[2024-01-24 13:41:41,347] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:41,348] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:41,349] [INFO] DQC Reference Directory: /var/lib/cwl/stga781eb27-8e27-4656-b6e0-45a22a2760a8/dqc_reference
[2024-01-24 13:41:42,617] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:42,619] [INFO] Task started: Prodigal
[2024-01-24 13:41:42,619] [INFO] Running command: gunzip -c /var/lib/cwl/stg61bc691a-1f03-4bcb-9fae-cfc90eafbfa3/GCF_000455445.1_4401737_genomic.fna.gz | prodigal -d GCF_000455445.1_4401737_genomic.fna/cds.fna -a GCF_000455445.1_4401737_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:42:00,012] [INFO] Task succeeded: Prodigal
[2024-01-24 13:42:00,012] [INFO] Task started: HMMsearch
[2024-01-24 13:42:00,012] [INFO] Running command: hmmsearch --tblout GCF_000455445.1_4401737_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga781eb27-8e27-4656-b6e0-45a22a2760a8/dqc_reference/reference_markers.hmm GCF_000455445.1_4401737_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:42:00,276] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:42:00,278] [INFO] Found 6/6 markers.
[2024-01-24 13:42:00,309] [INFO] Query marker FASTA was written to GCF_000455445.1_4401737_genomic.fna/markers.fasta
[2024-01-24 13:42:00,310] [INFO] Task started: Blastn
[2024-01-24 13:42:00,310] [INFO] Running command: blastn -query GCF_000455445.1_4401737_genomic.fna/markers.fasta -db /var/lib/cwl/stga781eb27-8e27-4656-b6e0-45a22a2760a8/dqc_reference/reference_markers.fasta -out GCF_000455445.1_4401737_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:00,958] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:00,962] [INFO] Selected 14 target genomes.
[2024-01-24 13:42:00,963] [INFO] Target genome list was writen to GCF_000455445.1_4401737_genomic.fna/target_genomes.txt
[2024-01-24 13:42:01,043] [INFO] Task started: fastANI
[2024-01-24 13:42:01,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg61bc691a-1f03-4bcb-9fae-cfc90eafbfa3/GCF_000455445.1_4401737_genomic.fna.gz --refList GCF_000455445.1_4401737_genomic.fna/target_genomes.txt --output GCF_000455445.1_4401737_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:10,096] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:10,097] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga781eb27-8e27-4656-b6e0-45a22a2760a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:10,097] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga781eb27-8e27-4656-b6e0-45a22a2760a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:10,110] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:42:10,110] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:10,110] [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 timonensis	strain=4401737	GCA_000455445.1	386414	386414	type	True	99.9998	1038	1060	95	conclusive
Prevotella timonensis	strain=JCM 15640	GCA_000614005.1	386414	386414	type	True	99.8912	943	1060	95	conclusive
Prevotella timonensis	strain=DSM 22865	GCA_000430565.1	386414	386414	suspected-type	True	99.8694	962	1060	95	conclusive
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	82.1827	112	1060	95	below_threshold
Prevotella pleuritidis	strain=JCM 14110	GCA_000613725.1	407975	407975	type	True	79.1614	88	1060	95	below_threshold
Prevotella loescheii	strain=DSM 19665	GCA_000378085.1	840	840	type	True	78.6897	83	1060	95	below_threshold
Prevotella oris	strain=DSM 18711	GCA_000377685.1	28135	28135	type	True	78.6405	105	1060	95	below_threshold
Prevotella phocaeensis	strain=SN19	GCA_900065875.1	1776388	1776388	type	True	78.1505	87	1060	95	below_threshold
Prevotella loescheii	strain=ATCC 15930	GCA_000698925.1	840	840	type	True	78.1158	84	1060	95	below_threshold
Prevotella dentasini	strain=JCM 15908	GCA_000614065.1	589537	589537	type	True	78.0426	76	1060	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:10,112] [INFO] DFAST Taxonomy check result was written to GCF_000455445.1_4401737_genomic.fna/tc_result.tsv
[2024-01-24 13:42:10,112] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:10,113] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:10,113] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga781eb27-8e27-4656-b6e0-45a22a2760a8/dqc_reference/checkm_data
[2024-01-24 13:42:10,115] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:10,148] [INFO] Task started: CheckM
[2024-01-24 13:42:10,148] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000455445.1_4401737_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000455445.1_4401737_genomic.fna/checkm_input GCF_000455445.1_4401737_genomic.fna/checkm_result
[2024-01-24 13:43:02,112] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:02,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:02,137] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:02,138] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:02,138] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000455445.1_4401737_genomic.fna/markers.fasta)
[2024-01-24 13:43:02,139] [INFO] Task started: Blastn
[2024-01-24 13:43:02,139] [INFO] Running command: blastn -query GCF_000455445.1_4401737_genomic.fna/markers.fasta -db /var/lib/cwl/stga781eb27-8e27-4656-b6e0-45a22a2760a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000455445.1_4401737_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:02,940] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:02,945] [INFO] Selected 17 target genomes.
[2024-01-24 13:43:02,945] [INFO] Target genome list was writen to GCF_000455445.1_4401737_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:02,958] [INFO] Task started: fastANI
[2024-01-24 13:43:02,958] [INFO] Running command: fastANI --query /var/lib/cwl/stg61bc691a-1f03-4bcb-9fae-cfc90eafbfa3/GCF_000455445.1_4401737_genomic.fna.gz --refList GCF_000455445.1_4401737_genomic.fna/target_genomes_gtdb.txt --output GCF_000455445.1_4401737_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:12,832] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:12,844] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:12,844] [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_000455445.1	s__Prevotella timonensis	99.9998	1038	1060	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0025	97.81	95.47	0.90	0.82	5	conclusive
GCF_000762405.1	s__Prevotella timonensis_A	94.9628	758	1060	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0025	96.56	96.39	0.83	0.81	3	-
GCF_000177075.1	s__Prevotella buccalis	85.7704	398	1060	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.19	95.19	0.85	0.85	2	-
GCF_000479005.1	s__Prevotella sp000479005	84.5985	388	1060	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.86	96.42	0.92	0.87	3	-
GCA_900547085.1	s__Prevotella sp900547085	84.0629	273	1060	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000599605.1	s__Prevotella sp000599605	81.605	116	1060	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.66	96.63	0.93	0.92	3	-
GCF_000378085.1	s__Prevotella loescheii	78.6207	85	1060	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.09	95.73	0.96	0.93	5	-
GCA_900199655.1	s__Prevotella sp900199655	78.1762	92	1060	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	78.0426	76	1060	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002449845.1	s__Prevotella sp002449845	76.2362	72	1060	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	96.99	0.89	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:12,846] [INFO] GTDB search result was written to GCF_000455445.1_4401737_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:12,846] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:12,849] [INFO] DFAST_QC result json was written to GCF_000455445.1_4401737_genomic.fna/dqc_result.json
[2024-01-24 13:43:12,850] [INFO] DFAST_QC completed!
[2024-01-24 13:43:12,850] [INFO] Total running time: 0h1m32s