[2024-01-24 13:22:42,356] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:42,362] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:42,363] [INFO] DQC Reference Directory: /var/lib/cwl/stg6cc1da91-38a4-4b7c-af50-5f4283d5b13f/dqc_reference
[2024-01-24 13:22:43,626] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:43,627] [INFO] Task started: Prodigal
[2024-01-24 13:22:43,627] [INFO] Running command: gunzip -c /var/lib/cwl/stg85af529e-db4c-41ed-9a91-a55dbc66e733/GCF_004340875.1_ASM434087v1_genomic.fna.gz | prodigal -d GCF_004340875.1_ASM434087v1_genomic.fna/cds.fna -a GCF_004340875.1_ASM434087v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:07,905] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:07,906] [INFO] Task started: HMMsearch
[2024-01-24 13:23:07,906] [INFO] Running command: hmmsearch --tblout GCF_004340875.1_ASM434087v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6cc1da91-38a4-4b7c-af50-5f4283d5b13f/dqc_reference/reference_markers.hmm GCF_004340875.1_ASM434087v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:08,270] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:08,271] [INFO] Found 6/6 markers.
[2024-01-24 13:23:08,339] [INFO] Query marker FASTA was written to GCF_004340875.1_ASM434087v1_genomic.fna/markers.fasta
[2024-01-24 13:23:08,339] [INFO] Task started: Blastn
[2024-01-24 13:23:08,340] [INFO] Running command: blastn -query GCF_004340875.1_ASM434087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6cc1da91-38a4-4b7c-af50-5f4283d5b13f/dqc_reference/reference_markers.fasta -out GCF_004340875.1_ASM434087v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:09,394] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:09,399] [INFO] Selected 25 target genomes.
[2024-01-24 13:23:09,400] [INFO] Target genome list was writen to GCF_004340875.1_ASM434087v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:09,439] [INFO] Task started: fastANI
[2024-01-24 13:23:09,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg85af529e-db4c-41ed-9a91-a55dbc66e733/GCF_004340875.1_ASM434087v1_genomic.fna.gz --refList GCF_004340875.1_ASM434087v1_genomic.fna/target_genomes.txt --output GCF_004340875.1_ASM434087v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:42,589] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:42,590] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6cc1da91-38a4-4b7c-af50-5f4283d5b13f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:42,591] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6cc1da91-38a4-4b7c-af50-5f4283d5b13f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:42,612] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:42,612] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:42,612] [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
Tamaricihabitans halophyticus	strain=DSM 45765	GCA_004340875.1	1262583	1262583	type	True	100.0	2105	2108	95	conclusive
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	77.8289	558	2108	95	below_threshold
Amycolatopsis nigrescens	strain=CSC17Ta-90	GCA_000384315.1	381445	381445	type	True	77.7145	612	2108	95	below_threshold
Amycolatopsis marina	strain=CGMCC 4.3568	GCA_900111885.1	490629	490629	type	True	77.5443	448	2108	95	below_threshold
Saccharopolyspora phatthalungensis	strain=DSM 45584	GCA_014203395.1	664693	664693	type	True	77.4804	390	2108	95	below_threshold
Amycolatopsis anabasis	strain=EGI 650086	GCA_009765355.1	1840409	1840409	type	True	77.4797	600	2108	95	below_threshold
Amycolatopsis suaedae	strain=8-3EHSu	GCA_004214935.1	2510978	2510978	type	True	77.4714	540	2108	95	below_threshold
Amycolatopsis viridis	strain=DSM 45668	GCA_011758765.1	185678	185678	type	True	77.4566	477	2108	95	below_threshold
Amycolatopsis albispora	strain=WP1	GCA_003312875.1	1804986	1804986	type	True	77.394	612	2108	95	below_threshold
Amycolatopsis rhizosphaerae	strain=TBRC 6029	GCA_007713715.1	2053003	2053003	type	True	77.3828	423	2108	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	77.3673	519	2108	95	below_threshold
Streptoalloteichus tenebrarius	strain=DSM 40477	GCA_024171885.1	1933	1933	type	True	77.2661	396	2108	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	77.2222	524	2108	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000739085.1	1814	1814	type	True	77.1947	524	2108	95	below_threshold
Amycolatopsis vastitatis	strain=H5	GCA_002234595.1	1905142	1905142	type	True	77.1892	496	2108	95	below_threshold
Actinophytocola xanthii	strain=11-183	GCA_001921205.1	1912961	1912961	type	True	77.1846	453	2108	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	77.1684	409	2108	95	below_threshold
Amycolatopsis thermoflava	strain=N1165	GCA_000473265.1	84480	84480	type	True	77.1548	561	2108	95	below_threshold
Actinokineospora auranticolor	strain=YU 961-1	GCA_002934265.1	155976	155976	type	True	77.1488	420	2108	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	77.1163	491	2108	95	below_threshold
Amycolatopsis keratiniphila subsp. keratiniphila	strain=DSM 44409	GCA_001620365.2	227715	129921	type	True	77.0427	483	2108	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	76.9248	449	2108	95	below_threshold
Actinopolyspora erythraea	strain=YIM 90600	GCA_000763095.1	414996	414996	type	True	76.9033	281	2108	95	below_threshold
Actinopolyspora erythraea	strain=YIM 90600	GCA_002263515.1	414996	414996	type	True	76.8972	285	2108	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	75.6272	289	2108	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:42,614] [INFO] DFAST Taxonomy check result was written to GCF_004340875.1_ASM434087v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:42,615] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:42,615] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:42,615] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6cc1da91-38a4-4b7c-af50-5f4283d5b13f/dqc_reference/checkm_data
[2024-01-24 13:23:42,616] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:42,674] [INFO] Task started: CheckM
[2024-01-24 13:23:42,674] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004340875.1_ASM434087v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004340875.1_ASM434087v1_genomic.fna/checkm_input GCF_004340875.1_ASM434087v1_genomic.fna/checkm_result
[2024-01-24 13:24:46,857] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:46,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:46,883] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:46,883] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:46,884] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004340875.1_ASM434087v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:46,884] [INFO] Task started: Blastn
[2024-01-24 13:24:46,884] [INFO] Running command: blastn -query GCF_004340875.1_ASM434087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6cc1da91-38a4-4b7c-af50-5f4283d5b13f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004340875.1_ASM434087v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:48,350] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:48,355] [INFO] Selected 23 target genomes.
[2024-01-24 13:24:48,355] [INFO] Target genome list was writen to GCF_004340875.1_ASM434087v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:48,376] [INFO] Task started: fastANI
[2024-01-24 13:24:48,376] [INFO] Running command: fastANI --query /var/lib/cwl/stg85af529e-db4c-41ed-9a91-a55dbc66e733/GCF_004340875.1_ASM434087v1_genomic.fna.gz --refList GCF_004340875.1_ASM434087v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004340875.1_ASM434087v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:17,651] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:17,669] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:17,669] [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_004340875.1	s__Tamaricihabitans halophyticus	100.0	2105	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Tamaricihabitans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009379845.1	s__Tamaricihabitans sp009379845	79.1772	749	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Tamaricihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715045.1	s__Amycolatopsis_D cihanbeyliensis	77.8393	533	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384315.1	s__Amycolatopsis nigrescens	77.7209	610	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001955.1	s__Saccharomonospora shujinwangii	77.5368	488	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111885.1	s__Amycolatopsis_D marina	77.5312	449	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011758745.1	s__Amycolatopsis granulosa	77.5224	456	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.9842	N/A	N/A	N/A	N/A	1	-
GCF_004214935.1	s__Amycolatopsis suaedae	77.4821	538	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464705.1	s__Saccharomonospora sp016464705	77.4538	487	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017309385.1	s__Amycolatopsis sp017309385	77.4153	600	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003312875.1	s__Amycolatopsis albispora	77.4041	610	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007713715.1	s__Amycolatopsis rhizosphaerae	77.3943	421	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385215.1	s__Amycolatopsis thermalba	77.3868	517	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.72	99.30	0.96	0.93	4	-
GCF_014653945.1	s__Amycolatopsis deserti	77.215	543	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001921205.1	s__Actinophytocola xanthii	77.1838	451	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203665.1	s__Actinosynnema tamanrassetense	77.178	424	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934265.1	s__Actinokineospora auranticolor	77.1484	420	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473265.1	s__Amycolatopsis thermoflava	77.1451	563	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	96.3446	98.72	98.72	0.92	0.92	2	-
GCF_902497555.1	s__Amycolatopsis sp902497555	77.117	490	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364075.1	s__Amycolatopsis sp013364075	77.0369	539	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634935.1	s__Actinosynnema australiense	76.925	448	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002263515.1	s__Actinopolyspora erythraea	76.8973	285	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	99.98	99.98	0.99	0.99	2	-
GCF_008923205.2	s__Spirillospora physcomitrii	75.6266	289	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:17,671] [INFO] GTDB search result was written to GCF_004340875.1_ASM434087v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:17,672] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:17,676] [INFO] DFAST_QC result json was written to GCF_004340875.1_ASM434087v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:17,676] [INFO] DFAST_QC completed!
[2024-01-24 13:25:17,676] [INFO] Total running time: 0h2m35s