[2024-01-24 11:35:11,664] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:11,666] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:11,667] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a6586ca-d537-44e7-8cef-a877a1e803df/dqc_reference
[2024-01-24 11:35:12,961] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:12,962] [INFO] Task started: Prodigal
[2024-01-24 11:35:12,962] [INFO] Running command: gunzip -c /var/lib/cwl/stgc62c7131-31a1-4549-8270-c0aae69b05a9/GCF_013408795.1_ASM1340879v1_genomic.fna.gz | prodigal -d GCF_013408795.1_ASM1340879v1_genomic.fna/cds.fna -a GCF_013408795.1_ASM1340879v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:31,472] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:31,472] [INFO] Task started: HMMsearch
[2024-01-24 11:35:31,472] [INFO] Running command: hmmsearch --tblout GCF_013408795.1_ASM1340879v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a6586ca-d537-44e7-8cef-a877a1e803df/dqc_reference/reference_markers.hmm GCF_013408795.1_ASM1340879v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:31,860] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:31,862] [INFO] Found 6/6 markers.
[2024-01-24 11:35:31,917] [INFO] Query marker FASTA was written to GCF_013408795.1_ASM1340879v1_genomic.fna/markers.fasta
[2024-01-24 11:35:31,918] [INFO] Task started: Blastn
[2024-01-24 11:35:31,918] [INFO] Running command: blastn -query GCF_013408795.1_ASM1340879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a6586ca-d537-44e7-8cef-a877a1e803df/dqc_reference/reference_markers.fasta -out GCF_013408795.1_ASM1340879v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:33,233] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:33,236] [INFO] Selected 19 target genomes.
[2024-01-24 11:35:33,237] [INFO] Target genome list was writen to GCF_013408795.1_ASM1340879v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:33,244] [INFO] Task started: fastANI
[2024-01-24 11:35:33,244] [INFO] Running command: fastANI --query /var/lib/cwl/stgc62c7131-31a1-4549-8270-c0aae69b05a9/GCF_013408795.1_ASM1340879v1_genomic.fna.gz --refList GCF_013408795.1_ASM1340879v1_genomic.fna/target_genomes.txt --output GCF_013408795.1_ASM1340879v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:59,807] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:59,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a6586ca-d537-44e7-8cef-a877a1e803df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:59,808] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a6586ca-d537-44e7-8cef-a877a1e803df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:59,829] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:59,830] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:59,830] [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
Nocardiopsis gilva	strain=YIM 90087	GCA_000341165.1	280236	280236	type	True	81.622	913	2228	95	below_threshold
Nocardiopsis mwathae	strain=DSM 46659	GCA_014201195.1	1472723	1472723	type	True	81.5933	1033	2228	95	below_threshold
Nocardiopsis gilva	strain=YIM 90087	GCA_002263495.1	280236	280236	type	True	81.5677	1013	2228	95	below_threshold
Thermobifida halotolerans	strain=DSM 44931	GCA_003574835.2	483545	483545	type	True	81.3446	974	2228	95	below_threshold
Thermobifida halotolerans	strain=YIM 90462	GCA_001660385.1	483545	483545	type	True	81.2801	943	2228	95	below_threshold
Thermobifida cellulosilytica	strain=TB100	GCA_001517975.1	144786	144786	type	True	81.1897	894	2228	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	81.0835	1100	2228	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	81.0785	940	2228	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	80.982	1065	2228	95	below_threshold
Streptomonospora alba	strain=YIM 90003	GCA_000826685.1	183763	183763	type	True	80.9347	1041	2228	95	below_threshold
Nocardiopsis composta	strain=DSM 44551	GCA_014200805.1	157465	157465	type	True	80.882	1210	2228	95	below_threshold
Streptomonospora salina	strain=DSM 44593	GCA_014204715.1	104205	104205	type	True	80.7073	986	2228	95	below_threshold
Nocardiopsis dassonvillei subsp. crassaminis	strain=D1	GCA_902825375.1	2580523	2014	type	True	80.2951	859	2228	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	80.1484	943	2228	95	below_threshold
Nocardiopsis halotolerans	strain=DSM 44410	GCA_000341065.1	124252	124252	type	True	80.0268	855	2228	95	below_threshold
Nocardiopsis deserti	strain=H13	GCA_008638355.1	2605988	2605988	type	True	79.9441	992	2228	95	below_threshold
Nocardiopsis aegyptia	strain=DSM 44442	GCA_013410755.1	220378	220378	type	True	79.8577	963	2228	95	below_threshold
Nocardiopsis flavescens	strain=CGMCC 4.5723	GCA_900141985.1	758803	758803	type	True	79.6946	962	2228	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	79.4598	891	2228	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:59,832] [INFO] DFAST Taxonomy check result was written to GCF_013408795.1_ASM1340879v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:59,832] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:59,833] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:59,833] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a6586ca-d537-44e7-8cef-a877a1e803df/dqc_reference/checkm_data
[2024-01-24 11:35:59,834] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:59,900] [INFO] Task started: CheckM
[2024-01-24 11:35:59,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013408795.1_ASM1340879v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013408795.1_ASM1340879v1_genomic.fna/checkm_input GCF_013408795.1_ASM1340879v1_genomic.fna/checkm_result
[2024-01-24 11:37:26,487] [INFO] Task succeeded: CheckM
[2024-01-24 11:37:26,488] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:37:26,510] [INFO] ===== Completeness check finished =====
[2024-01-24 11:37:26,511] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:37:26,511] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013408795.1_ASM1340879v1_genomic.fna/markers.fasta)
[2024-01-24 11:37:26,512] [INFO] Task started: Blastn
[2024-01-24 11:37:26,512] [INFO] Running command: blastn -query GCF_013408795.1_ASM1340879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a6586ca-d537-44e7-8cef-a877a1e803df/dqc_reference/reference_markers_gtdb.fasta -out GCF_013408795.1_ASM1340879v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:28,543] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:28,552] [INFO] Selected 13 target genomes.
[2024-01-24 11:37:28,552] [INFO] Target genome list was writen to GCF_013408795.1_ASM1340879v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:28,579] [INFO] Task started: fastANI
[2024-01-24 11:37:28,579] [INFO] Running command: fastANI --query /var/lib/cwl/stgc62c7131-31a1-4549-8270-c0aae69b05a9/GCF_013408795.1_ASM1340879v1_genomic.fna.gz --refList GCF_013408795.1_ASM1340879v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013408795.1_ASM1340879v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:47,523] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:47,537] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:47,537] [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_013408795.1	s__Spinactinospora alkalitolerans	100.0	2226	2228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spinactinospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900167435.1	s__Marinactinospora thermotolerans	82.2792	1118	2228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Marinactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363075.1	s__Actinorugispora endophytica	82.1208	1076	2228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinorugispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336425.1	s__Marinitenerispora sediminis	82.0589	1046	2228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Marinitenerispora	95.0	99.95	99.94	0.96	0.96	3	-
GCF_001552555.1	s__Nocardiopsis_B trehalosi	81.6369	1114	2228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201195.1	s__Nocardiopsis_C mwathae	81.6208	1033	2228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002263495.1	s__Nocardiopsis_C gilva	81.5348	1012	2228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_C	95.0	99.97	99.97	1.00	1.00	2	-
GCF_013410565.1	s__Streptomonospora nanhaiensis	81.4804	1139	2228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	99.69	99.69	0.95	0.95	2	-
GCF_001660385.1	s__Thermobifida halotolerans	81.2607	945	2228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida	95.0	99.91	99.91	0.97	0.97	2	-
GCF_001517975.1	s__Thermobifida cellulosilytica	81.2058	892	2228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014485.1	s__Murinocardiopsis flavida	80.7829	1159	2228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Murinocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204715.1	s__Streptomonospora salina	80.6832	992	2228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018316655.1	s__Nocardiopsis sp018316655	79.8132	1016	2228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:47,539] [INFO] GTDB search result was written to GCF_013408795.1_ASM1340879v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:47,540] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:47,544] [INFO] DFAST_QC result json was written to GCF_013408795.1_ASM1340879v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:47,544] [INFO] DFAST_QC completed!
[2024-01-24 11:37:47,544] [INFO] Total running time: 0h2m36s