[2024-01-24 13:09:48,488] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:48,490] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:48,490] [INFO] DQC Reference Directory: /var/lib/cwl/stg1debee02-cc0c-4230-9cb6-204cc90934a3/dqc_reference
[2024-01-24 13:09:49,840] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:49,841] [INFO] Task started: Prodigal
[2024-01-24 13:09:49,841] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4be657a-619f-4ff5-85e3-2f69c4599df8/GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna/cds.fna -a GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:07,840] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:07,840] [INFO] Task started: HMMsearch
[2024-01-24 13:10:07,841] [INFO] Running command: hmmsearch --tblout GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1debee02-cc0c-4230-9cb6-204cc90934a3/dqc_reference/reference_markers.hmm GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:08,159] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:08,161] [INFO] Found 6/6 markers.
[2024-01-24 13:10:08,209] [INFO] Query marker FASTA was written to GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:10:08,210] [INFO] Task started: Blastn
[2024-01-24 13:10:08,210] [INFO] Running command: blastn -query GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1debee02-cc0c-4230-9cb6-204cc90934a3/dqc_reference/reference_markers.fasta -out GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:09,505] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:09,508] [INFO] Selected 21 target genomes.
[2024-01-24 13:10:09,509] [INFO] Target genome list was writen to GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:10:09,516] [INFO] Task started: fastANI
[2024-01-24 13:10:09,516] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4be657a-619f-4ff5-85e3-2f69c4599df8/GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna.gz --refList GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:42,956] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:42,956] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1debee02-cc0c-4230-9cb6-204cc90934a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:42,957] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1debee02-cc0c-4230-9cb6-204cc90934a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:42,977] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:10:42,977] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:42,977] [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=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	100.0	1973	1975	95	conclusive
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	99.9948	1960	1975	95	conclusive
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	81.0862	1198	1975	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_003202285.1	588067	588067	type	True	81.0566	1127	1975	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_007993965.1	588067	588067	type	True	80.9922	1136	1975	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.7448	1051	1975	95	below_threshold
Amycolatopsis nigrescens	strain=CSC17Ta-90	GCA_000384315.1	381445	381445	type	True	80.6368	1210	1975	95	below_threshold
Amycolatopsis anabasis	strain=EGI 650086	GCA_009765355.1	1840409	1840409	type	True	80.5676	1193	1975	95	below_threshold
Amycolatopsis granulosa	strain=DSM 45669	GCA_011758745.1	185684	185684	type	True	80.528	987	1975	95	below_threshold
Amycolatopsis viridis	strain=DSM 45668	GCA_011758765.1	185678	185678	type	True	80.5006	983	1975	95	below_threshold
Amycolatopsis palatopharyngis	strain=DSM 44832	GCA_003385185.1	187982	187982	type	True	80.3182	1015	1975	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	80.2766	990	1975	95	below_threshold
Amycolatopsis acidiphila	strain=JCM 30562	GCA_007713745.1	715473	715473	type	True	80.2432	974	1975	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	80.2168	1019	1975	95	below_threshold
Amycolatopsis endophytica	strain=DSM 104006	GCA_013410405.1	860233	860233	type	True	80.0189	1004	1975	95	below_threshold
Amycolatopsis rhizosphaerae	strain=TBRC 6029	GCA_007713715.1	2053003	2053003	type	True	79.7623	804	1975	95	below_threshold
Amycolatopsis acidicola	strain=K81G1	GCA_007713735.2	2596893	2596893	type	True	79.5554	956	1975	95	below_threshold
Amycolatopsis taiwanensis	strain=DSM 45107	GCA_000519205.1	342230	342230	type	True	79.4615	880	1975	95	below_threshold
Saccharomonospora piscinae	strain=KCTC 19743	GCA_005862235.1	687388	687388	type	True	79.4129	796	1975	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	79.2071	814	1975	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	77.973	831	1975	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:42,979] [INFO] DFAST Taxonomy check result was written to GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:10:42,980] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:42,980] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:42,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1debee02-cc0c-4230-9cb6-204cc90934a3/dqc_reference/checkm_data
[2024-01-24 13:10:42,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:43,040] [INFO] Task started: CheckM
[2024-01-24 13:10:43,040] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna/checkm_input GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:11:48,640] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:48,642] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:48,669] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:48,670] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:48,670] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:11:48,671] [INFO] Task started: Blastn
[2024-01-24 13:11:48,671] [INFO] Running command: blastn -query GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1debee02-cc0c-4230-9cb6-204cc90934a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:50,663] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:50,667] [INFO] Selected 22 target genomes.
[2024-01-24 13:11:50,667] [INFO] Target genome list was writen to GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:51,181] [INFO] Task started: fastANI
[2024-01-24 13:11:51,182] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4be657a-619f-4ff5-85e3-2f69c4599df8/GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna.gz --refList GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:12:29,469] [INFO] Task succeeded: fastANI
[2024-01-24 13:12:29,493] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:12:29,493] [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	100.0	1973	1975	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	81.1086	1112	1975	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	81.0611	1204	1975	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	81.0202	1133	1975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006715045.1	s__Amycolatopsis_D cihanbeyliensis	80.9218	1189	1975	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_003385215.1	s__Amycolatopsis thermalba	80.706	1058	1975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.72	99.30	0.96	0.93	4	-
GCF_003202235.1	s__Saccharomonospora sp003202235	80.6515	1113	1975	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	80.6372	1211	1975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765355.1	s__Amycolatopsis anabasis	80.6325	1180	1975	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	80.5706	973	1975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.9842	N/A	N/A	N/A	N/A	1	-
GCF_011758745.1	s__Amycolatopsis granulosa	80.5046	991	1975	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	80.4819	1104	1975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.4849	N/A	N/A	N/A	N/A	1	-
GCF_003385185.1	s__Amycolatopsis_D palatopharyngis	80.2717	1021	1975	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_007713745.1	s__Amycolatopsis acidiphila	80.2698	970	1975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014191255.1	s__Amycolatopsis bartoniae	80.0978	1004	1975	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	79.9667	1015	1975	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	79.7761	1123	1975	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	79.7489	806	1975	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	79.591	1120	1975	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	79.5566	956	1975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519205.1	s__Amycolatopsis taiwanensis	79.4823	875	1975	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	79.4158	795	1975	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	98.79	98.27	0.95	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:12:29,495] [INFO] GTDB search result was written to GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:12:29,496] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:12:29,502] [INFO] DFAST_QC result json was written to GCF_900115565.1_IMG-taxon_2675903051_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:12:29,502] [INFO] DFAST_QC completed!
[2024-01-24 13:12:29,502] [INFO] Total running time: 0h2m41s