[2024-01-24 11:26:12,916] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:12,918] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:12,919] [INFO] DQC Reference Directory: /var/lib/cwl/stg3134dd68-9f0a-4b20-9db4-701ee087e665/dqc_reference
[2024-01-24 11:26:14,312] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:14,313] [INFO] Task started: Prodigal
[2024-01-24 11:26:14,313] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d106180-d445-4690-ab78-2789c46d82bf/GCF_013408335.1_ASM1340833v1_genomic.fna.gz | prodigal -d GCF_013408335.1_ASM1340833v1_genomic.fna/cds.fna -a GCF_013408335.1_ASM1340833v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:31,906] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:31,906] [INFO] Task started: HMMsearch
[2024-01-24 11:26:31,906] [INFO] Running command: hmmsearch --tblout GCF_013408335.1_ASM1340833v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3134dd68-9f0a-4b20-9db4-701ee087e665/dqc_reference/reference_markers.hmm GCF_013408335.1_ASM1340833v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:32,309] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:32,310] [INFO] Found 6/6 markers.
[2024-01-24 11:26:32,360] [INFO] Query marker FASTA was written to GCF_013408335.1_ASM1340833v1_genomic.fna/markers.fasta
[2024-01-24 11:26:32,361] [INFO] Task started: Blastn
[2024-01-24 11:26:32,361] [INFO] Running command: blastn -query GCF_013408335.1_ASM1340833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3134dd68-9f0a-4b20-9db4-701ee087e665/dqc_reference/reference_markers.fasta -out GCF_013408335.1_ASM1340833v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:33,576] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:33,580] [INFO] Selected 12 target genomes.
[2024-01-24 11:26:33,581] [INFO] Target genome list was writen to GCF_013408335.1_ASM1340833v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:33,586] [INFO] Task started: fastANI
[2024-01-24 11:26:33,586] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d106180-d445-4690-ab78-2789c46d82bf/GCF_013408335.1_ASM1340833v1_genomic.fna.gz --refList GCF_013408335.1_ASM1340833v1_genomic.fna/target_genomes.txt --output GCF_013408335.1_ASM1340833v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:48,950] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:48,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3134dd68-9f0a-4b20-9db4-701ee087e665/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:48,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3134dd68-9f0a-4b20-9db4-701ee087e665/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:48,962] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:48,962] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:48,962] [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
Nocardioides panzhihuensis	strain=DSM 26487	GCA_013408335.1	860243	860243	type	True	100.0	2087	2101	95	conclusive
Nocardioides albus	strain=JCM 3185	GCA_014648255.1	1841	1841	type	True	91.528	1514	2101	95	below_threshold
Nocardioides luteus	strain=JCM 3358	GCA_014648595.1	1844	1844	type	True	88.051	1344	2101	95	below_threshold
Nocardioides albertanoniae	strain=DSM 25218	GCA_006716315.1	1175486	1175486	type	True	87.4649	1344	2101	95	below_threshold
Nocardioides nematodiphilus	strain=R-N-C8	GCA_020216525.1	2849669	2849669	type	True	80.0379	638	2101	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	79.5099	663	2101	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	79.0931	650	2101	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	79.0735	630	2101	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	79.0613	627	2101	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	79.0585	719	2101	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	78.843	528	2101	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	78.8379	654	2101	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:48,964] [INFO] DFAST Taxonomy check result was written to GCF_013408335.1_ASM1340833v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:48,964] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:48,964] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:48,965] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3134dd68-9f0a-4b20-9db4-701ee087e665/dqc_reference/checkm_data
[2024-01-24 11:26:48,966] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:49,027] [INFO] Task started: CheckM
[2024-01-24 11:26:49,028] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013408335.1_ASM1340833v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013408335.1_ASM1340833v1_genomic.fna/checkm_input GCF_013408335.1_ASM1340833v1_genomic.fna/checkm_result
[2024-01-24 11:27:51,266] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:51,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:51,293] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:51,293] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:51,294] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013408335.1_ASM1340833v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:51,294] [INFO] Task started: Blastn
[2024-01-24 11:27:51,295] [INFO] Running command: blastn -query GCF_013408335.1_ASM1340833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3134dd68-9f0a-4b20-9db4-701ee087e665/dqc_reference/reference_markers_gtdb.fasta -out GCF_013408335.1_ASM1340833v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:53,138] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:53,142] [INFO] Selected 8 target genomes.
[2024-01-24 11:27:53,143] [INFO] Target genome list was writen to GCF_013408335.1_ASM1340833v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:53,151] [INFO] Task started: fastANI
[2024-01-24 11:27:53,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d106180-d445-4690-ab78-2789c46d82bf/GCF_013408335.1_ASM1340833v1_genomic.fna.gz --refList GCF_013408335.1_ASM1340833v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013408335.1_ASM1340833v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:07,644] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:07,658] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:07,659] [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_013408335.1	s__Nocardioides panzhihuensis	100.0	2087	2101	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014360585.1	s__Nocardioides sp014360585	94.2899	1439	2101	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648255.1	s__Nocardioides albus	91.51	1516	2101	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006715835.1	s__Nocardioides sp006715835	90.1753	1516	2101	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009858265.1	s__Nocardioides sp009858265	90.0766	1519	2101	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101045.1	s__Nocardioides sp900101045	89.7108	1519	2101	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752315.1	s__Nocardioides sp000192415	89.6668	1463	2101	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.29	98.29	0.91	0.91	2	-
GCF_014648595.1	s__Nocardioides luteus	88.0398	1345	2101	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:07,660] [INFO] GTDB search result was written to GCF_013408335.1_ASM1340833v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:07,661] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:07,666] [INFO] DFAST_QC result json was written to GCF_013408335.1_ASM1340833v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:07,666] [INFO] DFAST_QC completed!
[2024-01-24 11:28:07,666] [INFO] Total running time: 0h1m55s