[2024-01-24 13:37:04,996] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:04,998] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:04,998] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9e50df7-e333-419e-a05b-199009edb721/dqc_reference
[2024-01-24 13:37:06,385] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,386] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,387] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0abd8e3-420b-4cf0-bad1-d0ad9c798f5b/GCF_000373705.1_ASM37370v1_genomic.fna.gz | prodigal -d GCF_000373705.1_ASM37370v1_genomic.fna/cds.fna -a GCF_000373705.1_ASM37370v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:19,286] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:19,287] [INFO] Task started: HMMsearch
[2024-01-24 13:37:19,287] [INFO] Running command: hmmsearch --tblout GCF_000373705.1_ASM37370v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9e50df7-e333-419e-a05b-199009edb721/dqc_reference/reference_markers.hmm GCF_000373705.1_ASM37370v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:19,581] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:19,582] [INFO] Found 6/6 markers.
[2024-01-24 13:37:19,605] [INFO] Query marker FASTA was written to GCF_000373705.1_ASM37370v1_genomic.fna/markers.fasta
[2024-01-24 13:37:19,605] [INFO] Task started: Blastn
[2024-01-24 13:37:19,605] [INFO] Running command: blastn -query GCF_000373705.1_ASM37370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9e50df7-e333-419e-a05b-199009edb721/dqc_reference/reference_markers.fasta -out GCF_000373705.1_ASM37370v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:20,206] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:20,209] [INFO] Selected 17 target genomes.
[2024-01-24 13:37:20,209] [INFO] Target genome list was writen to GCF_000373705.1_ASM37370v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:20,231] [INFO] Task started: fastANI
[2024-01-24 13:37:20,232] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0abd8e3-420b-4cf0-bad1-d0ad9c798f5b/GCF_000373705.1_ASM37370v1_genomic.fna.gz --refList GCF_000373705.1_ASM37370v1_genomic.fna/target_genomes.txt --output GCF_000373705.1_ASM37370v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:29,656] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:29,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9e50df7-e333-419e-a05b-199009edb721/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:29,657] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9e50df7-e333-419e-a05b-199009edb721/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:29,667] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:29,667] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:29,667] [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 micans	strain=DSM 21469	GCA_000373705.1	189723	189723	type	True	100.0	783	785	95	conclusive
Prevotella micans	strain=JCM 16134	GCA_000614105.1	189723	189723	type	True	99.9007	738	785	95	conclusive
Prevotella maculosa	strain=JCM 15638	GCA_000613965.1	439703	439703	type	True	79.7753	61	785	95	below_threshold
Prevotella maculosa	strain=DSM 19339	GCA_000382385.1	439703	439703	type	True	79.6708	65	785	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	79.4502	69	785	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	79.1232	66	785	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	78.7595	63	785	95	below_threshold
Prevotella nigrescens	strain=ATCC 33563	GCA_000220235.1	28133	28133	type	True	78.5095	68	785	95	below_threshold
Prevotella nigrescens	strain=FDAARGOS_1486	GCA_019930605.1	28133	28133	type	True	78.1331	68	785	95	below_threshold
Prevotella brunnea	strain=A2672	GCA_008016795.1	2508867	2508867	type	True	77.9916	68	785	95	below_threshold
Prevotella dentasini	strain=JCM 15908	GCA_000614065.1	589537	589537	type	True	77.0429	72	785	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:29,670] [INFO] DFAST Taxonomy check result was written to GCF_000373705.1_ASM37370v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:29,671] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:29,671] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:29,671] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9e50df7-e333-419e-a05b-199009edb721/dqc_reference/checkm_data
[2024-01-24 13:37:29,673] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:29,703] [INFO] Task started: CheckM
[2024-01-24 13:37:29,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000373705.1_ASM37370v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000373705.1_ASM37370v1_genomic.fna/checkm_input GCF_000373705.1_ASM37370v1_genomic.fna/checkm_result
[2024-01-24 13:38:11,253] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:11,254] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:11,268] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:11,269] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:11,269] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000373705.1_ASM37370v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:11,270] [INFO] Task started: Blastn
[2024-01-24 13:38:11,270] [INFO] Running command: blastn -query GCF_000373705.1_ASM37370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9e50df7-e333-419e-a05b-199009edb721/dqc_reference/reference_markers_gtdb.fasta -out GCF_000373705.1_ASM37370v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:12,077] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:12,081] [INFO] Selected 27 target genomes.
[2024-01-24 13:38:12,082] [INFO] Target genome list was writen to GCF_000373705.1_ASM37370v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:12,166] [INFO] Task started: fastANI
[2024-01-24 13:38:12,166] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0abd8e3-420b-4cf0-bad1-d0ad9c798f5b/GCF_000373705.1_ASM37370v1_genomic.fna.gz --refList GCF_000373705.1_ASM37370v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000373705.1_ASM37370v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:24,299] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:24,313] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:24,313] [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_000614105.1	s__Prevotella micans	99.9007	738	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.39	98.24	0.98	0.95	4	conclusive
GCF_900454835.1	s__Prevotella denticola	79.4271	70	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.27	97.69	0.92	0.88	14	-
GCF_000688375.1	s__Prevotella sp000688375	78.9837	84	785	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	78.5244	68	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.14	97.70	0.92	0.78	13	-
GCF_008016795.1	s__Prevotella brunnea	77.9916	68	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.23	99.23	0.96	0.96	2	-
GCA_900199655.1	s__Prevotella sp900199655	77.3281	50	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.91	99.91	0.98	0.98	2	-
GCF_000614065.1	s__Prevotella dentasini	77.0429	72	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:24,315] [INFO] GTDB search result was written to GCF_000373705.1_ASM37370v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:24,315] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:24,318] [INFO] DFAST_QC result json was written to GCF_000373705.1_ASM37370v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:24,318] [INFO] DFAST_QC completed!
[2024-01-24 13:38:24,318] [INFO] Total running time: 0h1m19s