[2024-01-25 18:45:35,570] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:45:35,573] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:45:35,574] [INFO] DQC Reference Directory: /var/lib/cwl/stg58d4bd59-903b-487a-b3b4-3d9b60671317/dqc_reference
[2024-01-25 18:45:36,769] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:45:36,770] [INFO] Task started: Prodigal
[2024-01-25 18:45:36,770] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1e0ab75-ce0f-4ea1-a867-b0ffba9ef928/GCF_014180685.1_ASM1418068v1_genomic.fna.gz | prodigal -d GCF_014180685.1_ASM1418068v1_genomic.fna/cds.fna -a GCF_014180685.1_ASM1418068v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:45:46,761] [INFO] Task succeeded: Prodigal
[2024-01-25 18:45:46,761] [INFO] Task started: HMMsearch
[2024-01-25 18:45:46,761] [INFO] Running command: hmmsearch --tblout GCF_014180685.1_ASM1418068v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58d4bd59-903b-487a-b3b4-3d9b60671317/dqc_reference/reference_markers.hmm GCF_014180685.1_ASM1418068v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:45:46,983] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:45:46,984] [INFO] Found 6/6 markers.
[2024-01-25 18:45:47,021] [INFO] Query marker FASTA was written to GCF_014180685.1_ASM1418068v1_genomic.fna/markers.fasta
[2024-01-25 18:45:47,021] [INFO] Task started: Blastn
[2024-01-25 18:45:47,022] [INFO] Running command: blastn -query GCF_014180685.1_ASM1418068v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58d4bd59-903b-487a-b3b4-3d9b60671317/dqc_reference/reference_markers.fasta -out GCF_014180685.1_ASM1418068v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:48,135] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:48,138] [INFO] Selected 15 target genomes.
[2024-01-25 18:45:48,138] [INFO] Target genome list was writen to GCF_014180685.1_ASM1418068v1_genomic.fna/target_genomes.txt
[2024-01-25 18:45:48,155] [INFO] Task started: fastANI
[2024-01-25 18:45:48,155] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1e0ab75-ce0f-4ea1-a867-b0ffba9ef928/GCF_014180685.1_ASM1418068v1_genomic.fna.gz --refList GCF_014180685.1_ASM1418068v1_genomic.fna/target_genomes.txt --output GCF_014180685.1_ASM1418068v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:46:04,866] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:04,867] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58d4bd59-903b-487a-b3b4-3d9b60671317/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:46:04,867] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58d4bd59-903b-487a-b3b4-3d9b60671317/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:46:04,877] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:46:04,877] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:46:04,877] [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 pelophilus	strain=CGMCC 4.7388	GCA_014180685.1	2172019	2172019	type	True	100.0	1360	1373	95	conclusive
Nocardioides immobilis	strain=CCTCC AB 2017083	GCA_003515065.1	2049295	2049295	type	True	85.6436	962	1373	95	below_threshold
Nocardioides antri	strain=BN140041	GCA_008373765.1	2607659	2607659	type	True	85.4042	888	1373	95	below_threshold
Nocardioides silvaticus	strain=CCTCC AB 2018079	GCA_003160695.1	2201891	2201891	type	True	84.8422	935	1373	95	below_threshold
Nocardioides stalactiti	strain=1.0914	GCA_014180715.1	2755356	2755356	type	True	84.6168	885	1373	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	83.7587	895	1373	95	below_threshold
Nocardioides thalensis	strain=DSM 103833	GCA_013410655.1	1914755	1914755	type	True	82.3853	800	1373	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	81.3762	791	1373	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	80.9125	687	1373	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	80.6113	663	1373	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	80.534	685	1373	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	80.4867	716	1373	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	80.4409	717	1373	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	79.911	542	1373	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	79.8061	541	1373	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:46:04,880] [INFO] DFAST Taxonomy check result was written to GCF_014180685.1_ASM1418068v1_genomic.fna/tc_result.tsv
[2024-01-25 18:46:04,880] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:46:04,880] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:46:04,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58d4bd59-903b-487a-b3b4-3d9b60671317/dqc_reference/checkm_data
[2024-01-25 18:46:04,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:46:04,928] [INFO] Task started: CheckM
[2024-01-25 18:46:04,929] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014180685.1_ASM1418068v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014180685.1_ASM1418068v1_genomic.fna/checkm_input GCF_014180685.1_ASM1418068v1_genomic.fna/checkm_result
[2024-01-25 18:46:42,979] [INFO] Task succeeded: CheckM
[2024-01-25 18:46:42,980] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:46:42,999] [INFO] ===== Completeness check finished =====
[2024-01-25 18:46:42,999] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:46:43,000] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014180685.1_ASM1418068v1_genomic.fna/markers.fasta)
[2024-01-25 18:46:43,000] [INFO] Task started: Blastn
[2024-01-25 18:46:43,000] [INFO] Running command: blastn -query GCF_014180685.1_ASM1418068v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58d4bd59-903b-487a-b3b4-3d9b60671317/dqc_reference/reference_markers_gtdb.fasta -out GCF_014180685.1_ASM1418068v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:44,830] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:44,834] [INFO] Selected 12 target genomes.
[2024-01-25 18:46:44,834] [INFO] Target genome list was writen to GCF_014180685.1_ASM1418068v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:46:44,858] [INFO] Task started: fastANI
[2024-01-25 18:46:44,858] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1e0ab75-ce0f-4ea1-a867-b0ffba9ef928/GCF_014180685.1_ASM1418068v1_genomic.fna.gz --refList GCF_014180685.1_ASM1418068v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014180685.1_ASM1418068v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:46:58,436] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:58,444] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:46:58,445] [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_014180685.1	s__Nocardioides pelophilus	100.0	1360	1373	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_003515065.1	s__Nocardioides immobilis	85.5982	967	1373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008373765.1	s__Nocardioides antri	85.4255	886	1373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003160695.1	s__Nocardioides silvaticus	84.8491	934	1373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014180715.1	s__Nocardioides stalactiti	84.6195	886	1373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008373755.1	s__Nocardioides sp008373755	83.7351	898	1373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410655.1	s__Nocardioides thalensis	82.385	801	1373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011250565.1	s__Nocardioides sp011250565	80.8385	660	1373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014266025.1	s__Nocardioides deserti	80.6408	644	1373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001425175.1	s__Nocardioides sp001425175	80.4869	696	1373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900101465.1	s__Nocardioides lianchengensis	80.4306	718	1373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016462705.1	s__Nocardioides sp016462705	79.9878	574	1373	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:46:58,446] [INFO] GTDB search result was written to GCF_014180685.1_ASM1418068v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:46:58,446] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:46:58,449] [INFO] DFAST_QC result json was written to GCF_014180685.1_ASM1418068v1_genomic.fna/dqc_result.json
[2024-01-25 18:46:58,449] [INFO] DFAST_QC completed!
[2024-01-25 18:46:58,449] [INFO] Total running time: 0h1m23s