[2024-01-24 13:17:04,921] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:04,924] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:04,925] [INFO] DQC Reference Directory: /var/lib/cwl/stg52d27966-b007-4b4e-9140-20d706a42bf5/dqc_reference
[2024-01-24 13:17:06,269] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:06,270] [INFO] Task started: Prodigal
[2024-01-24 13:17:06,271] [INFO] Running command: gunzip -c /var/lib/cwl/stge8b7de5a-0e85-4939-b9a7-3a338de7f068/GCF_003710085.1_ASM371008v1_genomic.fna.gz | prodigal -d GCF_003710085.1_ASM371008v1_genomic.fna/cds.fna -a GCF_003710085.1_ASM371008v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:17,402] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:17,402] [INFO] Task started: HMMsearch
[2024-01-24 13:17:17,402] [INFO] Running command: hmmsearch --tblout GCF_003710085.1_ASM371008v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52d27966-b007-4b4e-9140-20d706a42bf5/dqc_reference/reference_markers.hmm GCF_003710085.1_ASM371008v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:17,676] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:17,677] [INFO] Found 6/6 markers.
[2024-01-24 13:17:17,711] [INFO] Query marker FASTA was written to GCF_003710085.1_ASM371008v1_genomic.fna/markers.fasta
[2024-01-24 13:17:17,712] [INFO] Task started: Blastn
[2024-01-24 13:17:17,712] [INFO] Running command: blastn -query GCF_003710085.1_ASM371008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52d27966-b007-4b4e-9140-20d706a42bf5/dqc_reference/reference_markers.fasta -out GCF_003710085.1_ASM371008v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:19,070] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:19,084] [INFO] Selected 25 target genomes.
[2024-01-24 13:17:19,085] [INFO] Target genome list was writen to GCF_003710085.1_ASM371008v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:19,101] [INFO] Task started: fastANI
[2024-01-24 13:17:19,102] [INFO] Running command: fastANI --query /var/lib/cwl/stge8b7de5a-0e85-4939-b9a7-3a338de7f068/GCF_003710085.1_ASM371008v1_genomic.fna.gz --refList GCF_003710085.1_ASM371008v1_genomic.fna/target_genomes.txt --output GCF_003710085.1_ASM371008v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:44,482] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:44,483] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52d27966-b007-4b4e-9140-20d706a42bf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:44,483] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52d27966-b007-4b4e-9140-20d706a42bf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:44,502] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:17:44,503] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:17:44,503] [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 dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	83.2626	885	1347	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	82.4881	885	1347	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	82.4597	788	1347	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	82.4403	877	1347	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	82.2618	815	1347	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	82.2072	752	1347	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	82.1127	802	1347	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	82.0217	785	1347	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	81.9753	769	1347	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	81.9183	773	1347	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	81.9051	738	1347	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	81.8652	741	1347	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	81.6675	763	1347	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	81.6154	779	1347	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	81.5835	782	1347	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	81.0721	705	1347	95	below_threshold
Nocardioides anomalus	strain=HKS04	GCA_011046535.1	2712223	2712223	type	True	80.9398	792	1347	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.8711	634	1347	95	below_threshold
Nocardioides sediminis	strain=KCTC 19271	GCA_003047295.1	433648	433648	type	True	80.8689	680	1347	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	80.6509	692	1347	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	80.4727	702	1347	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.4531	689	1347	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	80.4218	680	1347	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	80.244	656	1347	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	79.842	580	1347	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:44,505] [INFO] DFAST Taxonomy check result was written to GCF_003710085.1_ASM371008v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:44,505] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:44,506] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:44,506] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52d27966-b007-4b4e-9140-20d706a42bf5/dqc_reference/checkm_data
[2024-01-24 13:17:44,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:44,554] [INFO] Task started: CheckM
[2024-01-24 13:17:44,554] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003710085.1_ASM371008v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003710085.1_ASM371008v1_genomic.fna/checkm_input GCF_003710085.1_ASM371008v1_genomic.fna/checkm_result
[2024-01-24 13:18:44,008] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:44,010] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:44,029] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:44,029] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:44,030] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003710085.1_ASM371008v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:44,031] [INFO] Task started: Blastn
[2024-01-24 13:18:44,031] [INFO] Running command: blastn -query GCF_003710085.1_ASM371008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52d27966-b007-4b4e-9140-20d706a42bf5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003710085.1_ASM371008v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:46,099] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:46,103] [INFO] Selected 18 target genomes.
[2024-01-24 13:18:46,103] [INFO] Target genome list was writen to GCF_003710085.1_ASM371008v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:46,121] [INFO] Task started: fastANI
[2024-01-24 13:18:46,122] [INFO] Running command: fastANI --query /var/lib/cwl/stge8b7de5a-0e85-4939-b9a7-3a338de7f068/GCF_003710085.1_ASM371008v1_genomic.fna.gz --refList GCF_003710085.1_ASM371008v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003710085.1_ASM371008v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:04,501] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:04,520] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:04,520] [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_003710085.1	s__Nocardioides sp003710085	100.0	1347	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.05	99.05	0.97	0.97	2	conclusive
GCF_009557055.1	s__Nocardioides sp009557055	83.8976	919	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013155365.1	s__Nocardioides sp013155365	83.8486	905	1347	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	83.8362	906	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	99.38	0.96	0.96	2	-
GCF_014127485.1	s__Nocardioides sp014127485	83.2587	885	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCF_013177455.1	s__Nocardioides sp013177455	82.7629	834	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_900101465.1	s__Nocardioides lianchengensis	82.4494	875	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014266025.1	s__Nocardioides deserti	82.3581	798	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_011250565.1	s__Nocardioides sp011250565	82.3475	779	1347	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	82.2332	749	1347	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	82.0434	783	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016907435.1	s__Nocardioides salarius	81.9246	769	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_013778305.1	s__Nocardioides sp013778305	81.807	785	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015070375.1	s__Nocardioides kribbensis	81.6148	779	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCF_001425175.1	s__Nocardioides sp001425175	81.531	809	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003047295.1	s__Nocardioides sediminis	80.8823	679	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018275325.1	s__Nocardioides sp018275325	80.7907	732	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003057875.1	s__Nocardioides currus	80.4631	702	1347	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 13:19:04,522] [INFO] GTDB search result was written to GCF_003710085.1_ASM371008v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:04,523] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:04,528] [INFO] DFAST_QC result json was written to GCF_003710085.1_ASM371008v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:04,528] [INFO] DFAST_QC completed!
[2024-01-24 13:19:04,528] [INFO] Total running time: 0h1m60s