[2024-01-24 13:48:59,361] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,362] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,363] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c560960-a740-4460-90fe-0eeffe5f5d8f/dqc_reference
[2024-01-24 13:49:00,689] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:00,690] [INFO] Task started: Prodigal
[2024-01-24 13:49:00,690] [INFO] Running command: gunzip -c /var/lib/cwl/stg02a59550-d4d7-44f4-a106-5afd12b8bcf2/GCF_004168035.1_ASM416803v1_genomic.fna.gz | prodigal -d GCF_004168035.1_ASM416803v1_genomic.fna/cds.fna -a GCF_004168035.1_ASM416803v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:13,411] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:13,412] [INFO] Task started: HMMsearch
[2024-01-24 13:49:13,412] [INFO] Running command: hmmsearch --tblout GCF_004168035.1_ASM416803v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c560960-a740-4460-90fe-0eeffe5f5d8f/dqc_reference/reference_markers.hmm GCF_004168035.1_ASM416803v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:13,678] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:13,680] [INFO] Found 6/6 markers.
[2024-01-24 13:49:13,725] [INFO] Query marker FASTA was written to GCF_004168035.1_ASM416803v1_genomic.fna/markers.fasta
[2024-01-24 13:49:13,726] [INFO] Task started: Blastn
[2024-01-24 13:49:13,726] [INFO] Running command: blastn -query GCF_004168035.1_ASM416803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c560960-a740-4460-90fe-0eeffe5f5d8f/dqc_reference/reference_markers.fasta -out GCF_004168035.1_ASM416803v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:15,003] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:15,006] [INFO] Selected 21 target genomes.
[2024-01-24 13:49:15,006] [INFO] Target genome list was writen to GCF_004168035.1_ASM416803v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:15,073] [INFO] Task started: fastANI
[2024-01-24 13:49:15,073] [INFO] Running command: fastANI --query /var/lib/cwl/stg02a59550-d4d7-44f4-a106-5afd12b8bcf2/GCF_004168035.1_ASM416803v1_genomic.fna.gz --refList GCF_004168035.1_ASM416803v1_genomic.fna/target_genomes.txt --output GCF_004168035.1_ASM416803v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:35,430] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:35,431] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c560960-a740-4460-90fe-0eeffe5f5d8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:35,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c560960-a740-4460-90fe-0eeffe5f5d8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:35,447] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:35,447] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:35,448] [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 iriomotensis	strain=NBRC 105384	GCA_004168035.1	715784	715784	type	True	100.0	1548	1551	95	conclusive
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	82.0028	892	1551	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	80.8968	811	1551	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	80.6955	732	1551	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	80.3325	753	1551	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	80.2986	758	1551	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.2624	657	1551	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	80.2521	729	1551	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	80.2208	699	1551	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	80.1998	693	1551	95	below_threshold
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	80.0777	715	1551	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	80.0334	705	1551	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	80.0288	702	1551	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	79.9505	706	1551	95	below_threshold
Nocardioides gansuensis	strain=WSJ-1	GCA_003076135.1	2138300	2138300	type	True	79.9226	663	1551	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	79.9221	682	1551	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	79.8949	667	1551	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	79.8917	743	1551	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	79.8885	709	1551	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	79.8297	635	1551	95	below_threshold
Nocardioides cynanchi	strain=SB3-45	GCA_008761635.1	2558918	2558918	type	True	79.7933	628	1551	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:35,452] [INFO] DFAST Taxonomy check result was written to GCF_004168035.1_ASM416803v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:35,452] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:35,452] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:35,453] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c560960-a740-4460-90fe-0eeffe5f5d8f/dqc_reference/checkm_data
[2024-01-24 13:49:35,454] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:35,502] [INFO] Task started: CheckM
[2024-01-24 13:49:35,502] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004168035.1_ASM416803v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004168035.1_ASM416803v1_genomic.fna/checkm_input GCF_004168035.1_ASM416803v1_genomic.fna/checkm_result
[2024-01-24 13:50:36,065] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:36,067] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:36,089] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:36,090] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:36,090] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004168035.1_ASM416803v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:36,091] [INFO] Task started: Blastn
[2024-01-24 13:50:36,091] [INFO] Running command: blastn -query GCF_004168035.1_ASM416803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c560960-a740-4460-90fe-0eeffe5f5d8f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004168035.1_ASM416803v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:38,309] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:38,313] [INFO] Selected 16 target genomes.
[2024-01-24 13:50:38,314] [INFO] Target genome list was writen to GCF_004168035.1_ASM416803v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:38,334] [INFO] Task started: fastANI
[2024-01-24 13:50:38,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg02a59550-d4d7-44f4-a106-5afd12b8bcf2/GCF_004168035.1_ASM416803v1_genomic.fna.gz --refList GCF_004168035.1_ASM416803v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004168035.1_ASM416803v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:54,063] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:54,084] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:54,084] [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_004168035.1	s__Nocardioides_B iriomotensis	100.0	1548	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014395785.1	s__Nocardioides_B mesophilus	82.219	858	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019039255.1	s__JABFXA01 sp019039255	82.0212	889	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JABFXA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361955.1	s__JABFXA01 sp013361955	81.9364	797	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JABFXA01	95.0	99.75	99.75	0.92	0.92	2	-
GCA_002384855.1	s__UBA4001 sp002384855	80.7982	678	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__UBA4001	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014138045.1	s__Nocardioides ginsengisegetis	80.6946	732	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCF_002117935.1	s__Nocardioides sp002117935	80.5263	702	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013466985.1	s__Nocardioides ungokensis	80.3296	754	1551	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	80.2806	691	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409645.1	s__Nocardioides panaciterrulae	80.2608	728	1551	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	80.1738	696	1551	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	80.0907	774	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017916455.1	s__Nocardioides sp017916455	80.0628	648	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.92	98.92	0.96	0.96	2	-
GCF_013409425.1	s__Nocardioides perillae	79.9525	678	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013466785.1	s__Nocardioides marinisabuli	79.9503	712	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCA_902805865.1	s__Marmoricola_A sp902805865	79.8869	489	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:54,087] [INFO] GTDB search result was written to GCF_004168035.1_ASM416803v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:54,088] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:54,094] [INFO] DFAST_QC result json was written to GCF_004168035.1_ASM416803v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:54,094] [INFO] DFAST_QC completed!
[2024-01-24 13:50:54,095] [INFO] Total running time: 0h1m55s