[2024-01-24 12:47:18,715] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:18,718] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:18,719] [INFO] DQC Reference Directory: /var/lib/cwl/stgec19091b-b3bb-4e55-8ee8-0ce4cff684f2/dqc_reference
[2024-01-24 12:47:20,017] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:20,018] [INFO] Task started: Prodigal
[2024-01-24 12:47:20,018] [INFO] Running command: gunzip -c /var/lib/cwl/stgbaff0267-5b8c-4890-a9b5-8c930507842b/GCF_021555175.1_ASM2155517v1_genomic.fna.gz | prodigal -d GCF_021555175.1_ASM2155517v1_genomic.fna/cds.fna -a GCF_021555175.1_ASM2155517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:35,694] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:35,694] [INFO] Task started: HMMsearch
[2024-01-24 12:47:35,694] [INFO] Running command: hmmsearch --tblout GCF_021555175.1_ASM2155517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec19091b-b3bb-4e55-8ee8-0ce4cff684f2/dqc_reference/reference_markers.hmm GCF_021555175.1_ASM2155517v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:35,929] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:35,930] [INFO] Found 6/6 markers.
[2024-01-24 12:47:35,970] [INFO] Query marker FASTA was written to GCF_021555175.1_ASM2155517v1_genomic.fna/markers.fasta
[2024-01-24 12:47:35,970] [INFO] Task started: Blastn
[2024-01-24 12:47:35,971] [INFO] Running command: blastn -query GCF_021555175.1_ASM2155517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec19091b-b3bb-4e55-8ee8-0ce4cff684f2/dqc_reference/reference_markers.fasta -out GCF_021555175.1_ASM2155517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:37,043] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:37,047] [INFO] Selected 24 target genomes.
[2024-01-24 12:47:37,047] [INFO] Target genome list was writen to GCF_021555175.1_ASM2155517v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:37,056] [INFO] Task started: fastANI
[2024-01-24 12:47:37,057] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaff0267-5b8c-4890-a9b5-8c930507842b/GCF_021555175.1_ASM2155517v1_genomic.fna.gz --refList GCF_021555175.1_ASM2155517v1_genomic.fna/target_genomes.txt --output GCF_021555175.1_ASM2155517v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:57,119] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:57,119] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec19091b-b3bb-4e55-8ee8-0ce4cff684f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:57,120] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec19091b-b3bb-4e55-8ee8-0ce4cff684f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:57,138] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:57,138] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:57,139] [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 alcanivorans	strain=NGK65	GCA_021555175.1	2897352	2897352	type	True	100.0	1594	1615	95	conclusive
Nocardioides daejeonensis	strain=MJ31	GCA_003194585.1	1046556	1046556	type	True	82.0362	889	1615	95	below_threshold
Nocardioides jensenii	strain=NBRC 14755	GCA_001552535.1	1843	1843	type	True	80.2136	627	1615	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	79.9527	561	1615	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	79.8571	573	1615	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	79.8355	556	1615	95	below_threshold
Nocardioides daedukensis	strain=DSM 23819	GCA_013408415.1	634462	634462	type	True	79.7763	587	1615	95	below_threshold
Nocardioides daphniae	strain=CCM 7403	GCA_014635145.1	402297	402297	type	True	79.773	485	1615	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_016907435.1	374513	374513	type	True	79.7417	587	1615	95	below_threshold
Nocardioides jishulii	strain=dk3136	GCA_006007965.1	2575440	2575440	type	True	79.6628	478	1615	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	79.6096	555	1615	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	79.6038	583	1615	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	79.5888	589	1615	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	79.3889	543	1615	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	79.3563	501	1615	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	79.3478	494	1615	95	below_threshold
Nocardioides rubriscoriae	strain=DSM 23986	GCA_008087085.1	642762	642762	type	True	79.313	557	1615	95	below_threshold
Nocardioides jejuensis	strain=18JY15-6	GCA_004337475.1	2502782	2502782	type	True	79.3075	415	1615	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	79.2457	532	1615	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	79.2363	532	1615	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	79.2159	564	1615	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	78.7667	465	1615	95	below_threshold
Nocardioides albertanoniae	strain=DSM 25218	GCA_006716315.1	1175486	1175486	type	True	78.69	483	1615	95	below_threshold
Nocardioides agariphilus	strain=KCTC 19276	GCA_015352445.1	433664	433664	type	True	78.5183	438	1615	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:57,141] [INFO] DFAST Taxonomy check result was written to GCF_021555175.1_ASM2155517v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:57,141] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:57,141] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:57,142] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec19091b-b3bb-4e55-8ee8-0ce4cff684f2/dqc_reference/checkm_data
[2024-01-24 12:47:57,143] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:57,187] [INFO] Task started: CheckM
[2024-01-24 12:47:57,187] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021555175.1_ASM2155517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021555175.1_ASM2155517v1_genomic.fna/checkm_input GCF_021555175.1_ASM2155517v1_genomic.fna/checkm_result
[2024-01-24 12:49:04,842] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:04,844] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:04,865] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:04,865] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:04,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021555175.1_ASM2155517v1_genomic.fna/markers.fasta)
[2024-01-24 12:49:04,865] [INFO] Task started: Blastn
[2024-01-24 12:49:04,865] [INFO] Running command: blastn -query GCF_021555175.1_ASM2155517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec19091b-b3bb-4e55-8ee8-0ce4cff684f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_021555175.1_ASM2155517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:06,486] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:06,490] [INFO] Selected 27 target genomes.
[2024-01-24 12:49:06,490] [INFO] Target genome list was writen to GCF_021555175.1_ASM2155517v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:06,511] [INFO] Task started: fastANI
[2024-01-24 12:49:06,512] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaff0267-5b8c-4890-a9b5-8c930507842b/GCF_021555175.1_ASM2155517v1_genomic.fna.gz --refList GCF_021555175.1_ASM2155517v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021555175.1_ASM2155517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:27,735] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:27,756] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:49:27,756] [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_003194585.1	s__Nocardioides daejeonensis	82.0537	887	1615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552535.1	s__Nocardioides jensenii	80.2532	623	1615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426745.1	s__Nocardioides sp001426745	80.1262	645	1615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.99	98.75	0.96	0.95	3	-
GCF_017310035.1	s__Nocardioides sp017310035	80.0189	539	1615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012272695.1	s__Nocardioides sp012272695	79.9351	616	1615	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	79.9286	566	1615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004777465.1	s__Nocardioides daphniae	79.8414	488	1615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.94	99.94	1.00	1.00	2	-
GCF_011420305.2	s__Nocardioides sp011420305	79.8263	571	1615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	99.38	0.96	0.96	2	-
GCF_013408415.1	s__Nocardioides daedukensis	79.7578	587	1615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907435.1	s__Nocardioides salarius	79.747	587	1615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_006007965.1	s__Nocardioides sp006007965	79.7046	479	1615	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	79.6926	574	1615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015070375.1	s__Nocardioides kribbensis	79.6569	550	1615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCF_011250565.1	s__Nocardioides sp011250565	79.5862	576	1615	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	79.5611	563	1615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013778305.1	s__Nocardioides sp013778305	79.4706	575	1615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001428125.1	s__Nocardioides sp001428125	79.4672	513	1615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519545.1	s__Nocardioides guangzhouensis	79.4312	552	1615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429625.1	s__Nocardioides sp001429625	79.4071	510	1615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001627335.1	s__Nocardioides sp001627335	79.3888	475	1615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	96.50	0.91	0.88	12	-
GCF_001653335.1	s__Nocardioides dokdonensis	79.3307	559	1615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004337475.1	s__Nocardioides jejuensis	79.2683	416	1615	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	79.267	529	1615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005954645.2	s__Nocardioides dongxiaopingii	79.1937	534	1615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.98	98.98	0.96	0.96	2	-
GCF_013155375.1	s__Nocardioides sp013155375	79.0628	537	1615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716315.1	s__Nocardioides albertanoniae	78.764	479	1615	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015352445.1	s__Nocardioides agariphilus	78.5152	439	1615	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 12:49:27,758] [INFO] GTDB search result was written to GCF_021555175.1_ASM2155517v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:27,758] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:27,763] [INFO] DFAST_QC result json was written to GCF_021555175.1_ASM2155517v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:27,763] [INFO] DFAST_QC completed!
[2024-01-24 12:49:27,763] [INFO] Total running time: 0h2m9s