[2024-01-24 14:15:34,136] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:34,138] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:34,139] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f73b1c8-d9a7-43f2-9db8-caa4b6dfc9f6/dqc_reference
[2024-01-24 14:15:35,536] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:35,537] [INFO] Task started: Prodigal
[2024-01-24 14:15:35,537] [INFO] Running command: gunzip -c /var/lib/cwl/stg511675da-f64d-44b8-893c-597f9429cdab/GCF_003201355.1_ASM320135v1_genomic.fna.gz | prodigal -d GCF_003201355.1_ASM320135v1_genomic.fna/cds.fna -a GCF_003201355.1_ASM320135v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:55,484] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:55,485] [INFO] Task started: HMMsearch
[2024-01-24 14:15:55,485] [INFO] Running command: hmmsearch --tblout GCF_003201355.1_ASM320135v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f73b1c8-d9a7-43f2-9db8-caa4b6dfc9f6/dqc_reference/reference_markers.hmm GCF_003201355.1_ASM320135v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:55,847] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:55,848] [INFO] Found 6/6 markers.
[2024-01-24 14:15:55,903] [INFO] Query marker FASTA was written to GCF_003201355.1_ASM320135v1_genomic.fna/markers.fasta
[2024-01-24 14:15:55,904] [INFO] Task started: Blastn
[2024-01-24 14:15:55,904] [INFO] Running command: blastn -query GCF_003201355.1_ASM320135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f73b1c8-d9a7-43f2-9db8-caa4b6dfc9f6/dqc_reference/reference_markers.fasta -out GCF_003201355.1_ASM320135v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:56,549] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:56,562] [INFO] Selected 25 target genomes.
[2024-01-24 14:15:56,563] [INFO] Target genome list was writen to GCF_003201355.1_ASM320135v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:56,573] [INFO] Task started: fastANI
[2024-01-24 14:15:56,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg511675da-f64d-44b8-893c-597f9429cdab/GCF_003201355.1_ASM320135v1_genomic.fna.gz --refList GCF_003201355.1_ASM320135v1_genomic.fna/target_genomes.txt --output GCF_003201355.1_ASM320135v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:16:15,081] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:15,082] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f73b1c8-d9a7-43f2-9db8-caa4b6dfc9f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:16:15,082] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f73b1c8-d9a7-43f2-9db8-caa4b6dfc9f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:16:15,091] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:16:15,091] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:16:15,091] [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 alginatilytica	strain=DSM 100214	GCA_003201355.1	1605892	1605892	type	True	100.0	1667	1672	95	conclusive
Dysgonomonas capnocytophagoides	strain=DSM 22835	GCA_000426485.1	45254	45254	type	True	77.4877	253	1672	95	below_threshold
Dysgonomonas macrotermitis	strain=DSM 27370	GCA_900128985.1	1346286	1346286	type	True	77.2122	232	1672	95	below_threshold
Dysgonomonas macrotermitis	strain=JCM 19375	GCA_001047035.1	1346286	1346286	type	True	77.2102	233	1672	95	below_threshold
Dysgonomonas gadei	strain=ATCC BAA-286	GCA_000213555.1	156974	156974	type	True	76.7234	136	1672	95	below_threshold
Dysgonomonas mossii	strain=DSM 22836	GCA_000213575.1	163665	163665	suspected-type	True	76.6023	120	1672	95	below_threshold
Dysgonomonas massiliensis	strain=Marseille-P4356	GCA_900240225.1	2040292	2040292	type	True	76.5976	83	1672	95	below_threshold
Dysgonomonas mossii	strain=DSM 22836	GCA_000376405.1	163665	163665	suspected-type	True	76.4797	119	1672	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:16:15,097] [INFO] DFAST Taxonomy check result was written to GCF_003201355.1_ASM320135v1_genomic.fna/tc_result.tsv
[2024-01-24 14:16:15,098] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:16:15,098] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:16:15,098] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f73b1c8-d9a7-43f2-9db8-caa4b6dfc9f6/dqc_reference/checkm_data
[2024-01-24 14:16:15,101] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:16:15,160] [INFO] Task started: CheckM
[2024-01-24 14:16:15,161] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003201355.1_ASM320135v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003201355.1_ASM320135v1_genomic.fna/checkm_input GCF_003201355.1_ASM320135v1_genomic.fna/checkm_result
[2024-01-24 14:17:13,501] [INFO] Task succeeded: CheckM
[2024-01-24 14:17:13,503] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:17:13,531] [INFO] ===== Completeness check finished =====
[2024-01-24 14:17:13,532] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:17:13,532] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003201355.1_ASM320135v1_genomic.fna/markers.fasta)
[2024-01-24 14:17:13,533] [INFO] Task started: Blastn
[2024-01-24 14:17:13,533] [INFO] Running command: blastn -query GCF_003201355.1_ASM320135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f73b1c8-d9a7-43f2-9db8-caa4b6dfc9f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003201355.1_ASM320135v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:17:14,296] [INFO] Task succeeded: Blastn
[2024-01-24 14:17:14,300] [INFO] Selected 12 target genomes.
[2024-01-24 14:17:14,300] [INFO] Target genome list was writen to GCF_003201355.1_ASM320135v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:17:14,309] [INFO] Task started: fastANI
[2024-01-24 14:17:14,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg511675da-f64d-44b8-893c-597f9429cdab/GCF_003201355.1_ASM320135v1_genomic.fna.gz --refList GCF_003201355.1_ASM320135v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003201355.1_ASM320135v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:25,264] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:25,277] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:25,278] [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_003201355.1	s__Dysgonomonas alginatilytica	100.0	1667	1672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001261715.1	s__Dysgonomonas sp001261715	87.6793	1068	1672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	99.27	98.54	0.96	0.91	3	-
GCF_011299555.1	s__Dysgonomonas sp011299555	82.3052	898	1672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	97.14	97.14	0.92	0.92	2	-
GCF_011039205.1	s__Dysgonomonas sp011039205	79.4363	186	1672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	97.34	97.34	0.87	0.87	2	-
GCF_000426485.1	s__Dysgonomonas capnocytophagoides	77.4681	244	1672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	99.61	99.04	0.94	0.93	5	-
GCF_900128985.1	s__Dysgonomonas macrotermitis	77.2349	231	1672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900343125.1	s__Dysgonomonas sp900343125	77.0185	95	1672	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	76.9666	117	1672	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	76.716	123	1672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004569505.1	s__Dysgonomonas sp900079735	76.6004	145	1672	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Dysgonomonadaceae;g__Dysgonomonas	95.0	97.42	95.88	0.87	0.75	11	-
GCF_016652235.1	s__Dysgonomonas sp016652235	76.5693	116	1672	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 14:17:25,279] [INFO] GTDB search result was written to GCF_003201355.1_ASM320135v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:25,280] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:25,284] [INFO] DFAST_QC result json was written to GCF_003201355.1_ASM320135v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:25,284] [INFO] DFAST_QC completed!
[2024-01-24 14:17:25,284] [INFO] Total running time: 0h1m51s