[2024-01-25 18:09:50,663] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:50,665] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:50,666] [INFO] DQC Reference Directory: /var/lib/cwl/stgba81cf03-8280-452a-9832-e3f36ba05620/dqc_reference
[2024-01-25 18:09:51,789] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:51,790] [INFO] Task started: Prodigal
[2024-01-25 18:09:51,790] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8f170b8-eb73-42d4-bd98-45f307726899/GCF_014180715.1_ASM1418071v1_genomic.fna.gz | prodigal -d GCF_014180715.1_ASM1418071v1_genomic.fna/cds.fna -a GCF_014180715.1_ASM1418071v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:10:01,626] [INFO] Task succeeded: Prodigal
[2024-01-25 18:10:01,627] [INFO] Task started: HMMsearch
[2024-01-25 18:10:01,627] [INFO] Running command: hmmsearch --tblout GCF_014180715.1_ASM1418071v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba81cf03-8280-452a-9832-e3f36ba05620/dqc_reference/reference_markers.hmm GCF_014180715.1_ASM1418071v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:10:01,848] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:10:01,850] [INFO] Found 6/6 markers.
[2024-01-25 18:10:01,889] [INFO] Query marker FASTA was written to GCF_014180715.1_ASM1418071v1_genomic.fna/markers.fasta
[2024-01-25 18:10:01,889] [INFO] Task started: Blastn
[2024-01-25 18:10:01,889] [INFO] Running command: blastn -query GCF_014180715.1_ASM1418071v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba81cf03-8280-452a-9832-e3f36ba05620/dqc_reference/reference_markers.fasta -out GCF_014180715.1_ASM1418071v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:03,056] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:03,059] [INFO] Selected 15 target genomes.
[2024-01-25 18:10:03,059] [INFO] Target genome list was writen to GCF_014180715.1_ASM1418071v1_genomic.fna/target_genomes.txt
[2024-01-25 18:10:03,072] [INFO] Task started: fastANI
[2024-01-25 18:10:03,072] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8f170b8-eb73-42d4-bd98-45f307726899/GCF_014180715.1_ASM1418071v1_genomic.fna.gz --refList GCF_014180715.1_ASM1418071v1_genomic.fna/target_genomes.txt --output GCF_014180715.1_ASM1418071v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:10:18,535] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:18,535] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba81cf03-8280-452a-9832-e3f36ba05620/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:10:18,536] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba81cf03-8280-452a-9832-e3f36ba05620/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:10:18,545] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:10:18,545] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:10:18,545] [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 stalactiti	strain=1.0914	GCA_014180715.1	2755356	2755356	type	True	100.0	1380	1391	95	conclusive
Nocardioides pelophilus	strain=CGMCC 4.7388	GCA_014180685.1	2172019	2172019	type	True	84.5814	902	1391	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	84.311	1018	1391	95	below_threshold
Nocardioides antri	strain=BN140041	GCA_008373765.1	2607659	2607659	type	True	83.9905	874	1391	95	below_threshold
Nocardioides silvaticus	strain=CCTCC AB 2018079	GCA_003160695.1	2201891	2201891	type	True	83.8406	942	1391	95	below_threshold
Nocardioides immobilis	strain=CCTCC AB 2017083	GCA_003515065.1	2049295	2049295	type	True	83.7709	969	1391	95	below_threshold
Nocardioides thalensis	strain=DSM 103833	GCA_013410655.1	1914755	1914755	type	True	82.1003	824	1391	95	below_threshold
Pimelobacter simplex	strain=ATCC 6946	GCA_900114845.1	2045	2045	type	True	81.5498	830	1391	95	below_threshold
Pimelobacter simplex	strain=NBRC 12069	GCA_006538965.1	2045	2045	type	True	81.5461	839	1391	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	81.2319	783	1391	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	80.8191	681	1391	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	80.256	672	1391	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	80.215	666	1391	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	79.9309	577	1391	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	79.8279	539	1391	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:10:18,547] [INFO] DFAST Taxonomy check result was written to GCF_014180715.1_ASM1418071v1_genomic.fna/tc_result.tsv
[2024-01-25 18:10:18,547] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:10:18,547] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:10:18,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba81cf03-8280-452a-9832-e3f36ba05620/dqc_reference/checkm_data
[2024-01-25 18:10:18,548] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:10:18,602] [INFO] Task started: CheckM
[2024-01-25 18:10:18,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014180715.1_ASM1418071v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014180715.1_ASM1418071v1_genomic.fna/checkm_input GCF_014180715.1_ASM1418071v1_genomic.fna/checkm_result
[2024-01-25 18:11:06,211] [INFO] Task succeeded: CheckM
[2024-01-25 18:11:06,212] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:11:06,235] [INFO] ===== Completeness check finished =====
[2024-01-25 18:11:06,235] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:11:06,236] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014180715.1_ASM1418071v1_genomic.fna/markers.fasta)
[2024-01-25 18:11:06,236] [INFO] Task started: Blastn
[2024-01-25 18:11:06,236] [INFO] Running command: blastn -query GCF_014180715.1_ASM1418071v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba81cf03-8280-452a-9832-e3f36ba05620/dqc_reference/reference_markers_gtdb.fasta -out GCF_014180715.1_ASM1418071v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:08,242] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:08,244] [INFO] Selected 12 target genomes.
[2024-01-25 18:11:08,244] [INFO] Target genome list was writen to GCF_014180715.1_ASM1418071v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:11:08,263] [INFO] Task started: fastANI
[2024-01-25 18:11:08,263] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8f170b8-eb73-42d4-bd98-45f307726899/GCF_014180715.1_ASM1418071v1_genomic.fna.gz --refList GCF_014180715.1_ASM1418071v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014180715.1_ASM1418071v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:11:21,738] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:21,745] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:11:21,746] [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_014180715.1	s__Nocardioides stalactiti	100.0	1380	1391	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_014180685.1	s__Nocardioides pelophilus	84.5895	902	1391	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	84.3203	1017	1391	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	83.9837	874	1391	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	83.8663	939	1391	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003515065.1	s__Nocardioides immobilis	83.8096	965	1391	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519005.1	s__Nocardioides sp000519005	82.0263	753	1391	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.89	98.89	0.90	0.90	2	-
GCF_003054165.1	s__Nocardioides sp003054165	81.8834	816	1391	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428825.1	s__Nocardioides sp001428825	81.6517	835	1391	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001427795.1	s__Nocardioides sp001427795	81.1493	775	1391	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002117935.1	s__Nocardioides sp002117935	80.6499	636	1391	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001425175.1	s__Nocardioides sp001425175	80.4102	681	1391	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:11:21,747] [INFO] GTDB search result was written to GCF_014180715.1_ASM1418071v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:11:21,747] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:11:21,750] [INFO] DFAST_QC result json was written to GCF_014180715.1_ASM1418071v1_genomic.fna/dqc_result.json
[2024-01-25 18:11:21,750] [INFO] DFAST_QC completed!
[2024-01-25 18:11:21,750] [INFO] Total running time: 0h1m31s