[2024-01-24 14:22:31,852] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:31,854] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:31,854] [INFO] DQC Reference Directory: /var/lib/cwl/stg53c40b4d-5df5-4fa1-92e1-f21286c2e086/dqc_reference
[2024-01-24 14:22:33,119] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:33,119] [INFO] Task started: Prodigal
[2024-01-24 14:22:33,120] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d55efee-dd18-4fa8-af8c-c643c87c8025/GCF_017347605.1_ASM1734760v1_genomic.fna.gz | prodigal -d GCF_017347605.1_ASM1734760v1_genomic.fna/cds.fna -a GCF_017347605.1_ASM1734760v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:48,333] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:48,333] [INFO] Task started: HMMsearch
[2024-01-24 14:22:48,333] [INFO] Running command: hmmsearch --tblout GCF_017347605.1_ASM1734760v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53c40b4d-5df5-4fa1-92e1-f21286c2e086/dqc_reference/reference_markers.hmm GCF_017347605.1_ASM1734760v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:48,727] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:48,729] [INFO] Found 6/6 markers.
[2024-01-24 14:22:48,762] [INFO] Query marker FASTA was written to GCF_017347605.1_ASM1734760v1_genomic.fna/markers.fasta
[2024-01-24 14:22:48,763] [INFO] Task started: Blastn
[2024-01-24 14:22:48,763] [INFO] Running command: blastn -query GCF_017347605.1_ASM1734760v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53c40b4d-5df5-4fa1-92e1-f21286c2e086/dqc_reference/reference_markers.fasta -out GCF_017347605.1_ASM1734760v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:49,353] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:49,447] [INFO] Selected 13 target genomes.
[2024-01-24 14:22:49,448] [INFO] Target genome list was writen to GCF_017347605.1_ASM1734760v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:49,459] [INFO] Task started: fastANI
[2024-01-24 14:22:49,459] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d55efee-dd18-4fa8-af8c-c643c87c8025/GCF_017347605.1_ASM1734760v1_genomic.fna.gz --refList GCF_017347605.1_ASM1734760v1_genomic.fna/target_genomes.txt --output GCF_017347605.1_ASM1734760v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:58,487] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:58,488] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53c40b4d-5df5-4fa1-92e1-f21286c2e086/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:58,488] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53c40b4d-5df5-4fa1-92e1-f21286c2e086/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:58,503] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:58,503] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:58,503] [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 herbatica	strain=WR041	GCA_017347605.1	2801997	2801997	type	True	100.0	1172	1174	95	conclusive
Prevotella paludivivens	strain=JCM 13650	GCA_000613605.1	185294	185294	type	True	92.0981	969	1174	95	below_threshold
Prevotella paludivivens	strain=DSM 17968	GCA_000373185.1	185294	185294	type	True	92.0742	976	1174	95	below_threshold
Prevotella oryzae	strain=DSM 17970	GCA_000585355.1	185293	185293	type	True	79.6519	167	1174	95	below_threshold
Prevotella melaninogenica	strain=ATCC 25845	GCA_000144405.1	28132	28132	suspected-type	True	78.8611	97	1174	95	below_threshold
Prevotella melaninogenica	strain=FDAARGOS_1566	GCA_020735785.1	28132	28132	suspected-type	True	78.7589	96	1174	95	below_threshold
Prevotella bryantii	strain=DSM 11371	GCA_019973295.1	77095	77095	type	True	78.3545	128	1174	95	below_threshold
Prevotella bryantii	strain=B14	GCA_022024235.1	77095	77095	type	True	78.1088	128	1174	95	below_threshold
Prevotella salivae	strain=DSM 15606	GCA_000185845.1	228604	228604	type	True	77.8624	105	1174	95	below_threshold
Prevotella jejuni	strain=DSM 26989	GCA_900187995.1	1177574	1177574	type	True	77.669	84	1174	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	77.6575	100	1174	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	77.5112	149	1174	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:58,505] [INFO] DFAST Taxonomy check result was written to GCF_017347605.1_ASM1734760v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:58,506] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:58,506] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:58,506] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53c40b4d-5df5-4fa1-92e1-f21286c2e086/dqc_reference/checkm_data
[2024-01-24 14:22:58,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:58,545] [INFO] Task started: CheckM
[2024-01-24 14:22:58,545] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017347605.1_ASM1734760v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017347605.1_ASM1734760v1_genomic.fna/checkm_input GCF_017347605.1_ASM1734760v1_genomic.fna/checkm_result
[2024-01-24 14:23:45,493] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:45,494] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:45,516] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:45,517] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:45,518] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017347605.1_ASM1734760v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:45,518] [INFO] Task started: Blastn
[2024-01-24 14:23:45,518] [INFO] Running command: blastn -query GCF_017347605.1_ASM1734760v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53c40b4d-5df5-4fa1-92e1-f21286c2e086/dqc_reference/reference_markers_gtdb.fasta -out GCF_017347605.1_ASM1734760v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:46,409] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:46,414] [INFO] Selected 11 target genomes.
[2024-01-24 14:23:46,414] [INFO] Target genome list was writen to GCF_017347605.1_ASM1734760v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:46,428] [INFO] Task started: fastANI
[2024-01-24 14:23:46,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d55efee-dd18-4fa8-af8c-c643c87c8025/GCF_017347605.1_ASM1734760v1_genomic.fna.gz --refList GCF_017347605.1_ASM1734760v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017347605.1_ASM1734760v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:55,474] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:55,487] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:55,487] [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_017347605.1	s__Prevotella sp017347605	100.0	1171	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000373185.1	s__Prevotella paludivivens	92.0692	976	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.98	0.99	0.99	2	-
GCA_018053665.1	s__Prevotella sp018053665	88.3161	606	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.38	99.32	0.87	0.85	3	-
GCA_018054505.1	s__Prevotella sp018054505	85.7881	465	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.05	98.05	0.52	0.52	2	-
GCF_000144405.1	s__Prevotella melaninogenica	78.8065	96	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.46	95.36	0.87	0.78	36	-
GCF_000179055.1	s__Prevotella bryantii	78.0559	125	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.02	98.58	0.88	0.73	13	-
GCF_900187995.1	s__Prevotella jejuni	77.6604	83	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.57	0.92	0.88	7	-
GCA_905236755.1	s__Prevotella sp905236755	77.5535	157	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.83	97.34	0.84	0.68	4	-
GCA_902775075.1	s__Prevotella sp902775075	77.5358	107	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905236815.1	s__Prevotella sp905236815	76.8194	115	1174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554835.1	s__Prevotella sp900554835	76.5852	84	1174	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 14:23:55,489] [INFO] GTDB search result was written to GCF_017347605.1_ASM1734760v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:55,490] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:55,498] [INFO] DFAST_QC result json was written to GCF_017347605.1_ASM1734760v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:55,498] [INFO] DFAST_QC completed!
[2024-01-24 14:23:55,499] [INFO] Total running time: 0h1m24s