[2024-01-24 13:28:02,570] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:02,572] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:02,572] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1aa832a-1417-46ed-b9b2-cdbc19d9cedc/dqc_reference
[2024-01-24 13:28:03,863] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:03,864] [INFO] Task started: Prodigal
[2024-01-24 13:28:03,864] [INFO] Running command: gunzip -c /var/lib/cwl/stg06f58820-b5b4-4977-8b68-d317e4cfb072/GCF_022024235.1_ASM2202423v1_genomic.fna.gz | prodigal -d GCF_022024235.1_ASM2202423v1_genomic.fna/cds.fna -a GCF_022024235.1_ASM2202423v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:19,312] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:19,313] [INFO] Task started: HMMsearch
[2024-01-24 13:28:19,313] [INFO] Running command: hmmsearch --tblout GCF_022024235.1_ASM2202423v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1aa832a-1417-46ed-b9b2-cdbc19d9cedc/dqc_reference/reference_markers.hmm GCF_022024235.1_ASM2202423v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:19,556] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:19,557] [INFO] Found 6/6 markers.
[2024-01-24 13:28:19,590] [INFO] Query marker FASTA was written to GCF_022024235.1_ASM2202423v1_genomic.fna/markers.fasta
[2024-01-24 13:28:19,591] [INFO] Task started: Blastn
[2024-01-24 13:28:19,591] [INFO] Running command: blastn -query GCF_022024235.1_ASM2202423v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1aa832a-1417-46ed-b9b2-cdbc19d9cedc/dqc_reference/reference_markers.fasta -out GCF_022024235.1_ASM2202423v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:20,229] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:20,233] [INFO] Selected 12 target genomes.
[2024-01-24 13:28:20,233] [INFO] Target genome list was writen to GCF_022024235.1_ASM2202423v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:20,240] [INFO] Task started: fastANI
[2024-01-24 13:28:20,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg06f58820-b5b4-4977-8b68-d317e4cfb072/GCF_022024235.1_ASM2202423v1_genomic.fna.gz --refList GCF_022024235.1_ASM2202423v1_genomic.fna/target_genomes.txt --output GCF_022024235.1_ASM2202423v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:28,137] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:28,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1aa832a-1417-46ed-b9b2-cdbc19d9cedc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:28,138] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1aa832a-1417-46ed-b9b2-cdbc19d9cedc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:28,147] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:28:28,147] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:28,148] [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 bryantii	strain=B14	GCA_022024235.1	77095	77095	type	True	100.0	1208	1209	95	conclusive
Prevotella bryantii	strain=DSM 11371	GCA_019973295.1	77095	77095	type	True	99.9863	1197	1209	95	conclusive
Prevotella bryantii	strain=B14	GCA_900110745.1	77095	77095	type	True	99.9526	1164	1209	95	conclusive
Prevotella bryantii	strain=B14	GCA_000179055.1	77095	77095	type	True	99.9196	1128	1209	95	conclusive
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	78.8724	171	1209	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	78.8132	123	1209	95	below_threshold
Prevotella disiens	strain=ATCC 29426	GCA_000467875.1	28130	28130	type	True	78.125	60	1209	95	below_threshold
Prevotella amnii	strain=DSM 23384	GCA_000378745.1	419005	419005	type	True	77.6275	60	1209	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:28,149] [INFO] DFAST Taxonomy check result was written to GCF_022024235.1_ASM2202423v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:28,150] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:28,150] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:28,150] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1aa832a-1417-46ed-b9b2-cdbc19d9cedc/dqc_reference/checkm_data
[2024-01-24 13:28:28,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:28,192] [INFO] Task started: CheckM
[2024-01-24 13:28:28,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022024235.1_ASM2202423v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022024235.1_ASM2202423v1_genomic.fna/checkm_input GCF_022024235.1_ASM2202423v1_genomic.fna/checkm_result
[2024-01-24 13:29:15,967] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:15,968] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:15,987] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:15,987] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:15,988] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022024235.1_ASM2202423v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:15,988] [INFO] Task started: Blastn
[2024-01-24 13:29:15,988] [INFO] Running command: blastn -query GCF_022024235.1_ASM2202423v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1aa832a-1417-46ed-b9b2-cdbc19d9cedc/dqc_reference/reference_markers_gtdb.fasta -out GCF_022024235.1_ASM2202423v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:16,775] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:16,777] [INFO] Selected 26 target genomes.
[2024-01-24 13:29:16,778] [INFO] Target genome list was writen to GCF_022024235.1_ASM2202423v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:16,810] [INFO] Task started: fastANI
[2024-01-24 13:29:16,810] [INFO] Running command: fastANI --query /var/lib/cwl/stg06f58820-b5b4-4977-8b68-d317e4cfb072/GCF_022024235.1_ASM2202423v1_genomic.fna.gz --refList GCF_022024235.1_ASM2202423v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022024235.1_ASM2202423v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:29,447] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:29,462] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:29,463] [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_000179055.1	s__Prevotella bryantii	99.9195	1128	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.02	98.58	0.88	0.73	13	conclusive
GCF_018127785.1	s__Prevotella scopos	79.672	93	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.97	1.00	1.00	4	-
GCF_900637655.1	s__Prevotella oris	79.3587	77	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.96	97.06	0.90	0.82	10	-
GCA_902775075.1	s__Prevotella sp902775075	78.8947	142	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426565.1	s__Prevotella albensis	78.7807	171	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.96	99.96	1.00	1.00	2	-
GCF_900290275.1	s__Prevotella sp900290275	78.7678	71	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.80	97.71	0.90	0.86	4	-
GCF_000157935.1	s__Prevotella copri	78.5219	125	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	-
GCA_905236755.1	s__Prevotella sp905236755	78.5056	137	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.83	97.34	0.84	0.68	4	-
GCA_019249655.1	s__Prevotella sp900767615	78.4918	107	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.47	95.77	0.82	0.75	7	-
GCF_000613345.1	s__Prevotella disiens	78.3404	65	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.74	97.99	0.90	0.82	7	-
GCF_019127135.1	s__Prevotella sp900551275	78.1165	118	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0063	98.12	96.96	0.86	0.77	7	-
GCF_900100635.1	s__Prevotella sp900100635	78.004	71	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	96.60	0.86	0.83	10	-
GCF_000378745.1	s__Prevotella amnii	77.609	59	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.70	98.21	0.90	0.86	5	-
GCA_018053665.1	s__Prevotella sp018053665	77.4924	91	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.38	99.32	0.87	0.85	3	-
GCA_003483565.1	s__Prevotella sp003483565	77.4391	124	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.31	99.31	0.72	0.72	2	-
GCA_000436915.1	s__Prevotella sp000436915	77.2345	72	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.18	97.08	0.77	0.76	4	-
GCA_902762325.1	s__Prevotella sp902762325	77.2164	72	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.14	98.03	0.81	0.79	4	-
GCA_017410365.1	s__Prevotella sp017410365	77.0337	57	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.93	96.60	0.79	0.74	5	-
GCA_018054505.1	s__Prevotella sp018054505	76.7957	90	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.05	98.05	0.52	0.52	2	-
GCA_900556395.1	s__Prevotella sp900556395	76.7492	63	1209	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.82	97.81	0.83	0.82	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:29,464] [INFO] GTDB search result was written to GCF_022024235.1_ASM2202423v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:29,465] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:29,468] [INFO] DFAST_QC result json was written to GCF_022024235.1_ASM2202423v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:29,469] [INFO] DFAST_QC completed!
[2024-01-24 13:29:29,469] [INFO] Total running time: 0h1m27s