[2023-06-19 06:45:24,071] [INFO] DFAST_QC pipeline started.
[2023-06-19 06:45:24,074] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 06:45:24,074] [INFO] DQC Reference Directory: /var/lib/cwl/stg5940d3ce-3c4e-41d3-b14a-dc5dbbd73889/dqc_reference
[2023-06-19 06:45:25,348] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 06:45:25,349] [INFO] Task started: Prodigal
[2023-06-19 06:45:25,349] [INFO] Running command: gunzip -c /var/lib/cwl/stg0329ffe5-b6a2-42a6-8a6d-ea725be5daae/GCA_013696785.1_ASM1369678v1_genomic.fna.gz | prodigal -d GCA_013696785.1_ASM1369678v1_genomic.fna/cds.fna -a GCA_013696785.1_ASM1369678v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 06:45:33,742] [INFO] Task succeeded: Prodigal
[2023-06-19 06:45:33,743] [INFO] Task started: HMMsearch
[2023-06-19 06:45:33,743] [INFO] Running command: hmmsearch --tblout GCA_013696785.1_ASM1369678v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5940d3ce-3c4e-41d3-b14a-dc5dbbd73889/dqc_reference/reference_markers.hmm GCA_013696785.1_ASM1369678v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 06:45:34,025] [INFO] Task succeeded: HMMsearch
[2023-06-19 06:45:34,026] [INFO] Found 6/6 markers.
[2023-06-19 06:45:34,074] [INFO] Query marker FASTA was written to GCA_013696785.1_ASM1369678v1_genomic.fna/markers.fasta
[2023-06-19 06:45:34,074] [INFO] Task started: Blastn
[2023-06-19 06:45:34,074] [INFO] Running command: blastn -query GCA_013696785.1_ASM1369678v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5940d3ce-3c4e-41d3-b14a-dc5dbbd73889/dqc_reference/reference_markers.fasta -out GCA_013696785.1_ASM1369678v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:45:35,042] [INFO] Task succeeded: Blastn
[2023-06-19 06:45:35,047] [INFO] Selected 25 target genomes.
[2023-06-19 06:45:35,047] [INFO] Target genome list was writen to GCA_013696785.1_ASM1369678v1_genomic.fna/target_genomes.txt
[2023-06-19 06:45:35,075] [INFO] Task started: fastANI
[2023-06-19 06:45:35,076] [INFO] Running command: fastANI --query /var/lib/cwl/stg0329ffe5-b6a2-42a6-8a6d-ea725be5daae/GCA_013696785.1_ASM1369678v1_genomic.fna.gz --refList GCA_013696785.1_ASM1369678v1_genomic.fna/target_genomes.txt --output GCA_013696785.1_ASM1369678v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 06:45:55,283] [INFO] Task succeeded: fastANI
[2023-06-19 06:45:55,284] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5940d3ce-3c4e-41d3-b14a-dc5dbbd73889/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 06:45:55,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5940d3ce-3c4e-41d3-b14a-dc5dbbd73889/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 06:45:55,302] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 06:45:55,302] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 06:45:55,303] [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
Geodermatophilus poikilotrophus	strain=DSM 44209	GCA_900111455.1	1333667	1333667	type	True	77.5622	259	892	95	below_threshold
Geodermatophilus pulveris	strain=DSM 46839	GCA_900188375.1	1564159	1564159	type	True	77.5061	263	892	95	below_threshold
Geodermatophilus chilensis	strain=B12	GCA_002802985.1	2035835	2035835	type	True	77.505	268	892	95	below_threshold
Geodermatophilus tzadiensis	strain=DSM 45416	GCA_003002915.1	1137988	1137988	type	True	77.4695	281	892	95	below_threshold
Modestobacter excelsi	strain=1G6	GCA_005930495.1	2213161	2213161	type	True	77.4409	246	892	95	below_threshold
Geodermatophilus siccatus	strain=DSM 45419	GCA_900103785.1	1137991	1137991	type	True	77.4026	285	892	95	below_threshold
Geodermatophilus normandii	strain=DSM 45417	GCA_003182485.1	1137989	1137989	type	True	77.3926	271	892	95	below_threshold
Geodermatophilus daqingensis	strain=DSM 104001	GCA_013408985.1	2026353	2026353	type	True	77.3066	304	892	95	below_threshold
Blastococcus xanthinilyticus	strain=DSM 46842	GCA_008124835.1	1564164	1564164	type	True	77.3018	263	892	95	below_threshold
Blastococcus saxobsidens	strain=DSM 44509	GCA_004217455.1	138336	138336	type	True	77.2956	230	892	95	below_threshold
Blastococcus saxobsidens	strain=DSM 44509	GCA_002938435.1	138336	138336	type	True	77.2862	226	892	95	below_threshold
Modestobacter roseus	strain=DSM 45764	GCA_007994135.1	1181884	1181884	type	True	77.1482	262	892	95	below_threshold
Geodermatophilus nigrescens	strain=DSM 45408	GCA_900129495.1	1070870	1070870	type	True	77.1397	286	892	95	below_threshold
Blastococcus colisei	strain=DSM 46837	GCA_006717095.1	1564162	1564162	type	True	77.0858	244	892	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	76.6167	121	892	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	76.2663	141	892	95	below_threshold
Kribbella flavida	strain=DSM 17836	GCA_000024345.1	182640	182640	type	True	76.2637	209	892	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	76.2448	141	892	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	76.2332	129	892	95	below_threshold
Amycolatopsis nigrescens	strain=CSC17Ta-90	GCA_000384315.1	381445	381445	type	True	76.1863	196	892	95	below_threshold
Jiangella mangrovi	strain=DSM 102122	GCA_014204975.1	1524084	1524084	type	True	76.1617	218	892	95	below_threshold
Nocardiopsis prasina	strain=DSM 43845	GCA_000341265.1	2015	2015	type	True	76.0995	114	892	95	below_threshold
Pilimelia anulata	strain=JCM 3090	GCA_014647895.1	53371	53371	type	True	76.0881	220	892	95	below_threshold
Planobispora longispora	strain=NBRC 13918	GCA_016863135.1	28887	28887	type	True	76.0677	229	892	95	below_threshold
Streptomyces aureoverticillatus	strain=JCM 4347	GCA_014649395.1	66871	66871	type	True	75.7396	164	892	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 06:45:55,305] [INFO] DFAST Taxonomy check result was written to GCA_013696785.1_ASM1369678v1_genomic.fna/tc_result.tsv
[2023-06-19 06:45:55,305] [INFO] ===== Taxonomy check completed =====
[2023-06-19 06:45:55,305] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 06:45:55,306] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5940d3ce-3c4e-41d3-b14a-dc5dbbd73889/dqc_reference/checkm_data
[2023-06-19 06:45:55,307] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 06:45:55,342] [INFO] Task started: CheckM
[2023-06-19 06:45:55,342] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013696785.1_ASM1369678v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013696785.1_ASM1369678v1_genomic.fna/checkm_input GCA_013696785.1_ASM1369678v1_genomic.fna/checkm_result
[2023-06-19 06:46:24,450] [INFO] Task succeeded: CheckM
[2023-06-19 06:46:24,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.25%
Contamintation: 5.09%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-19 06:46:24,477] [INFO] ===== Completeness check finished =====
[2023-06-19 06:46:24,477] [INFO] ===== Start GTDB Search =====
[2023-06-19 06:46:24,477] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013696785.1_ASM1369678v1_genomic.fna/markers.fasta)
[2023-06-19 06:46:24,477] [INFO] Task started: Blastn
[2023-06-19 06:46:24,477] [INFO] Running command: blastn -query GCA_013696785.1_ASM1369678v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5940d3ce-3c4e-41d3-b14a-dc5dbbd73889/dqc_reference/reference_markers_gtdb.fasta -out GCA_013696785.1_ASM1369678v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:46:25,850] [INFO] Task succeeded: Blastn
[2023-06-19 06:46:25,856] [INFO] Selected 15 target genomes.
[2023-06-19 06:46:25,856] [INFO] Target genome list was writen to GCA_013696785.1_ASM1369678v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 06:46:25,924] [INFO] Task started: fastANI
[2023-06-19 06:46:25,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg0329ffe5-b6a2-42a6-8a6d-ea725be5daae/GCA_013696785.1_ASM1369678v1_genomic.fna.gz --refList GCA_013696785.1_ASM1369678v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013696785.1_ASM1369678v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 06:46:36,172] [INFO] Task succeeded: fastANI
[2023-06-19 06:46:36,184] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 06:46:36,184] [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_013696785.1	s__JACCTY01 sp013696785	100.0	877	892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__JACCTY01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013695685.1	s__JACCTY01 sp013695685	82.1652	523	892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__JACCTY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812145.1	s__JACCTY01 sp013812145	81.8417	548	892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__JACCTY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695665.1	s__JACCTY01 sp013695665	81.3787	398	892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__JACCTY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813215.1	s__JACCSC01 sp013813215	79.2222	428	892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__JACCSC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188375.1	s__Geodermatophilus pulveris	77.5058	263	892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002915.1	s__Geodermatophilus tzadiensis	77.4806	280	892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004571065.1	s__Geodermatophilus sp004571065	77.464	233	892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124835.1	s__Blastococcus xanthinilyticus	77.2906	264	892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129495.1	s__Geodermatophilus nigrescens	77.121	288	892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805565.1	s__CADCTP01 sp902805565	77.0455	253	892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__CADCTP01;g__CADCTP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109665.1	s__Blastococcus sp900109665	76.9808	266	892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001942415.1	s__Pseudonocardia sp001942415	76.4512	212	892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726955.1	s__Mycobacterium fallax	76.2687	142	892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.97	0.97	2	-
GCA_003244095.1	s__QHCA01 sp003244095	76.1364	149	892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__QHCA01;g__QHCA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 06:46:36,186] [INFO] GTDB search result was written to GCA_013696785.1_ASM1369678v1_genomic.fna/result_gtdb.tsv
[2023-06-19 06:46:36,187] [INFO] ===== GTDB Search completed =====
[2023-06-19 06:46:36,193] [INFO] DFAST_QC result json was written to GCA_013696785.1_ASM1369678v1_genomic.fna/dqc_result.json
[2023-06-19 06:46:36,194] [INFO] DFAST_QC completed!
[2023-06-19 06:46:36,194] [INFO] Total running time: 0h1m12s