[2024-01-25 17:43:05,794] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:43:05,796] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:43:05,796] [INFO] DQC Reference Directory: /var/lib/cwl/stgac3f6f30-a55c-498f-a6b0-c7abd547b83a/dqc_reference
[2024-01-25 17:43:06,920] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:43:06,921] [INFO] Task started: Prodigal
[2024-01-25 17:43:06,921] [INFO] Running command: gunzip -c /var/lib/cwl/stg203072fd-4322-4c54-8e56-5b1f9c3f826d/GCF_014196915.1_ASM1419691v1_genomic.fna.gz | prodigal -d GCF_014196915.1_ASM1419691v1_genomic.fna/cds.fna -a GCF_014196915.1_ASM1419691v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:43:24,221] [INFO] Task succeeded: Prodigal
[2024-01-25 17:43:24,221] [INFO] Task started: HMMsearch
[2024-01-25 17:43:24,221] [INFO] Running command: hmmsearch --tblout GCF_014196915.1_ASM1419691v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac3f6f30-a55c-498f-a6b0-c7abd547b83a/dqc_reference/reference_markers.hmm GCF_014196915.1_ASM1419691v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:43:24,503] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:43:24,504] [INFO] Found 6/6 markers.
[2024-01-25 17:43:24,544] [INFO] Query marker FASTA was written to GCF_014196915.1_ASM1419691v1_genomic.fna/markers.fasta
[2024-01-25 17:43:24,544] [INFO] Task started: Blastn
[2024-01-25 17:43:24,544] [INFO] Running command: blastn -query GCF_014196915.1_ASM1419691v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac3f6f30-a55c-498f-a6b0-c7abd547b83a/dqc_reference/reference_markers.fasta -out GCF_014196915.1_ASM1419691v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:25,113] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:25,115] [INFO] Selected 15 target genomes.
[2024-01-25 17:43:25,116] [INFO] Target genome list was writen to GCF_014196915.1_ASM1419691v1_genomic.fna/target_genomes.txt
[2024-01-25 17:43:25,129] [INFO] Task started: fastANI
[2024-01-25 17:43:25,129] [INFO] Running command: fastANI --query /var/lib/cwl/stg203072fd-4322-4c54-8e56-5b1f9c3f826d/GCF_014196915.1_ASM1419691v1_genomic.fna.gz --refList GCF_014196915.1_ASM1419691v1_genomic.fna/target_genomes.txt --output GCF_014196915.1_ASM1419691v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:43:36,277] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:36,277] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac3f6f30-a55c-498f-a6b0-c7abd547b83a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:43:36,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac3f6f30-a55c-498f-a6b0-c7abd547b83a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:43:36,283] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:43:36,283] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:43:36,283] [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 hofstadii	strain=DSM 104969	GCA_014196915.1	637886	637886	type	True	100.0	1652	1657	95	conclusive
Dysgonomonas capnocytophagoides	strain=DSM 22835	GCA_000426485.1	45254	45254	type	True	80.2447	121	1657	95	below_threshold
Dysgonomonas mossii	strain=DSM 22836	GCA_000213575.1	163665	163665	suspected-type	True	79.6434	249	1657	95	below_threshold
Dysgonomonas mossii	strain=DSM 22836	GCA_000376405.1	163665	163665	suspected-type	True	79.6113	252	1657	95	below_threshold
Dysgonomonas gadei	strain=ATCC BAA-286	GCA_000213555.1	156974	156974	type	True	79.2095	410	1657	95	below_threshold
Dysgonomonas macrotermitis	strain=DSM 27370	GCA_900128985.1	1346286	1346286	type	True	78.1398	124	1657	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:43:36,285] [INFO] DFAST Taxonomy check result was written to GCF_014196915.1_ASM1419691v1_genomic.fna/tc_result.tsv
[2024-01-25 17:43:36,285] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:43:36,285] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:43:36,285] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac3f6f30-a55c-498f-a6b0-c7abd547b83a/dqc_reference/checkm_data
[2024-01-25 17:43:36,286] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:43:36,336] [INFO] Task started: CheckM
[2024-01-25 17:43:36,336] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196915.1_ASM1419691v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196915.1_ASM1419691v1_genomic.fna/checkm_input GCF_014196915.1_ASM1419691v1_genomic.fna/checkm_result
[2024-01-25 17:44:25,821] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:25,822] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:25,867] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:25,868] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:25,869] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196915.1_ASM1419691v1_genomic.fna/markers.fasta)
[2024-01-25 17:44:25,869] [INFO] Task started: Blastn
[2024-01-25 17:44:25,869] [INFO] Running command: blastn -query GCF_014196915.1_ASM1419691v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac3f6f30-a55c-498f-a6b0-c7abd547b83a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196915.1_ASM1419691v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:26,794] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:26,797] [INFO] Selected 19 target genomes.
[2024-01-25 17:44:26,797] [INFO] Target genome list was writen to GCF_014196915.1_ASM1419691v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:44:26,834] [INFO] Task started: fastANI
[2024-01-25 17:44:26,835] [INFO] Running command: fastANI --query /var/lib/cwl/stg203072fd-4322-4c54-8e56-5b1f9c3f826d/GCF_014196915.1_ASM1419691v1_genomic.fna.gz --refList GCF_014196915.1_ASM1419691v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196915.1_ASM1419691v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:44:42,177] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:42,187] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:44:42,188] [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_014196915.1	s__Dysgonomonas hofstadii	100.0	1652	1657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	99.76	99.76	1.00	1.00	2	conclusive
GCF_000213575.1	s__Dysgonomonas mossii	79.6329	250	1657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000213555.1	s__Dysgonomonas gadei	79.2574	406	1657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	99.21	98.41	0.94	0.88	3	-
GCA_900079725.1	s__Dysgonomonas sp900079725	79.0597	392	1657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004569505.1	s__Dysgonomonas sp900079735	78.7843	235	1657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	97.42	95.88	0.87	0.75	11	-
GCA_002409595.1	s__Dysgonomonas sp002409595	78.7116	212	1657	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	78.3818	288	1657	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	78.3323	325	1657	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	78.0892	147	1657	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	77.9156	322	1657	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	77.6132	292	1657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556485.1	s__Dysgonomonas sp900556485	77.3421	176	1657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010501075.1	s__Dysgonomonas sp010501075	77.2409	154	1657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015550595.1	s__Parabacteroides sp900540715	76.8258	71	1657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.96	99.96	0.98	0.97	3	-
GCF_011299555.1	s__Dysgonomonas sp011299555	76.539	106	1657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	97.14	97.14	0.92	0.92	2	-
GCA_905196875.1	s__Parabacteroides sp905196875	75.8529	57	1657	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:44:42,190] [INFO] GTDB search result was written to GCF_014196915.1_ASM1419691v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:44:42,191] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:44:42,193] [INFO] DFAST_QC result json was written to GCF_014196915.1_ASM1419691v1_genomic.fna/dqc_result.json
[2024-01-25 17:44:42,194] [INFO] DFAST_QC completed!
[2024-01-25 17:44:42,194] [INFO] Total running time: 0h1m36s