[2023-06-30 14:27:25,910] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:27:25,913] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:27:25,913] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ec51ec5-84f2-4d8c-aec6-c894987aab48/dqc_reference
[2023-06-30 14:27:28,473] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:27:28,475] [INFO] Task started: Prodigal
[2023-06-30 14:27:28,475] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9f19b5b-c08d-4e24-9867-ebebff4f1b1e/GCA_025923955.1_ASM2592395v1_genomic.fna.gz | prodigal -d GCA_025923955.1_ASM2592395v1_genomic.fna/cds.fna -a GCA_025923955.1_ASM2592395v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:27:36,946] [INFO] Task succeeded: Prodigal
[2023-06-30 14:27:36,946] [INFO] Task started: HMMsearch
[2023-06-30 14:27:36,947] [INFO] Running command: hmmsearch --tblout GCA_025923955.1_ASM2592395v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ec51ec5-84f2-4d8c-aec6-c894987aab48/dqc_reference/reference_markers.hmm GCA_025923955.1_ASM2592395v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:27:37,195] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:27:37,197] [INFO] Found 6/6 markers.
[2023-06-30 14:27:37,227] [INFO] Query marker FASTA was written to GCA_025923955.1_ASM2592395v1_genomic.fna/markers.fasta
[2023-06-30 14:27:37,227] [INFO] Task started: Blastn
[2023-06-30 14:27:37,227] [INFO] Running command: blastn -query GCA_025923955.1_ASM2592395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ec51ec5-84f2-4d8c-aec6-c894987aab48/dqc_reference/reference_markers.fasta -out GCA_025923955.1_ASM2592395v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:27:37,829] [INFO] Task succeeded: Blastn
[2023-06-30 14:27:37,833] [INFO] Selected 24 target genomes.
[2023-06-30 14:27:37,834] [INFO] Target genome list was writen to GCA_025923955.1_ASM2592395v1_genomic.fna/target_genomes.txt
[2023-06-30 14:27:37,837] [INFO] Task started: fastANI
[2023-06-30 14:27:37,838] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9f19b5b-c08d-4e24-9867-ebebff4f1b1e/GCA_025923955.1_ASM2592395v1_genomic.fna.gz --refList GCA_025923955.1_ASM2592395v1_genomic.fna/target_genomes.txt --output GCA_025923955.1_ASM2592395v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:27:57,914] [INFO] Task succeeded: fastANI
[2023-06-30 14:27:57,914] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ec51ec5-84f2-4d8c-aec6-c894987aab48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:27:57,915] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ec51ec5-84f2-4d8c-aec6-c894987aab48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:27:57,924] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 14:27:57,925] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 14:27:57,925] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	75.5139	59	921	95	below_threshold
Jatrophihabitans endophyticus	strain=DSM 45627	GCA_900129455.1	1206085	1206085	type	True	75.3458	52	921	95	below_threshold
Nocardioides halotolerans	strain=DSM 19273	GCA_000422805.1	433660	433660	type	True	75.262	51	921	95	below_threshold
Streptomyces smaragdinus	strain=RB5	GCA_009604385.1	2585196	2585196	type	True	75.143	50	921	95	below_threshold
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	75.088	64	921	95	below_threshold
Planobispora longispora	strain=NBRC 13918	GCA_016863135.1	28887	28887	type	True	75.0721	68	921	95	below_threshold
Planomonospora sphaerica	strain=JCM 9374	GCA_001653075.1	161355	161355	type	True	75.0383	65	921	95	below_threshold
Planobispora takensis	strain=NBRC 109077	GCA_016863195.1	1367882	1367882	type	True	74.9131	81	921	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=JCM 3094	GCA_014647955.1	97193	58119	type	True	74.8265	71	921	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=NBRC 15869	GCA_016863235.1	97193	58119	type	True	74.8265	71	921	95	below_threshold
Herbidospora cretacea	strain=NBRC 15474	GCA_001570605.1	28444	28444	type	True	74.813	70	921	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 14:27:57,927] [INFO] DFAST Taxonomy check result was written to GCA_025923955.1_ASM2592395v1_genomic.fna/tc_result.tsv
[2023-06-30 14:27:57,928] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:27:57,928] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:27:57,928] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ec51ec5-84f2-4d8c-aec6-c894987aab48/dqc_reference/checkm_data
[2023-06-30 14:27:57,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:27:57,966] [INFO] Task started: CheckM
[2023-06-30 14:27:57,966] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025923955.1_ASM2592395v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025923955.1_ASM2592395v1_genomic.fna/checkm_input GCA_025923955.1_ASM2592395v1_genomic.fna/checkm_result
[2023-06-30 14:28:27,430] [INFO] Task succeeded: CheckM
[2023-06-30 14:28:27,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 14:28:27,458] [INFO] ===== Completeness check finished =====
[2023-06-30 14:28:27,458] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:28:27,459] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025923955.1_ASM2592395v1_genomic.fna/markers.fasta)
[2023-06-30 14:28:27,459] [INFO] Task started: Blastn
[2023-06-30 14:28:27,459] [INFO] Running command: blastn -query GCA_025923955.1_ASM2592395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ec51ec5-84f2-4d8c-aec6-c894987aab48/dqc_reference/reference_markers_gtdb.fasta -out GCA_025923955.1_ASM2592395v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:28:28,259] [INFO] Task succeeded: Blastn
[2023-06-30 14:28:28,264] [INFO] Selected 20 target genomes.
[2023-06-30 14:28:28,264] [INFO] Target genome list was writen to GCA_025923955.1_ASM2592395v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:28:28,272] [INFO] Task started: fastANI
[2023-06-30 14:28:28,272] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9f19b5b-c08d-4e24-9867-ebebff4f1b1e/GCA_025923955.1_ASM2592395v1_genomic.fna.gz --refList GCA_025923955.1_ASM2592395v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025923955.1_ASM2592395v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:28:41,648] [INFO] Task succeeded: fastANI
[2023-06-30 14:28:41,664] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 14:28:41,665] [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
GCA_003242515.1	s__ZC4RG35 sp003242515	77.4783	127	921	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__ZC4RG35;g__ZC4RG35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004356805.1	s__SZUA-217 sp004356805	76.8224	59	921	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__ZC4RG35;g__SZUA-217	95.0	99.12	98.89	0.80	0.78	3	-
GCA_017577575.1	s__ZC4RG17 sp017577575	76.8069	139	921	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__ZC4RG35;g__ZC4RG17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377435.1	s__WHTL01 sp009377435	76.7425	80	921	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__ZC4RG35;g__WHTL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003388545.1	s__MA-ANB-1 sp003388545	76.4269	76	921	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__ZC4RG35;g__MA-ANB-1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015488325.1	s__S012-128 sp015488325	76.4084	104	921	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__S012-128;g__S012-128	95.0	99.25	99.12	0.90	0.88	5	-
GCA_003230435.1	s__SZUA-217 sp003230435	76.3893	56	921	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__ZC4RG35;g__SZUA-217	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403855.1	s__UBA4744 sp002403855	75.8126	50	921	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__UBA4744;g__UBA4744	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124535.1	s__Geodermatophilus sp008124535	75.3099	54	921	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015711605.1	s__Planomonospora_A sp015711605	75.0559	72	921	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002950945.1	s__Sorangium cellulosum_E	74.7108	60	921	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 14:28:41,667] [INFO] GTDB search result was written to GCA_025923955.1_ASM2592395v1_genomic.fna/result_gtdb.tsv
[2023-06-30 14:28:41,668] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:28:41,673] [INFO] DFAST_QC result json was written to GCA_025923955.1_ASM2592395v1_genomic.fna/dqc_result.json
[2023-06-30 14:28:41,673] [INFO] DFAST_QC completed!
[2023-06-30 14:28:41,673] [INFO] Total running time: 0h1m16s