[2023-06-18 17:21:39,642] [INFO] DFAST_QC pipeline started.
[2023-06-18 17:21:39,644] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 17:21:39,644] [INFO] DQC Reference Directory: /var/lib/cwl/stgc319767c-d640-4c65-b8da-47daea6f37c7/dqc_reference
[2023-06-18 17:21:40,746] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 17:21:40,746] [INFO] Task started: Prodigal
[2023-06-18 17:21:40,747] [INFO] Running command: gunzip -c /var/lib/cwl/stg49ac6b43-3707-406f-b6dc-123392c7f3de/GCA_013698135.1_ASM1369813v1_genomic.fna.gz | prodigal -d GCA_013698135.1_ASM1369813v1_genomic.fna/cds.fna -a GCA_013698135.1_ASM1369813v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 17:21:45,082] [INFO] Task succeeded: Prodigal
[2023-06-18 17:21:45,082] [INFO] Task started: HMMsearch
[2023-06-18 17:21:45,082] [INFO] Running command: hmmsearch --tblout GCA_013698135.1_ASM1369813v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc319767c-d640-4c65-b8da-47daea6f37c7/dqc_reference/reference_markers.hmm GCA_013698135.1_ASM1369813v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 17:21:45,255] [INFO] Task succeeded: HMMsearch
[2023-06-18 17:21:45,256] [INFO] Found 6/6 markers.
[2023-06-18 17:21:45,275] [INFO] Query marker FASTA was written to GCA_013698135.1_ASM1369813v1_genomic.fna/markers.fasta
[2023-06-18 17:21:45,275] [INFO] Task started: Blastn
[2023-06-18 17:21:45,275] [INFO] Running command: blastn -query GCA_013698135.1_ASM1369813v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc319767c-d640-4c65-b8da-47daea6f37c7/dqc_reference/reference_markers.fasta -out GCA_013698135.1_ASM1369813v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:21:46,035] [INFO] Task succeeded: Blastn
[2023-06-18 17:21:46,037] [INFO] Selected 29 target genomes.
[2023-06-18 17:21:46,038] [INFO] Target genome list was writen to GCA_013698135.1_ASM1369813v1_genomic.fna/target_genomes.txt
[2023-06-18 17:21:46,045] [INFO] Task started: fastANI
[2023-06-18 17:21:46,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg49ac6b43-3707-406f-b6dc-123392c7f3de/GCA_013698135.1_ASM1369813v1_genomic.fna.gz --refList GCA_013698135.1_ASM1369813v1_genomic.fna/target_genomes.txt --output GCA_013698135.1_ASM1369813v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 17:22:04,704] [INFO] Task succeeded: fastANI
[2023-06-18 17:22:04,704] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc319767c-d640-4c65-b8da-47daea6f37c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 17:22:04,704] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc319767c-d640-4c65-b8da-47daea6f37c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 17:22:04,716] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 17:22:04,716] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 17:22:04,716] [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
Egibacter rhizosphaerae	strain=EGI 80759	GCA_004322855.1	1670831	1670831	type	True	76.6513	99	509	95	below_threshold
Euzebya rosea	strain=DSW09	GCA_003073135.1	2052804	2052804	type	True	76.4175	114	509	95	below_threshold
Euzebya tangerina	strain=F10	GCA_003074135.1	591198	591198	type	True	76.0592	76	509	95	below_threshold
Egicoccus halophilus	strain=EGI 80432	GCA_004300825.1	1670830	1670830	type	True	75.5653	103	509	95	below_threshold
Egicoccus halophilus	strain=CGMCC 1.14988	GCA_014640475.1	1670830	1670830	type	True	75.557	104	509	95	below_threshold
Salsipaludibacter albus	strain=AS10	GCA_019798055.1	2849650	2849650	type	True	75.5422	71	509	95	below_threshold
Mycolicibacterium chitae	strain=JCM 12403	GCA_010727725.1	1792	1792	type	True	75.5221	66	509	95	below_threshold
Actinomycetospora chiangmaiensis	strain=DSM 45062	GCA_000379625.1	402650	402650	type	True	75.5067	76	509	95	below_threshold
Mycolicibacterium chitae	strain=NCTC10485	GCA_900637205.1	1792	1792	type	True	75.5051	67	509	95	below_threshold
Micromonospora marina	strain=DSM 45555	GCA_900091565.1	307120	307120	type	True	75.4345	78	509	95	below_threshold
Actinomycetospora corticicola	strain=DSM 45772	GCA_013409505.1	663602	663602	type	True	75.305	81	509	95	below_threshold
Microbacterium marinilacus	strain=YM11-607	GCA_019753765.1	415209	415209	type	True	75.2937	60	509	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	75.2914	62	509	95	below_threshold
Ornithinicoccus hortensis	strain=DSM 12335	GCA_006716185.1	82346	82346	type	True	75.2125	53	509	95	below_threshold
Frankia torreyi	strain=CpI1	GCA_000948395.1	1856	1856	type	True	75.2125	75	509	95	below_threshold
Catellatospora tritici	strain=NEAU-YM18	GCA_019083965.1	2851566	2851566	type	True	75.2099	101	509	95	below_threshold
Glycomyces terrestris	strain=YIM 121974	GCA_003933745.1	2493553	2493553	type	True	75.2023	70	509	95	below_threshold
Micromonospora nigra	strain=DSM 43818	GCA_900091585.1	145857	145857	type	True	75.2021	90	509	95	below_threshold
Ornithinicoccus hortensis	strain=HKI0125	GCA_009602515.1	82346	82346	type	True	75.2016	54	509	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	75.2008	120	509	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 17:22:04,718] [INFO] DFAST Taxonomy check result was written to GCA_013698135.1_ASM1369813v1_genomic.fna/tc_result.tsv
[2023-06-18 17:22:04,718] [INFO] ===== Taxonomy check completed =====
[2023-06-18 17:22:04,718] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 17:22:04,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc319767c-d640-4c65-b8da-47daea6f37c7/dqc_reference/checkm_data
[2023-06-18 17:22:04,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 17:22:04,744] [INFO] Task started: CheckM
[2023-06-18 17:22:04,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013698135.1_ASM1369813v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013698135.1_ASM1369813v1_genomic.fna/checkm_input GCA_013698135.1_ASM1369813v1_genomic.fna/checkm_result
[2023-06-18 17:22:22,194] [INFO] Task succeeded: CheckM
[2023-06-18 17:22:22,196] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.86%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 17:22:22,228] [INFO] ===== Completeness check finished =====
[2023-06-18 17:22:22,228] [INFO] ===== Start GTDB Search =====
[2023-06-18 17:22:22,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013698135.1_ASM1369813v1_genomic.fna/markers.fasta)
[2023-06-18 17:22:22,229] [INFO] Task started: Blastn
[2023-06-18 17:22:22,229] [INFO] Running command: blastn -query GCA_013698135.1_ASM1369813v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc319767c-d640-4c65-b8da-47daea6f37c7/dqc_reference/reference_markers_gtdb.fasta -out GCA_013698135.1_ASM1369813v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:22:23,342] [INFO] Task succeeded: Blastn
[2023-06-18 17:22:23,346] [INFO] Selected 19 target genomes.
[2023-06-18 17:22:23,347] [INFO] Target genome list was writen to GCA_013698135.1_ASM1369813v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 17:22:23,355] [INFO] Task started: fastANI
[2023-06-18 17:22:23,355] [INFO] Running command: fastANI --query /var/lib/cwl/stg49ac6b43-3707-406f-b6dc-123392c7f3de/GCA_013698135.1_ASM1369813v1_genomic.fna.gz --refList GCA_013698135.1_ASM1369813v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013698135.1_ASM1369813v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 17:22:33,393] [INFO] Task succeeded: fastANI
[2023-06-18 17:22:33,402] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 17:22:33,402] [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_013698135.1	s__JACCTL01 sp013698135	100.0	496	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__JACCTL01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013812395.1	s__JACCTL01 sp013812395	86.3161	309	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__JACCTL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013696915.1	s__JACCXR01 sp013696915	77.3864	186	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__JACCXR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377835.1	s__WHTG01 sp009377835	77.2769	131	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__WHTG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009379795.1	s__WHTC01 sp009379795	77.0671	130	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__WHTC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003553795.1	s__T1Sed10-49 sp003553795	76.7324	124	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__T1Sed10-49	95.0	99.28	99.23	0.95	0.92	4	-
GCA_007126835.1	s__SLAO01 sp007126835	76.3998	76	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__SLAO01	95.0	98.77	98.77	0.62	0.62	2	-
GCF_003073135.1	s__Euzebya rosea	76.3858	116	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Euzebyaceae;g__Euzebya	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007119305.1	s__SKPY01 sp007119305	76.3821	99	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__SKPY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003553565.1	s__PUKE01 sp003553565	76.3087	119	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__PUKE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003550425.1	s__PUKE01 sp003550425	76.2352	109	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__PUKE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805775.1	s__SCTD01 sp902805775	75.7048	82	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__SCTD01;g__SCTD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637205.1	s__Mycobacterium chitae	75.489	68	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009604375.1	s__Spirillospora macrotermitis	75.1958	121	509	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 17:22:33,404] [INFO] GTDB search result was written to GCA_013698135.1_ASM1369813v1_genomic.fna/result_gtdb.tsv
[2023-06-18 17:22:33,404] [INFO] ===== GTDB Search completed =====
[2023-06-18 17:22:33,409] [INFO] DFAST_QC result json was written to GCA_013698135.1_ASM1369813v1_genomic.fna/dqc_result.json
[2023-06-18 17:22:33,409] [INFO] DFAST_QC completed!
[2023-06-18 17:22:33,409] [INFO] Total running time: 0h0m54s