[2023-06-13 19:29:48,605] [INFO] DFAST_QC pipeline started.
[2023-06-13 19:29:48,607] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 19:29:48,608] [INFO] DQC Reference Directory: /var/lib/cwl/stg9bdad9af-a9a2-45b9-b8ec-4c286faf40d9/dqc_reference
[2023-06-13 19:29:50,179] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 19:29:50,180] [INFO] Task started: Prodigal
[2023-06-13 19:29:50,180] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc97ae6e-24d7-4cc0-be94-845533c3b78e/GCA_022483425.1_ASM2248342v1_genomic.fna.gz | prodigal -d GCA_022483425.1_ASM2248342v1_genomic.fna/cds.fna -a GCA_022483425.1_ASM2248342v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 19:30:05,027] [INFO] Task succeeded: Prodigal
[2023-06-13 19:30:05,027] [INFO] Task started: HMMsearch
[2023-06-13 19:30:05,027] [INFO] Running command: hmmsearch --tblout GCA_022483425.1_ASM2248342v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9bdad9af-a9a2-45b9-b8ec-4c286faf40d9/dqc_reference/reference_markers.hmm GCA_022483425.1_ASM2248342v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 19:30:05,220] [INFO] Task succeeded: HMMsearch
[2023-06-13 19:30:05,222] [INFO] Found 6/6 markers.
[2023-06-13 19:30:05,248] [INFO] Query marker FASTA was written to GCA_022483425.1_ASM2248342v1_genomic.fna/markers.fasta
[2023-06-13 19:30:05,248] [INFO] Task started: Blastn
[2023-06-13 19:30:05,248] [INFO] Running command: blastn -query GCA_022483425.1_ASM2248342v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bdad9af-a9a2-45b9-b8ec-4c286faf40d9/dqc_reference/reference_markers.fasta -out GCA_022483425.1_ASM2248342v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:30:05,824] [INFO] Task succeeded: Blastn
[2023-06-13 19:30:05,829] [INFO] Selected 25 target genomes.
[2023-06-13 19:30:05,829] [INFO] Target genome list was writen to GCA_022483425.1_ASM2248342v1_genomic.fna/target_genomes.txt
[2023-06-13 19:30:05,830] [INFO] Task started: fastANI
[2023-06-13 19:30:05,830] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc97ae6e-24d7-4cc0-be94-845533c3b78e/GCA_022483425.1_ASM2248342v1_genomic.fna.gz --refList GCA_022483425.1_ASM2248342v1_genomic.fna/target_genomes.txt --output GCA_022483425.1_ASM2248342v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 19:30:18,617] [INFO] Task succeeded: fastANI
[2023-06-13 19:30:18,618] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9bdad9af-a9a2-45b9-b8ec-4c286faf40d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 19:30:18,618] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9bdad9af-a9a2-45b9-b8ec-4c286faf40d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 19:30:18,629] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 19:30:18,629] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 19:30:18,629] [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 cerevisiae	strain=DSM 100619	GCA_024054555.1	2053716	2053716	type	True	80.9398	438	1056	95	below_threshold
Prevotella herbatica	strain=WR041	GCA_017347605.1	2801997	2801997	type	True	78.1976	56	1056	95	below_threshold
Prevotella oris	strain=NCTC13071	GCA_900637655.1	28135	28135	type	True	78.0303	52	1056	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	77.5185	66	1056	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	77.262	69	1056	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	77.1857	69	1056	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	76.9662	72	1056	95	below_threshold
Prevotella paludivivens	strain=JCM 13650	GCA_000613605.1	185294	185294	type	True	76.8257	60	1056	95	below_threshold
Prevotella albensis	strain=DSM 11370	GCA_000426565.1	77768	77768	type	True	76.7054	75	1056	95	below_threshold
Prevotella paludivivens	strain=DSM 17968	GCA_000373185.1	185294	185294	type	True	76.3773	63	1056	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.3542	64	1056	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	76.2768	68	1056	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 19:30:18,631] [INFO] DFAST Taxonomy check result was written to GCA_022483425.1_ASM2248342v1_genomic.fna/tc_result.tsv
[2023-06-13 19:30:18,632] [INFO] ===== Taxonomy check completed =====
[2023-06-13 19:30:18,632] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 19:30:18,632] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9bdad9af-a9a2-45b9-b8ec-4c286faf40d9/dqc_reference/checkm_data
[2023-06-13 19:30:18,633] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 19:30:18,663] [INFO] Task started: CheckM
[2023-06-13 19:30:18,663] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022483425.1_ASM2248342v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022483425.1_ASM2248342v1_genomic.fna/checkm_input GCA_022483425.1_ASM2248342v1_genomic.fna/checkm_result
[2023-06-13 19:31:04,610] [INFO] Task succeeded: CheckM
[2023-06-13 19:31:04,611] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 19:31:04,627] [INFO] ===== Completeness check finished =====
[2023-06-13 19:31:04,628] [INFO] ===== Start GTDB Search =====
[2023-06-13 19:31:04,628] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022483425.1_ASM2248342v1_genomic.fna/markers.fasta)
[2023-06-13 19:31:04,628] [INFO] Task started: Blastn
[2023-06-13 19:31:04,628] [INFO] Running command: blastn -query GCA_022483425.1_ASM2248342v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bdad9af-a9a2-45b9-b8ec-4c286faf40d9/dqc_reference/reference_markers_gtdb.fasta -out GCA_022483425.1_ASM2248342v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:31:05,386] [INFO] Task succeeded: Blastn
[2023-06-13 19:31:05,390] [INFO] Selected 27 target genomes.
[2023-06-13 19:31:05,391] [INFO] Target genome list was writen to GCA_022483425.1_ASM2248342v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 19:31:05,392] [INFO] Task started: fastANI
[2023-06-13 19:31:05,392] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc97ae6e-24d7-4cc0-be94-845533c3b78e/GCA_022483425.1_ASM2248342v1_genomic.fna.gz --refList GCA_022483425.1_ASM2248342v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022483425.1_ASM2248342v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 19:31:16,653] [INFO] Task succeeded: fastANI
[2023-06-13 19:31:16,663] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 19:31:16,663] [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
GCA_002409785.1	s__Prevotella sp002409785	99.0354	774	1056	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.35	99.13	0.87	0.82	3	conclusive
GCA_003483565.1	s__Prevotella sp003483565	78.8465	82	1056	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.31	99.31	0.72	0.72	2	-
GCF_900637655.1	s__Prevotella oris	78.08	52	1056	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.96	97.06	0.90	0.82	10	-
GCF_000157935.1	s__Prevotella copri	77.256	70	1056	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	-
GCF_015074785.1	s__Prevotella sp015074785	77.1072	67	1056	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	-
GCF_000426565.1	s__Prevotella albensis	76.7274	76	1056	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.96	99.96	1.00	1.00	2	-
GCF_000424185.1	s__Prevotella sp000424185	76.6152	76	1056	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019127135.1	s__Prevotella sp900551275	76.5752	68	1056	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0063	98.12	96.96	0.86	0.77	7	-
GCA_019249655.1	s__Prevotella sp900767615	76.3232	65	1056	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.47	95.77	0.82	0.75	7	-
GCF_009494395.1	s__Prevotella sp900546535	76.3187	55	1056	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.78	96.11	0.82	0.79	8	-
--------------------------------------------------------------------------------
[2023-06-13 19:31:16,665] [INFO] GTDB search result was written to GCA_022483425.1_ASM2248342v1_genomic.fna/result_gtdb.tsv
[2023-06-13 19:31:16,666] [INFO] ===== GTDB Search completed =====
[2023-06-13 19:31:16,669] [INFO] DFAST_QC result json was written to GCA_022483425.1_ASM2248342v1_genomic.fna/dqc_result.json
[2023-06-13 19:31:16,669] [INFO] DFAST_QC completed!
[2023-06-13 19:31:16,670] [INFO] Total running time: 0h1m28s