[2024-01-24 10:57:38,632] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:38,635] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:38,635] [INFO] DQC Reference Directory: /var/lib/cwl/stg08cebf8f-df70-418b-b4ae-d4ab7dbedfdd/dqc_reference
[2024-01-24 10:57:39,996] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:39,997] [INFO] Task started: Prodigal
[2024-01-24 10:57:39,998] [INFO] Running command: gunzip -c /var/lib/cwl/stgc38a58bd-ef2d-48e0-9994-919c2a03dcde/GCF_001653335.1_ASM165333v1_genomic.fna.gz | prodigal -d GCF_001653335.1_ASM165333v1_genomic.fna/cds.fna -a GCF_001653335.1_ASM165333v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:52,454] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:52,454] [INFO] Task started: HMMsearch
[2024-01-24 10:57:52,454] [INFO] Running command: hmmsearch --tblout GCF_001653335.1_ASM165333v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08cebf8f-df70-418b-b4ae-d4ab7dbedfdd/dqc_reference/reference_markers.hmm GCF_001653335.1_ASM165333v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:52,742] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:52,743] [INFO] Found 6/6 markers.
[2024-01-24 10:57:52,786] [INFO] Query marker FASTA was written to GCF_001653335.1_ASM165333v1_genomic.fna/markers.fasta
[2024-01-24 10:57:52,787] [INFO] Task started: Blastn
[2024-01-24 10:57:52,787] [INFO] Running command: blastn -query GCF_001653335.1_ASM165333v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08cebf8f-df70-418b-b4ae-d4ab7dbedfdd/dqc_reference/reference_markers.fasta -out GCF_001653335.1_ASM165333v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:54,060] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:54,064] [INFO] Selected 12 target genomes.
[2024-01-24 10:57:54,065] [INFO] Target genome list was writen to GCF_001653335.1_ASM165333v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:54,069] [INFO] Task started: fastANI
[2024-01-24 10:57:54,070] [INFO] Running command: fastANI --query /var/lib/cwl/stgc38a58bd-ef2d-48e0-9994-919c2a03dcde/GCF_001653335.1_ASM165333v1_genomic.fna.gz --refList GCF_001653335.1_ASM165333v1_genomic.fna/target_genomes.txt --output GCF_001653335.1_ASM165333v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:07,520] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:07,521] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08cebf8f-df70-418b-b4ae-d4ab7dbedfdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:07,521] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08cebf8f-df70-418b-b4ae-d4ab7dbedfdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:07,535] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:07,535] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:07,535] [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 dokdonensis	strain=FR1436	GCA_001653335.1	450734	450734	type	True	100.0	1455	1458	95	conclusive
Nocardioides salarius	strain=DSM 18239	GCA_016907435.1	374513	374513	type	True	87.4727	1113	1458	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	87.4607	1101	1458	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	87.4451	1108	1458	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	87.4352	1110	1458	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	87.4211	1107	1458	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	82.8931	878	1458	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.9592	693	1458	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.6655	656	1458	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	80.2161	705	1458	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	80.2097	648	1458	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	79.8286	638	1458	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:07,537] [INFO] DFAST Taxonomy check result was written to GCF_001653335.1_ASM165333v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:07,537] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:07,538] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:07,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08cebf8f-df70-418b-b4ae-d4ab7dbedfdd/dqc_reference/checkm_data
[2024-01-24 10:58:07,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:07,580] [INFO] Task started: CheckM
[2024-01-24 10:58:07,580] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001653335.1_ASM165333v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001653335.1_ASM165333v1_genomic.fna/checkm_input GCF_001653335.1_ASM165333v1_genomic.fna/checkm_result
[2024-01-24 10:59:21,591] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:21,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:21,614] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:21,614] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:21,615] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001653335.1_ASM165333v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:21,615] [INFO] Task started: Blastn
[2024-01-24 10:59:21,615] [INFO] Running command: blastn -query GCF_001653335.1_ASM165333v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08cebf8f-df70-418b-b4ae-d4ab7dbedfdd/dqc_reference/reference_markers_gtdb.fasta -out GCF_001653335.1_ASM165333v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:23,583] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:23,587] [INFO] Selected 15 target genomes.
[2024-01-24 10:59:23,587] [INFO] Target genome list was writen to GCF_001653335.1_ASM165333v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:23,597] [INFO] Task started: fastANI
[2024-01-24 10:59:23,597] [INFO] Running command: fastANI --query /var/lib/cwl/stgc38a58bd-ef2d-48e0-9994-919c2a03dcde/GCF_001653335.1_ASM165333v1_genomic.fna.gz --refList GCF_001653335.1_ASM165333v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001653335.1_ASM165333v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:39,582] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:39,608] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:39,608] [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_001653335.1	s__Nocardioides dokdonensis	100.0	1455	1458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016907435.1	s__Nocardioides salarius	87.4759	1114	1458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_013466785.1	s__Nocardioides marinisabuli	87.4495	1106	1458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013408145.1	s__Nocardioides marinus	82.9012	876	1458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.85	95.82	0.82	0.73	3	-
GCA_001627335.1	s__Nocardioides sp001627335	82.5992	766	1458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	96.50	0.91	0.88	12	-
GCF_015070375.1	s__Nocardioides kribbensis	82.5536	821	1458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCF_014127485.1	s__Nocardioides sp014127485	82.2086	794	1458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCF_013155365.1	s__Nocardioides sp013155365	81.9173	780	1458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011420305.2	s__Nocardioides sp011420305	81.8683	774	1458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	99.38	0.96	0.96	2	-
GCF_018459925.1	s__Nocardioides aquaticus	81.3245	773	1458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620705.1	s__Nocardioides sp000620705	81.2329	757	1458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506435.1	s__Nocardioides sp902506435	81.1138	736	1458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003047265.1	s__Nocardioides terrigena	80.9928	737	1458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	95.44	95.44	0.86	0.86	2	-
GCF_003047295.1	s__Nocardioides sediminis	80.9661	711	1458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076135.1	s__Nocardioides gansuensis	80.2706	661	1458	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 10:59:39,610] [INFO] GTDB search result was written to GCF_001653335.1_ASM165333v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:39,610] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:39,614] [INFO] DFAST_QC result json was written to GCF_001653335.1_ASM165333v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:39,614] [INFO] DFAST_QC completed!
[2024-01-24 10:59:39,614] [INFO] Total running time: 0h2m1s