[2024-01-24 10:47:40,961] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,967] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,967] [INFO] DQC Reference Directory: /var/lib/cwl/stg2af58e65-44ef-476f-a0f3-db1c01a1d171/dqc_reference
[2024-01-24 10:47:44,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,789] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,789] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5a26f95-4e2d-4714-8fff-8f3ab362ee4f/GCF_013410565.1_ASM1341056v1_genomic.fna.gz | prodigal -d GCF_013410565.1_ASM1341056v1_genomic.fna/cds.fna -a GCF_013410565.1_ASM1341056v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:03,573] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:03,574] [INFO] Task started: HMMsearch
[2024-01-24 10:48:03,574] [INFO] Running command: hmmsearch --tblout GCF_013410565.1_ASM1341056v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2af58e65-44ef-476f-a0f3-db1c01a1d171/dqc_reference/reference_markers.hmm GCF_013410565.1_ASM1341056v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:03,906] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:03,908] [INFO] Found 6/6 markers.
[2024-01-24 10:48:03,957] [INFO] Query marker FASTA was written to GCF_013410565.1_ASM1341056v1_genomic.fna/markers.fasta
[2024-01-24 10:48:03,957] [INFO] Task started: Blastn
[2024-01-24 10:48:03,957] [INFO] Running command: blastn -query GCF_013410565.1_ASM1341056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2af58e65-44ef-476f-a0f3-db1c01a1d171/dqc_reference/reference_markers.fasta -out GCF_013410565.1_ASM1341056v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:05,321] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:05,325] [INFO] Selected 15 target genomes.
[2024-01-24 10:48:05,325] [INFO] Target genome list was writen to GCF_013410565.1_ASM1341056v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:05,333] [INFO] Task started: fastANI
[2024-01-24 10:48:05,333] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5a26f95-4e2d-4714-8fff-8f3ab362ee4f/GCF_013410565.1_ASM1341056v1_genomic.fna.gz --refList GCF_013410565.1_ASM1341056v1_genomic.fna/target_genomes.txt --output GCF_013410565.1_ASM1341056v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:27,799] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:27,799] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2af58e65-44ef-476f-a0f3-db1c01a1d171/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:27,799] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2af58e65-44ef-476f-a0f3-db1c01a1d171/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:27,812] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:48:27,812] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:48:27,812] [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
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	83.3801	1277	2093	95	below_threshold
Streptomonospora alba	strain=YIM 90003	GCA_000826685.1	183763	183763	type	True	83.0623	1219	2093	95	below_threshold
Streptomonospora salina	strain=DSM 44593	GCA_014204715.1	104205	104205	type	True	82.5686	1204	2093	95	below_threshold
Nocardiopsis mwathae	strain=DSM 46659	GCA_014201195.1	1472723	1472723	type	True	81.4344	1005	2093	95	below_threshold
Nocardiopsis gilva	strain=YIM 90087	GCA_000341165.1	280236	280236	type	True	81.3876	879	2093	95	below_threshold
Nocardiopsis chromatogenes	strain=YIM 90109	GCA_000341185.1	280239	280239	type	True	81.128	1064	2093	95	below_threshold
Nocardiopsis composta	strain=DSM 44551	GCA_014200805.1	157465	157465	type	True	80.8982	1227	2093	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	80.787	1168	2093	95	below_threshold
Thermobifida cellulosilytica	strain=TB100	GCA_001517975.1	144786	144786	type	True	80.5427	843	2093	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	80.3863	883	2093	95	below_threshold
Thermobifida halotolerans	strain=DSM 44931	GCA_003574835.2	483545	483545	type	True	80.3421	898	2093	95	below_threshold
Thermobifida halotolerans	strain=YIM 90462	GCA_001660385.1	483545	483545	type	True	80.2337	883	2093	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	80.0807	989	2093	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	79.6918	922	2093	95	below_threshold
Nocardiopsis metallicus	strain=DSM 44598	GCA_014201115.1	179819	179819	type	True	79.488	947	2093	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:27,814] [INFO] DFAST Taxonomy check result was written to GCF_013410565.1_ASM1341056v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:27,814] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:27,815] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:27,815] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2af58e65-44ef-476f-a0f3-db1c01a1d171/dqc_reference/checkm_data
[2024-01-24 10:48:27,816] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:27,874] [INFO] Task started: CheckM
[2024-01-24 10:48:27,875] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013410565.1_ASM1341056v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013410565.1_ASM1341056v1_genomic.fna/checkm_input GCF_013410565.1_ASM1341056v1_genomic.fna/checkm_result
[2024-01-24 10:49:34,926] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:34,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:34,952] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:34,952] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:34,953] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013410565.1_ASM1341056v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:34,953] [INFO] Task started: Blastn
[2024-01-24 10:49:34,953] [INFO] Running command: blastn -query GCF_013410565.1_ASM1341056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2af58e65-44ef-476f-a0f3-db1c01a1d171/dqc_reference/reference_markers_gtdb.fasta -out GCF_013410565.1_ASM1341056v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:36,985] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:36,989] [INFO] Selected 10 target genomes.
[2024-01-24 10:49:36,990] [INFO] Target genome list was writen to GCF_013410565.1_ASM1341056v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:36,998] [INFO] Task started: fastANI
[2024-01-24 10:49:36,998] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5a26f95-4e2d-4714-8fff-8f3ab362ee4f/GCF_013410565.1_ASM1341056v1_genomic.fna.gz --refList GCF_013410565.1_ASM1341056v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013410565.1_ASM1341056v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:53,277] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:53,295] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:53,296] [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_013410565.1	s__Streptomonospora nanhaiensis	100.0	2091	2093	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	99.69	99.69	0.95	0.95	2	conclusive
GCF_009728995.1	s__Streptomonospora sp009728995	83.904	1298	2093	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004323735.1	s__Streptomonospora sp004323735	83.3612	1277	2093	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826685.1	s__Streptomonospora alba	83.0409	1222	2093	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552555.1	s__Nocardiopsis_B trehalosi	82.8228	1191	2093	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_014204715.1	s__Streptomonospora salina	82.5548	1201	2093	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201195.1	s__Nocardiopsis_C mwathae	81.4292	1013	2093	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_003336425.1	s__Marinitenerispora sediminis	80.817	1020	2093	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Marinitenerispora	95.0	99.95	99.94	0.96	0.96	3	-
GCF_001517975.1	s__Thermobifida cellulosilytica	80.5876	837	2093	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000981225.1	s__Allosalinactinospora lopnorensis	80.1991	883	2093	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Allosalinactinospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:53,298] [INFO] GTDB search result was written to GCF_013410565.1_ASM1341056v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:53,299] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:53,302] [INFO] DFAST_QC result json was written to GCF_013410565.1_ASM1341056v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:53,302] [INFO] DFAST_QC completed!
[2024-01-24 10:49:53,302] [INFO] Total running time: 0h2m12s