was written to GCF_000421205.1_ASM42120v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:53,556] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:53,556] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:53,557] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1903438-0f60-4f48-b864-e1231dce8f1c/dqc_reference/checkm_data
[2024-01-24 13:28:53,558] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:53,596] [INFO] Task started: CheckM
[2024-01-24 13:28:53,596] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000421205.1_ASM42120v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000421205.1_ASM42120v1_genomic.fna/checkm_input GCF_000421205.1_ASM42120v1_genomic.fna/checkm_result
[2024-01-24 13:29:43,172] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:43,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:43,197] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:43,197] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:43,198] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000421205.1_ASM42120v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:43,198] [INFO] Task started: Blastn
[2024-01-24 13:29:43,198] [INFO] Running command: blastn -query GCF_000421205.1_ASM42120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1903438-0f60-4f48-b864-e1231dce8f1c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000421205.1_ASM42120v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:44,107] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:44,111] [INFO] Selected 15 target genomes.
[2024-01-24 13:29:44,111] [INFO] Target genome list was writen to GCF_000421205.1_ASM42120v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:44,136] [INFO] Task started: fastANI
[2024-01-24 13:29:44,136] [INFO] Running command: fastANI --query /var/lib/cwl/stga54c5200-3de5-4bd2-a0b2-2da52bbf8e83/GCF_000421205.1_ASM42120v1_genomic.fna.gz --refList GCF_000421205.1_ASM42120v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000421205.1_ASM42120v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:53,130] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:53,143] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:53,143] [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_900454835.1	s__Prevotella denticola	99.995	985	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.27	97.69	0.92	0.88	14	conclusive
GCF_000191065.1	s__Prevotella multiformis	89.6688	722	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.87	97.87	0.89	0.89	2	-
GCF_001262015.1	s__Prevotella fusca	81.0287	526	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.97	1.00	1.00	3	-
GCF_000377625.1	s__Prevotella veroralis	80.8171	253	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.76	96.65	0.91	0.86	4	-
GCF_018128065.1	s__Prevotella sp000467895	80.3717	378	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.71	96.42	0.91	0.83	4	-
GCF_000144405.1	s__Prevotella melaninogenica	79.738	330	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.46	95.36	0.87	0.78	36	-
GCF_018127965.1	s__Prevotella melaninogenica_B	79.7352	311	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.77	95.72	0.91	0.89	4	-
GCF_018127925.1	s__Prevotella melaninogenica_C	79.7168	346	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220235.1	s__Prevotella nigrescens	79.4316	114	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.14	97.70	0.92	0.78	13	-
GCF_000613925.1	s__Prevotella histicola	79.1627	253	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.82	97.59	0.91	0.86	21	-
GCF_000614065.1	s__Prevotella dentasini	78.1049	227	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900762125.1	s__Prevotella sp900762125	76.8634	126	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543975.1	s__Prevotella sp900543975	76.1364	94	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.48	97.34	0.84	0.79	5	-
GCA_017471245.1	s__Prevotella sp017471245	76.0268	73	988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.04	98.04	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:53,145] [INFO] GTDB search result was written to GCF_000421205.1_ASM42120v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:53,145] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:53,149] [INFO] DFAST_QC result json was written to GCF_000421205.1_ASM42120v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:53,149] [INFO] DFAST_QC completed!
[2024-01-24 13:29:53,149] [INFO] Total running time: 0h1m27s