[2024-01-24 10:57:37,956] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:37,959] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:37,959] [INFO] DQC Reference Directory: /var/lib/cwl/stg12dd1266-3a61-48ce-8215-46c6f376ad4c/dqc_reference
[2024-01-24 10:57:39,314] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:39,315] [INFO] Task started: Prodigal
[2024-01-24 10:57:39,315] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a7af44d-80dd-4600-8fcd-a629e869a6d1/GCF_003688855.1_ASM368885v1_genomic.fna.gz | prodigal -d GCF_003688855.1_ASM368885v1_genomic.fna/cds.fna -a GCF_003688855.1_ASM368885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:51,886] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:51,887] [INFO] Task started: HMMsearch
[2024-01-24 10:57:51,887] [INFO] Running command: hmmsearch --tblout GCF_003688855.1_ASM368885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12dd1266-3a61-48ce-8215-46c6f376ad4c/dqc_reference/reference_markers.hmm GCF_003688855.1_ASM368885v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:52,166] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:52,167] [INFO] Found 6/6 markers.
[2024-01-24 10:57:52,197] [INFO] Query marker FASTA was written to GCF_003688855.1_ASM368885v1_genomic.fna/markers.fasta
[2024-01-24 10:57:52,198] [INFO] Task started: Blastn
[2024-01-24 10:57:52,198] [INFO] Running command: blastn -query GCF_003688855.1_ASM368885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12dd1266-3a61-48ce-8215-46c6f376ad4c/dqc_reference/reference_markers.fasta -out GCF_003688855.1_ASM368885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:53,213] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:53,217] [INFO] Selected 16 target genomes.
[2024-01-24 10:57:53,217] [INFO] Target genome list was writen to GCF_003688855.1_ASM368885v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:53,246] [INFO] Task started: fastANI
[2024-01-24 10:57:53,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a7af44d-80dd-4600-8fcd-a629e869a6d1/GCF_003688855.1_ASM368885v1_genomic.fna.gz --refList GCF_003688855.1_ASM368885v1_genomic.fna/target_genomes.txt --output GCF_003688855.1_ASM368885v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:04,003] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:04,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12dd1266-3a61-48ce-8215-46c6f376ad4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:04,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12dd1266-3a61-48ce-8215-46c6f376ad4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:04,018] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:04,018] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:04,018] [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
Tessaracoccus antarcticus	strain=JDX10	GCA_003688855.1	2479848	2479848	type	True	100.0	1211	1212	95	conclusive
Tessaracoccus rhinocerotis	strain=YIM 101269	GCA_007197885.1	1689449	1689449	type	True	79.0891	439	1212	95	below_threshold
Tessaracoccus lapidicaptus	strain=IPBSL-7	GCA_001693815.1	1427523	1427523	type	True	78.6148	363	1212	95	below_threshold
Tessaracoccus aquimaris	strain=NSG39	GCA_001997345.1	1332264	1332264	type	True	78.4625	359	1212	95	below_threshold
Tessaracoccus oleiagri	strain=CGMCC 1.9159	GCA_900103275.1	686624	686624	type	True	78.4014	323	1212	95	below_threshold
Tessaracoccus defluvii	strain=JCM 17540	GCA_014489575.1	1285901	1285901	type	True	78.3397	356	1212	95	below_threshold
Tessaracoccus coleopterorum	strain=HDW20	GCA_011174705.1	2714950	2714950	type	True	78.3018	360	1212	95	below_threshold
[Pseudopropionibacterium] massiliense	strain=Marseille-P6184	GCA_900607225.1	2220000	2220000	type	True	78.2094	248	1212	95	below_threshold
Tessaracoccus flavescens	strain=SST-39T	GCA_001998865.1	399497	399497	type	True	78.0764	338	1212	95	below_threshold
Arachnia propionica	strain=NBRC 14587	GCA_001592325.1	1750	1750	type	True	77.9636	257	1212	95	below_threshold
Arachnia propionica	strain=NCTC12967	GCA_900637725.1	1750	1750	type	True	77.956	255	1212	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	77.551	221	1212	95	below_threshold
Propioniciclava sinopodophylli	strain=KCTC 33808	GCA_004324755.1	1837344	1837344	type	True	77.5401	228	1212	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	76.8096	160	1212	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	76.5757	175	1212	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002811705.2	1257026	1257026	type	True	76.3281	153	1212	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:04,020] [INFO] DFAST Taxonomy check result was written to GCF_003688855.1_ASM368885v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:04,021] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:04,021] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:04,021] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12dd1266-3a61-48ce-8215-46c6f376ad4c/dqc_reference/checkm_data
[2024-01-24 10:58:04,023] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:04,064] [INFO] Task started: CheckM
[2024-01-24 10:58:04,064] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003688855.1_ASM368885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003688855.1_ASM368885v1_genomic.fna/checkm_input GCF_003688855.1_ASM368885v1_genomic.fna/checkm_result
[2024-01-24 10:59:19,438] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:19,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:19,459] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:19,459] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:19,459] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003688855.1_ASM368885v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:19,460] [INFO] Task started: Blastn
[2024-01-24 10:59:19,460] [INFO] Running command: blastn -query GCF_003688855.1_ASM368885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12dd1266-3a61-48ce-8215-46c6f376ad4c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003688855.1_ASM368885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:20,995] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:20,998] [INFO] Selected 18 target genomes.
[2024-01-24 10:59:20,998] [INFO] Target genome list was writen to GCF_003688855.1_ASM368885v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:21,025] [INFO] Task started: fastANI
[2024-01-24 10:59:21,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a7af44d-80dd-4600-8fcd-a629e869a6d1/GCF_003688855.1_ASM368885v1_genomic.fna.gz --refList GCF_003688855.1_ASM368885v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003688855.1_ASM368885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:32,534] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:32,562] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:32,562] [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_003688855.1	s__Arachnia antarctica	100.0	1211	1212	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007197885.1	s__Arachnia rhinocerotis	79.0833	439	1212	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693815.1	s__Arachnia lapidicapta	78.6523	361	1212	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	98.86	97.76	0.95	0.93	4	-
GCF_014164775.1	s__Arachnia sp014164775	78.5822	340	1212	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	97.46	97.46	0.87	0.87	2	-
GCF_017815535.1	s__Arachnia sp001956895	78.5152	340	1212	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	97.64	95.92	0.92	0.88	4	-
GCA_016714275.1	s__Arachnia sp016714275	78.4759	305	1212	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001997345.1	s__Arachnia aquimaris	78.4672	358	1212	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103275.1	s__Arachnia oleiagri	78.3895	324	1212	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489575.1	s__Arachnia defluvii	78.3188	358	1212	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012837465.1	s__Arachnia sp012837465	78.2657	311	1212	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003859805.1	s__Arachnia propionica_C	78.2436	254	1212	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900607225.1	s__Arachnia sp900607225	78.2094	248	1212	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001998865.1	s__Arachnia flavescens	78.0777	337	1212	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001997295.1	s__Arachnia flava	78.0537	336	1212	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003932785.1	s__Arachnia propionica_B	78.049	278	1212	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637725.1	s__Arachnia propionica	77.951	257	1212	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	98.87	97.26	0.96	0.91	9	-
GCA_905372155.1	s__Arachnia sp905372155	77.9386	241	1212	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141915.1	s__Arachnia bendigoensis	77.7445	277	1212	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:32,564] [INFO] GTDB search result was written to GCF_003688855.1_ASM368885v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:32,565] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:32,571] [INFO] DFAST_QC result json was written to GCF_003688855.1_ASM368885v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:32,571] [INFO] DFAST_QC completed!
[2024-01-24 10:59:32,571] [INFO] Total running time: 0h1m55s