[2024-01-24 12:13:42,237] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:42,240] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:42,240] [INFO] DQC Reference Directory: /var/lib/cwl/stgb005578d-201b-4d63-8222-e4769fe51e82/dqc_reference
[2024-01-24 12:13:43,628] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:43,631] [INFO] Task started: Prodigal
[2024-01-24 12:13:43,632] [INFO] Running command: gunzip -c /var/lib/cwl/stg225e4fdf-d0cc-4751-8463-db5938a34f58/GCF_019679455.1_ASM1967945v1_genomic.fna.gz | prodigal -d GCF_019679455.1_ASM1967945v1_genomic.fna/cds.fna -a GCF_019679455.1_ASM1967945v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:54,873] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:54,874] [INFO] Task started: HMMsearch
[2024-01-24 12:13:54,874] [INFO] Running command: hmmsearch --tblout GCF_019679455.1_ASM1967945v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb005578d-201b-4d63-8222-e4769fe51e82/dqc_reference/reference_markers.hmm GCF_019679455.1_ASM1967945v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:55,241] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:55,242] [INFO] Found 6/6 markers.
[2024-01-24 12:13:55,284] [INFO] Query marker FASTA was written to GCF_019679455.1_ASM1967945v1_genomic.fna/markers.fasta
[2024-01-24 12:13:55,284] [INFO] Task started: Blastn
[2024-01-24 12:13:55,285] [INFO] Running command: blastn -query GCF_019679455.1_ASM1967945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb005578d-201b-4d63-8222-e4769fe51e82/dqc_reference/reference_markers.fasta -out GCF_019679455.1_ASM1967945v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:56,649] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:56,653] [INFO] Selected 20 target genomes.
[2024-01-24 12:13:56,653] [INFO] Target genome list was writen to GCF_019679455.1_ASM1967945v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:56,660] [INFO] Task started: fastANI
[2024-01-24 12:13:56,661] [INFO] Running command: fastANI --query /var/lib/cwl/stg225e4fdf-d0cc-4751-8463-db5938a34f58/GCF_019679455.1_ASM1967945v1_genomic.fna.gz --refList GCF_019679455.1_ASM1967945v1_genomic.fna/target_genomes.txt --output GCF_019679455.1_ASM1967945v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:15,564] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:15,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb005578d-201b-4d63-8222-e4769fe51e82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:15,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb005578d-201b-4d63-8222-e4769fe51e82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:15,582] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:14:15,583] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:14:15,583] [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 panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	82.2777	821	1320	95	below_threshold
Nocardioides iriomotensis	strain=NBRC 105384	GCA_004168035.1	715784	715784	type	True	81.8563	817	1320	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	80.838	672	1320	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	80.7483	697	1320	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	80.6342	691	1320	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	80.6009	663	1320	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.5196	616	1320	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	80.4794	655	1320	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	80.3623	644	1320	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	80.2793	644	1320	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	80.2646	643	1320	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	80.2624	633	1320	95	below_threshold
Nocardioides speluncae	strain=YIM ART13	GCA_003121585.1	2670337	2670337	type	True	80.2153	617	1320	95	below_threshold
Nocardioides jensenii	strain=NBRC 14755	GCA_001552535.1	1843	1843	type	True	79.9591	549	1320	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	79.8415	598	1320	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	79.8214	646	1320	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	79.7043	581	1320	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	79.668	609	1320	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	79.5477	585	1320	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	79.5404	571	1320	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:15,585] [INFO] DFAST Taxonomy check result was written to GCF_019679455.1_ASM1967945v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:15,585] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:15,585] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:15,586] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb005578d-201b-4d63-8222-e4769fe51e82/dqc_reference/checkm_data
[2024-01-24 12:14:15,587] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:15,634] [INFO] Task started: CheckM
[2024-01-24 12:14:15,687] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019679455.1_ASM1967945v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019679455.1_ASM1967945v1_genomic.fna/checkm_input GCF_019679455.1_ASM1967945v1_genomic.fna/checkm_result
[2024-01-24 12:15:10,892] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:10,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:10,918] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:10,918] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:10,919] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019679455.1_ASM1967945v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:10,919] [INFO] Task started: Blastn
[2024-01-24 12:15:10,919] [INFO] Running command: blastn -query GCF_019679455.1_ASM1967945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb005578d-201b-4d63-8222-e4769fe51e82/dqc_reference/reference_markers_gtdb.fasta -out GCF_019679455.1_ASM1967945v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:13,092] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:13,096] [INFO] Selected 17 target genomes.
[2024-01-24 12:15:13,097] [INFO] Target genome list was writen to GCF_019679455.1_ASM1967945v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:13,129] [INFO] Task started: fastANI
[2024-01-24 12:15:13,130] [INFO] Running command: fastANI --query /var/lib/cwl/stg225e4fdf-d0cc-4751-8463-db5938a34f58/GCF_019679455.1_ASM1967945v1_genomic.fna.gz --refList GCF_019679455.1_ASM1967945v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019679455.1_ASM1967945v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:28,889] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:28,909] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:15:28,909] [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
GCA_002384855.1	s__UBA4001 sp002384855	82.4397	738	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__UBA4001	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019039255.1	s__JABFXA01 sp019039255	82.2576	824	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JABFXA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014395785.1	s__Nocardioides_B mesophilus	82.1458	802	1320	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_004168035.1	s__Nocardioides_B iriomotensis	81.9	813	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361955.1	s__JABFXA01 sp013361955	81.6617	671	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JABFXA01	95.0	99.75	99.75	0.92	0.92	2	-
GCF_004519545.1	s__Nocardioides guangzhouensis	80.7589	697	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014138045.1	s__Nocardioides ginsengisegetis	80.518	672	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCA_902805855.1	s__UBA4001 sp902805855	80.5142	541	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__UBA4001	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014842875.1	s__Nocardioides sp014842875	80.4995	618	1320	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	80.3325	610	1320	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	80.2204	648	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013778305.1	s__Nocardioides sp013778305	80.2001	653	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013177455.1	s__Nocardioides sp013177455	80.1352	667	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_001425175.1	s__Nocardioides sp001425175	80.035	660	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018275325.1	s__Nocardioides sp018275325	79.9943	629	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916455.1	s__Nocardioides sp017916455	79.9175	565	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.92	98.92	0.96	0.96	2	-
GCA_001627335.1	s__Nocardioides sp001627335	79.8489	513	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	96.50	0.91	0.88	12	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:28,911] [INFO] GTDB search result was written to GCF_019679455.1_ASM1967945v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:28,912] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:28,917] [INFO] DFAST_QC result json was written to GCF_019679455.1_ASM1967945v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:28,917] [INFO] DFAST_QC completed!
[2024-01-24 12:15:28,918] [INFO] Total running time: 0h1m47s