[2024-01-24 14:19:15,658] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:15,660] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:15,660] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f8056f9-a618-4ab5-af50-06c2ec4b20a6/dqc_reference
[2024-01-24 14:19:18,321] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:18,322] [INFO] Task started: Prodigal
[2024-01-24 14:19:18,322] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b9649e6-25f0-4b7a-8740-92e2a898ae6f/GCF_000376405.1_ASM37640v1_genomic.fna.gz | prodigal -d GCF_000376405.1_ASM37640v1_genomic.fna/cds.fna -a GCF_000376405.1_ASM37640v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:34,964] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:34,965] [INFO] Task started: HMMsearch
[2024-01-24 14:19:34,965] [INFO] Running command: hmmsearch --tblout GCF_000376405.1_ASM37640v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f8056f9-a618-4ab5-af50-06c2ec4b20a6/dqc_reference/reference_markers.hmm GCF_000376405.1_ASM37640v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:35,392] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:35,393] [INFO] Found 6/6 markers.
[2024-01-24 14:19:35,437] [INFO] Query marker FASTA was written to GCF_000376405.1_ASM37640v1_genomic.fna/markers.fasta
[2024-01-24 14:19:35,438] [INFO] Task started: Blastn
[2024-01-24 14:19:35,438] [INFO] Running command: blastn -query GCF_000376405.1_ASM37640v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f8056f9-a618-4ab5-af50-06c2ec4b20a6/dqc_reference/reference_markers.fasta -out GCF_000376405.1_ASM37640v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:36,342] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:36,346] [INFO] Selected 15 target genomes.
[2024-01-24 14:19:36,346] [INFO] Target genome list was writen to GCF_000376405.1_ASM37640v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:36,359] [INFO] Task started: fastANI
[2024-01-24 14:19:36,359] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b9649e6-25f0-4b7a-8740-92e2a898ae6f/GCF_000376405.1_ASM37640v1_genomic.fna.gz --refList GCF_000376405.1_ASM37640v1_genomic.fna/target_genomes.txt --output GCF_000376405.1_ASM37640v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:54,117] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:54,118] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f8056f9-a618-4ab5-af50-06c2ec4b20a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:54,118] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f8056f9-a618-4ab5-af50-06c2ec4b20a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:54,127] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:19:54,128] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:54,128] [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	100.0	1292	1292	95	conclusive
Dysgonomonas mossii	strain=DSM 22836	GCA_000213575.1	163665	163665	suspected-type	True	99.9973	1291	1292	95	conclusive
Dysgonomonas capnocytophagoides	strain=DSM 22835	GCA_000426485.1	45254	45254	type	True	79.5121	143	1292	95	below_threshold
Dysgonomonas hofstadii	strain=DSM 104969	GCA_014196915.1	637886	637886	type	True	79.3702	264	1292	95	below_threshold
Dysgonomonas gadei	strain=ATCC BAA-286	GCA_000213555.1	156974	156974	type	True	79.0461	305	1292	95	below_threshold
Dysgonomonas macrotermitis	strain=DSM 27370	GCA_900128985.1	1346286	1346286	type	True	77.3637	123	1292	95	below_threshold
Dysgonomonas macrotermitis	strain=JCM 19375	GCA_001047035.1	1346286	1346286	type	True	77.3429	121	1292	95	below_threshold
Dysgonomonas alginatilytica	strain=DSM 100214	GCA_003201355.1	1605892	1605892	type	True	76.6116	119	1292	95	below_threshold
Dysgonomonas massiliensis	strain=Marseille-P4356	GCA_900240225.1	2040292	2040292	type	True	76.5008	104	1292	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:54,133] [INFO] DFAST Taxonomy check result was written to GCF_000376405.1_ASM37640v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:54,134] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:54,134] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:54,135] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f8056f9-a618-4ab5-af50-06c2ec4b20a6/dqc_reference/checkm_data
[2024-01-24 14:19:54,137] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:54,192] [INFO] Task started: CheckM
[2024-01-24 14:19:54,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000376405.1_ASM37640v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000376405.1_ASM37640v1_genomic.fna/checkm_input GCF_000376405.1_ASM37640v1_genomic.fna/checkm_result
[2024-01-24 14:20:46,079] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:46,080] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:46,100] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:46,101] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:46,101] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000376405.1_ASM37640v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:46,101] [INFO] Task started: Blastn
[2024-01-24 14:20:46,102] [INFO] Running command: blastn -query GCF_000376405.1_ASM37640v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f8056f9-a618-4ab5-af50-06c2ec4b20a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000376405.1_ASM37640v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:47,070] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:47,075] [INFO] Selected 18 target genomes.
[2024-01-24 14:20:47,075] [INFO] Target genome list was writen to GCF_000376405.1_ASM37640v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:47,105] [INFO] Task started: fastANI
[2024-01-24 14:20:47,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b9649e6-25f0-4b7a-8740-92e2a898ae6f/GCF_000376405.1_ASM37640v1_genomic.fna.gz --refList GCF_000376405.1_ASM37640v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000376405.1_ASM37640v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:00,356] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:00,381] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:00,381] [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_000213575.1	s__Dysgonomonas mossii	99.9973	1291	1292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_004569505.1	s__Dysgonomonas sp900079735	94.0507	1086	1292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	97.42	95.88	0.87	0.75	11	-
GCF_000426485.1	s__Dysgonomonas capnocytophagoides	79.5282	143	1292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	99.61	99.04	0.94	0.93	5	-
GCF_014196915.1	s__Dysgonomonas hofstadii	79.3332	266	1292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	99.76	99.76	1.00	1.00	2	-
GCA_900556485.1	s__Dysgonomonas sp900556485	79.1377	144	1292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900079725.1	s__Dysgonomonas sp900079725	79.0077	333	1292	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	78.8246	464	1292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001261735.1	s__Dysgonomonas sp001261735	78.7946	251	1292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002409595.1	s__Dysgonomonas sp002409595	78.3224	257	1292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	99.42	99.42	0.78	0.78	2	-
GCF_010501105.1	s__Dysgonomonas sp010501105	78.0299	174	1292	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	78.0286	179	1292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711235.1	s__Dysgonomonas sp000711235	77.497	234	1292	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	77.3593	124	1292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003201355.1	s__Dysgonomonas alginatilytica	76.6131	120	1292	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:00,384] [INFO] GTDB search result was written to GCF_000376405.1_ASM37640v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:00,385] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:00,389] [INFO] DFAST_QC result json was written to GCF_000376405.1_ASM37640v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:00,389] [INFO] DFAST_QC completed!
[2024-01-24 14:21:00,390] [INFO] Total running time: 0h1m45s