[2024-01-24 14:28:15,832] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:15,836] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:15,836] [INFO] DQC Reference Directory: /var/lib/cwl/stgd720ed75-44c5-4bb5-bda2-151c57dcc4e5/dqc_reference
[2024-01-24 14:28:17,937] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:17,938] [INFO] Task started: Prodigal
[2024-01-24 14:28:17,938] [INFO] Running command: gunzip -c /var/lib/cwl/stg8679d94b-4dde-4d9e-8fbc-7308ce172152/GCF_009728485.1_ASM972848v1_genomic.fna.gz | prodigal -d GCF_009728485.1_ASM972848v1_genomic.fna/cds.fna -a GCF_009728485.1_ASM972848v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:31,423] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:31,424] [INFO] Task started: HMMsearch
[2024-01-24 14:28:31,424] [INFO] Running command: hmmsearch --tblout GCF_009728485.1_ASM972848v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd720ed75-44c5-4bb5-bda2-151c57dcc4e5/dqc_reference/reference_markers.hmm GCF_009728485.1_ASM972848v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:31,686] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:31,687] [INFO] Found 6/6 markers.
[2024-01-24 14:28:31,717] [INFO] Query marker FASTA was written to GCF_009728485.1_ASM972848v1_genomic.fna/markers.fasta
[2024-01-24 14:28:31,718] [INFO] Task started: Blastn
[2024-01-24 14:28:31,718] [INFO] Running command: blastn -query GCF_009728485.1_ASM972848v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd720ed75-44c5-4bb5-bda2-151c57dcc4e5/dqc_reference/reference_markers.fasta -out GCF_009728485.1_ASM972848v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:32,405] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:32,409] [INFO] Selected 12 target genomes.
[2024-01-24 14:28:32,409] [INFO] Target genome list was writen to GCF_009728485.1_ASM972848v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:32,472] [INFO] Task started: fastANI
[2024-01-24 14:28:32,472] [INFO] Running command: fastANI --query /var/lib/cwl/stg8679d94b-4dde-4d9e-8fbc-7308ce172152/GCF_009728485.1_ASM972848v1_genomic.fna.gz --refList GCF_009728485.1_ASM972848v1_genomic.fna/target_genomes.txt --output GCF_009728485.1_ASM972848v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:39,714] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:39,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd720ed75-44c5-4bb5-bda2-151c57dcc4e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:39,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd720ed75-44c5-4bb5-bda2-151c57dcc4e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:39,724] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:39,725] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:39,725] [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 vespertina	strain=A2879	GCA_009728485.1	2608404	2608404	type	True	100.0	926	926	95	conclusive
Prevotella veroralis	strain=DSM 19559	GCA_000377625.1	28137	28137	type	True	92.2086	713	926	95	below_threshold
Prevotella veroralis	strain=JCM 6290	GCA_000613325.1	28137	28137	type	True	92.1885	704	926	95	below_threshold
Prevotella scopos	strain=W2052	GCA_001683355.1	589437	589437	type	True	81.7047	393	926	95	below_threshold
Prevotella scopos	strain=W2052	GCA_018127785.1	589437	589437	type	True	81.6828	387	926	95	below_threshold
Prevotella melaninogenica	strain=ATCC 25845	GCA_000144405.1	28132	28132	suspected-type	True	81.3852	389	926	95	below_threshold
Prevotella melaninogenica	strain=FDAARGOS_1566	GCA_020735785.1	28132	28132	suspected-type	True	81.3445	396	926	95	below_threshold
Prevotella histicola	strain=JCM 15637	GCA_000613925.1	470565	470565	type	True	81.1733	343	926	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	81.1082	64	926	95	below_threshold
Prevotella brunnea	strain=A2672	GCA_008016795.1	2508867	2508867	type	True	79.3173	89	926	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:39,726] [INFO] DFAST Taxonomy check result was written to GCF_009728485.1_ASM972848v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:39,727] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:39,727] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:39,727] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd720ed75-44c5-4bb5-bda2-151c57dcc4e5/dqc_reference/checkm_data
[2024-01-24 14:28:39,728] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:39,759] [INFO] Task started: CheckM
[2024-01-24 14:28:39,759] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009728485.1_ASM972848v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009728485.1_ASM972848v1_genomic.fna/checkm_input GCF_009728485.1_ASM972848v1_genomic.fna/checkm_result
[2024-01-24 14:29:20,499] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:20,500] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:20,519] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:20,519] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:20,519] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009728485.1_ASM972848v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:20,520] [INFO] Task started: Blastn
[2024-01-24 14:29:20,520] [INFO] Running command: blastn -query GCF_009728485.1_ASM972848v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd720ed75-44c5-4bb5-bda2-151c57dcc4e5/dqc_reference/reference_markers_gtdb.fasta -out GCF_009728485.1_ASM972848v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:21,404] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:21,407] [INFO] Selected 11 target genomes.
[2024-01-24 14:29:21,408] [INFO] Target genome list was writen to GCF_009728485.1_ASM972848v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:21,416] [INFO] Task started: fastANI
[2024-01-24 14:29:21,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg8679d94b-4dde-4d9e-8fbc-7308ce172152/GCF_009728485.1_ASM972848v1_genomic.fna.gz --refList GCF_009728485.1_ASM972848v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009728485.1_ASM972848v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:28,878] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:28,889] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:28,889] [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_000257925.1	s__Prevotella sp000257925	96.9413	810	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.40	96.99	0.92	0.83	10	conclusive
GCF_000377625.1	s__Prevotella veroralis	92.2086	713	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.76	96.65	0.91	0.86	4	-
GCF_900187995.1	s__Prevotella jejuni	82.3399	425	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.57	0.92	0.88	7	-
GCF_018127925.1	s__Prevotella melaninogenica_C	82.0621	393	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018127785.1	s__Prevotella scopos	81.6819	388	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.97	1.00	1.00	4	-
GCF_018127965.1	s__Prevotella melaninogenica_B	81.495	380	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.77	95.72	0.91	0.89	4	-
GCF_000144405.1	s__Prevotella melaninogenica	81.3287	393	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.46	95.36	0.87	0.78	36	-
GCF_000613925.1	s__Prevotella histicola	81.1809	343	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.82	97.59	0.91	0.86	21	-
GCF_003609775.1	s__Prevotella melaninogenica_A	80.6599	387	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008016795.1	s__Prevotella brunnea	79.3236	88	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.23	99.23	0.96	0.96	2	-
GCF_000157935.1	s__Prevotella copri	78.361	77	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:28,892] [INFO] GTDB search result was written to GCF_009728485.1_ASM972848v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:28,893] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:28,897] [INFO] DFAST_QC result json was written to GCF_009728485.1_ASM972848v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:28,897] [INFO] DFAST_QC completed!
[2024-01-24 14:29:28,897] [INFO] Total running time: 0h1m13s