[2024-01-24 13:12:55,769] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:55,771] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:55,771] [INFO] DQC Reference Directory: /var/lib/cwl/stga146753f-8631-4e83-98e2-65b946df34ba/dqc_reference
[2024-01-24 13:12:57,118] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:57,119] [INFO] Task started: Prodigal
[2024-01-24 13:12:57,119] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb5cee28-2cee-4d8e-a3f1-1fb8281f469b/GCF_004365925.1_ASM436592v1_genomic.fna.gz | prodigal -d GCF_004365925.1_ASM436592v1_genomic.fna/cds.fna -a GCF_004365925.1_ASM436592v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:16,109] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:16,110] [INFO] Task started: HMMsearch
[2024-01-24 13:13:16,110] [INFO] Running command: hmmsearch --tblout GCF_004365925.1_ASM436592v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga146753f-8631-4e83-98e2-65b946df34ba/dqc_reference/reference_markers.hmm GCF_004365925.1_ASM436592v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:16,424] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:16,426] [INFO] Found 6/6 markers.
[2024-01-24 13:13:16,493] [INFO] Query marker FASTA was written to GCF_004365925.1_ASM436592v1_genomic.fna/markers.fasta
[2024-01-24 13:13:16,493] [INFO] Task started: Blastn
[2024-01-24 13:13:16,494] [INFO] Running command: blastn -query GCF_004365925.1_ASM436592v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga146753f-8631-4e83-98e2-65b946df34ba/dqc_reference/reference_markers.fasta -out GCF_004365925.1_ASM436592v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:17,839] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:17,843] [INFO] Selected 21 target genomes.
[2024-01-24 13:13:17,843] [INFO] Target genome list was writen to GCF_004365925.1_ASM436592v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:17,855] [INFO] Task started: fastANI
[2024-01-24 13:13:17,855] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb5cee28-2cee-4d8e-a3f1-1fb8281f469b/GCF_004365925.1_ASM436592v1_genomic.fna.gz --refList GCF_004365925.1_ASM436592v1_genomic.fna/target_genomes.txt --output GCF_004365925.1_ASM436592v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:51,376] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:51,377] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga146753f-8631-4e83-98e2-65b946df34ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:51,377] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga146753f-8631-4e83-98e2-65b946df34ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:51,399] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:13:51,400] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:51,400] [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
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	100.0	1985	1986	95	conclusive
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	99.9973	1964	1986	95	conclusive
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	81.0426	1208	1986	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_007993965.1	588067	588067	type	True	80.9549	1144	1986	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_003202285.1	588067	588067	type	True	80.954	1122	1986	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.7547	1052	1986	95	below_threshold
Amycolatopsis granulosa	strain=DSM 45669	GCA_011758745.1	185684	185684	type	True	80.6763	966	1986	95	below_threshold
Amycolatopsis anabasis	strain=EGI 650086	GCA_009765355.1	1840409	1840409	type	True	80.6427	1184	1986	95	below_threshold
Amycolatopsis nigrescens	strain=CSC17Ta-90	GCA_000384315.1	381445	381445	type	True	80.6025	1209	1986	95	below_threshold
Amycolatopsis viridis	strain=DSM 45668	GCA_011758765.1	185678	185678	type	True	80.5898	980	1986	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	80.3355	991	1986	95	below_threshold
Amycolatopsis acidiphila	strain=JCM 30562	GCA_007713745.1	715473	715473	type	True	80.3348	961	1986	95	below_threshold
Amycolatopsis palatopharyngis	strain=DSM 44832	GCA_003385185.1	187982	187982	type	True	80.2876	1015	1986	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	80.2747	998	1986	95	below_threshold
Amycolatopsis endophytica	strain=DSM 104006	GCA_013410405.1	860233	860233	type	True	80.0789	988	1986	95	below_threshold
Amycolatopsis rhizosphaerae	strain=TBRC 6029	GCA_007713715.1	2053003	2053003	type	True	79.8393	808	1986	95	below_threshold
Amycolatopsis acidicola	strain=K81G1	GCA_007713735.2	2596893	2596893	type	True	79.6452	953	1986	95	below_threshold
Saccharomonospora piscinae	strain=KCTC 19743	GCA_005862235.1	687388	687388	type	True	79.3553	805	1986	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	79.3467	776	1986	95	below_threshold
Amycolatopsis taiwanensis	strain=DSM 45107	GCA_000519205.1	342230	342230	type	True	79.318	884	1986	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	77.8976	842	1986	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:51,402] [INFO] DFAST Taxonomy check result was written to GCF_004365925.1_ASM436592v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:51,402] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:51,402] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:51,402] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga146753f-8631-4e83-98e2-65b946df34ba/dqc_reference/checkm_data
[2024-01-24 13:13:51,403] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:51,459] [INFO] Task started: CheckM
[2024-01-24 13:13:51,459] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004365925.1_ASM436592v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004365925.1_ASM436592v1_genomic.fna/checkm_input GCF_004365925.1_ASM436592v1_genomic.fna/checkm_result
[2024-01-24 13:14:58,278] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:58,279] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:58,303] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:58,304] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:58,304] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004365925.1_ASM436592v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:58,304] [INFO] Task started: Blastn
[2024-01-24 13:14:58,305] [INFO] Running command: blastn -query GCF_004365925.1_ASM436592v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga146753f-8631-4e83-98e2-65b946df34ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_004365925.1_ASM436592v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:00,568] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:00,572] [INFO] Selected 22 target genomes.
[2024-01-24 13:15:00,573] [INFO] Target genome list was writen to GCF_004365925.1_ASM436592v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:00,606] [INFO] Task started: fastANI
[2024-01-24 13:15:00,607] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb5cee28-2cee-4d8e-a3f1-1fb8281f469b/GCF_004365925.1_ASM436592v1_genomic.fna.gz --refList GCF_004365925.1_ASM436592v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004365925.1_ASM436592v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:37,843] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:37,866] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:37,866] [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_900115565.1	s__Yuhushiella arida	99.9973	1964	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_003001955.1	s__Saccharomonospora shujinwangii	81.1312	1106	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018885265.1	s__Amycolatopsis_D sp018885265	81.0256	1211	1986	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_006715045.1	s__Amycolatopsis_D cihanbeyliensis	80.9707	1185	1986	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_003202285.1	s__Saccharomonospora muralis	80.9301	1126	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003385215.1	s__Amycolatopsis thermalba	80.7534	1052	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.72	99.30	0.96	0.93	4	-
GCF_011758745.1	s__Amycolatopsis granulosa	80.6632	968	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.9842	N/A	N/A	N/A	N/A	1	-
GCF_009765355.1	s__Amycolatopsis anabasis	80.6427	1183	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202235.1	s__Saccharomonospora sp003202235	80.6281	1112	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384315.1	s__Amycolatopsis nigrescens	80.5963	1210	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011758765.1	s__Amycolatopsis viridis	80.58	982	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.9842	N/A	N/A	N/A	N/A	1	-
GCF_000231075.2	s__Amycolatopsis sp000231075	80.5131	1104	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.4849	N/A	N/A	N/A	N/A	1	-
GCF_007713745.1	s__Amycolatopsis acidiphila	80.3298	963	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003385185.1	s__Amycolatopsis_D palatopharyngis	80.3175	1010	1986	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_014191255.1	s__Amycolatopsis bartoniae	80.1235	977	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	0.99	0.99	3	-
GCF_013410405.1	s__Amycolatopsis endophytica	80.1075	983	1986	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	79.8733	803	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018736145.1	s__Amycolatopsis sp018736145	79.7219	1105	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119165.1	s__Amycolatopsis australiensis	79.6852	1126	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007713735.2	s__Amycolatopsis acidicola	79.643	953	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005862235.1	s__Saccharomonospora piscinae	79.3755	802	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	98.79	98.27	0.95	0.94	3	-
GCF_000519205.1	s__Amycolatopsis taiwanensis	79.3278	882	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:37,868] [INFO] GTDB search result was written to GCF_004365925.1_ASM436592v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:37,868] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:37,873] [INFO] DFAST_QC result json was written to GCF_004365925.1_ASM436592v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:37,873] [INFO] DFAST_QC completed!
[2024-01-24 13:15:37,873] [INFO] Total running time: 0h2m42s