[2023-06-19 13:14:34,932] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:14:34,937] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:14:34,937] [INFO] DQC Reference Directory: /var/lib/cwl/stg277acfb8-62ce-4ee3-83f8-0331e36f255d/dqc_reference
[2023-06-19 13:14:36,155] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:14:36,156] [INFO] Task started: Prodigal
[2023-06-19 13:14:36,156] [INFO] Running command: gunzip -c /var/lib/cwl/stga6a46972-e65d-4897-a5fb-798aadb65c08/GCA_018372255.1_ASM1837225v1_genomic.fna.gz | prodigal -d GCA_018372255.1_ASM1837225v1_genomic.fna/cds.fna -a GCA_018372255.1_ASM1837225v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:14:52,440] [INFO] Task succeeded: Prodigal
[2023-06-19 13:14:52,441] [INFO] Task started: HMMsearch
[2023-06-19 13:14:52,441] [INFO] Running command: hmmsearch --tblout GCA_018372255.1_ASM1837225v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg277acfb8-62ce-4ee3-83f8-0331e36f255d/dqc_reference/reference_markers.hmm GCA_018372255.1_ASM1837225v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:14:52,768] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:14:52,769] [INFO] Found 6/6 markers.
[2023-06-19 13:14:52,820] [INFO] Query marker FASTA was written to GCA_018372255.1_ASM1837225v1_genomic.fna/markers.fasta
[2023-06-19 13:14:52,820] [INFO] Task started: Blastn
[2023-06-19 13:14:52,820] [INFO] Running command: blastn -query GCA_018372255.1_ASM1837225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg277acfb8-62ce-4ee3-83f8-0331e36f255d/dqc_reference/reference_markers.fasta -out GCA_018372255.1_ASM1837225v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:14:53,426] [INFO] Task succeeded: Blastn
[2023-06-19 13:14:53,431] [INFO] Selected 15 target genomes.
[2023-06-19 13:14:53,432] [INFO] Target genome list was writen to GCA_018372255.1_ASM1837225v1_genomic.fna/target_genomes.txt
[2023-06-19 13:14:53,433] [INFO] Task started: fastANI
[2023-06-19 13:14:53,433] [INFO] Running command: fastANI --query /var/lib/cwl/stga6a46972-e65d-4897-a5fb-798aadb65c08/GCA_018372255.1_ASM1837225v1_genomic.fna.gz --refList GCA_018372255.1_ASM1837225v1_genomic.fna/target_genomes.txt --output GCA_018372255.1_ASM1837225v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:15:04,957] [INFO] Task succeeded: fastANI
[2023-06-19 13:15:04,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg277acfb8-62ce-4ee3-83f8-0331e36f255d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:15:04,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg277acfb8-62ce-4ee3-83f8-0331e36f255d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:15:04,973] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:15:04,973] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 13:15:04,973] [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
Dysgonomonas mossii	strain=DSM 22836	GCA_000376405.1	163665	163665	suspected-type	True	94.0412	1070	1358	95	below_threshold
Dysgonomonas mossii	strain=DSM 22836	GCA_000213575.1	163665	163665	suspected-type	True	93.9772	1076	1358	95	below_threshold
Dysgonomonas hofstadii	strain=DSM 104969	GCA_014196915.1	637886	637886	type	True	80.1685	246	1358	95	below_threshold
Dysgonomonas gadei	strain=ATCC BAA-286	GCA_000213555.1	156974	156974	type	True	79.7747	321	1358	95	below_threshold
Dysgonomonas massiliensis	strain=Marseille-P4356	GCA_900240225.1	2040292	2040292	type	True	77.0193	91	1358	95	below_threshold
Dysgonomonas alginatilytica	strain=DSM 100214	GCA_003201355.1	1605892	1605892	type	True	76.9355	121	1358	95	below_threshold
Dysgonomonas macrotermitis	strain=DSM 27370	GCA_900128985.1	1346286	1346286	type	True	76.8293	108	1358	95	below_threshold
Dysgonomonas macrotermitis	strain=JCM 19375	GCA_001047035.1	1346286	1346286	type	True	76.8255	110	1358	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 13:15:04,975] [INFO] DFAST Taxonomy check result was written to GCA_018372255.1_ASM1837225v1_genomic.fna/tc_result.tsv
[2023-06-19 13:15:04,976] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:15:04,976] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:15:04,976] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg277acfb8-62ce-4ee3-83f8-0331e36f255d/dqc_reference/checkm_data
[2023-06-19 13:15:04,977] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:15:05,017] [INFO] Task started: CheckM
[2023-06-19 13:15:05,018] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018372255.1_ASM1837225v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018372255.1_ASM1837225v1_genomic.fna/checkm_input GCA_018372255.1_ASM1837225v1_genomic.fna/checkm_result
[2023-06-19 13:15:53,314] [INFO] Task succeeded: CheckM
[2023-06-19 13:15:53,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 13:15:53,340] [INFO] ===== Completeness check finished =====
[2023-06-19 13:15:53,340] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:15:53,341] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018372255.1_ASM1837225v1_genomic.fna/markers.fasta)
[2023-06-19 13:15:53,341] [INFO] Task started: Blastn
[2023-06-19 13:15:53,341] [INFO] Running command: blastn -query GCA_018372255.1_ASM1837225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg277acfb8-62ce-4ee3-83f8-0331e36f255d/dqc_reference/reference_markers_gtdb.fasta -out GCA_018372255.1_ASM1837225v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:15:54,164] [INFO] Task succeeded: Blastn
[2023-06-19 13:15:54,168] [INFO] Selected 18 target genomes.
[2023-06-19 13:15:54,169] [INFO] Target genome list was writen to GCA_018372255.1_ASM1837225v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:15:54,171] [INFO] Task started: fastANI
[2023-06-19 13:15:54,171] [INFO] Running command: fastANI --query /var/lib/cwl/stga6a46972-e65d-4897-a5fb-798aadb65c08/GCA_018372255.1_ASM1837225v1_genomic.fna.gz --refList GCA_018372255.1_ASM1837225v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018372255.1_ASM1837225v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:16:06,169] [INFO] Task succeeded: fastANI
[2023-06-19 13:16:06,184] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:16:06,184] [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_004569505.1	s__Dysgonomonas sp900079735	97.2959	1147	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	97.42	95.88	0.87	0.75	11	conclusive
GCF_000213575.1	s__Dysgonomonas mossii	93.9977	1075	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014196915.1	s__Dysgonomonas hofstadii	80.1685	246	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	99.76	99.76	1.00	1.00	2	-
GCA_900079725.1	s__Dysgonomonas sp900079725	79.3362	330	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002409595.1	s__Dysgonomonas sp002409595	79.32	233	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	99.42	99.42	0.78	0.78	2	-
GCF_001261735.1	s__Dysgonomonas sp001261735	78.7634	267	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002482385.1	s__Dysgonomonas sp002482385	78.5138	311	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010501055.1	s__Dysgonomonas sp010501055	78.4087	419	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900343125.1	s__Dysgonomonas sp900343125	77.7841	181	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201355.1	s__Dysgonomonas alginatilytica	76.9155	122	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128985.1	s__Dysgonomonas macrotermitis	76.8293	108	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-19 13:16:06,186] [INFO] GTDB search result was written to GCA_018372255.1_ASM1837225v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:16:06,187] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:16:06,190] [INFO] DFAST_QC result json was written to GCA_018372255.1_ASM1837225v1_genomic.fna/dqc_result.json
[2023-06-19 13:16:06,190] [INFO] DFAST_QC completed!
[2023-06-19 13:16:06,190] [INFO] Total running time: 0h1m31s