[2023-06-30 23:36:32,737] [INFO] DFAST_QC pipeline started.
[2023-06-30 23:36:32,739] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 23:36:32,739] [INFO] DQC Reference Directory: /var/lib/cwl/stg0aff2b03-6986-4923-a964-81160a5d52cd/dqc_reference
[2023-06-30 23:36:33,977] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 23:36:33,978] [INFO] Task started: Prodigal
[2023-06-30 23:36:33,979] [INFO] Running command: gunzip -c /var/lib/cwl/stgd60d513e-5aa8-41af-a0dd-d9d35a791356/GCA_025928855.1_ASM2592885v1_genomic.fna.gz | prodigal -d GCA_025928855.1_ASM2592885v1_genomic.fna/cds.fna -a GCA_025928855.1_ASM2592885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 23:36:42,829] [INFO] Task succeeded: Prodigal
[2023-06-30 23:36:42,830] [INFO] Task started: HMMsearch
[2023-06-30 23:36:42,830] [INFO] Running command: hmmsearch --tblout GCA_025928855.1_ASM2592885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0aff2b03-6986-4923-a964-81160a5d52cd/dqc_reference/reference_markers.hmm GCA_025928855.1_ASM2592885v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 23:36:43,083] [INFO] Task succeeded: HMMsearch
[2023-06-30 23:36:43,085] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd60d513e-5aa8-41af-a0dd-d9d35a791356/GCA_025928855.1_ASM2592885v1_genomic.fna.gz]
[2023-06-30 23:36:43,119] [INFO] Query marker FASTA was written to GCA_025928855.1_ASM2592885v1_genomic.fna/markers.fasta
[2023-06-30 23:36:43,120] [INFO] Task started: Blastn
[2023-06-30 23:36:43,120] [INFO] Running command: blastn -query GCA_025928855.1_ASM2592885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0aff2b03-6986-4923-a964-81160a5d52cd/dqc_reference/reference_markers.fasta -out GCA_025928855.1_ASM2592885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 23:36:44,221] [INFO] Task succeeded: Blastn
[2023-06-30 23:36:44,226] [INFO] Selected 30 target genomes.
[2023-06-30 23:36:44,227] [INFO] Target genome list was writen to GCA_025928855.1_ASM2592885v1_genomic.fna/target_genomes.txt
[2023-06-30 23:36:44,230] [INFO] Task started: fastANI
[2023-06-30 23:36:44,231] [INFO] Running command: fastANI --query /var/lib/cwl/stgd60d513e-5aa8-41af-a0dd-d9d35a791356/GCA_025928855.1_ASM2592885v1_genomic.fna.gz --refList GCA_025928855.1_ASM2592885v1_genomic.fna/target_genomes.txt --output GCA_025928855.1_ASM2592885v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 23:37:09,248] [INFO] Task succeeded: fastANI
[2023-06-30 23:37:09,249] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0aff2b03-6986-4923-a964-81160a5d52cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 23:37:09,250] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0aff2b03-6986-4923-a964-81160a5d52cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 23:37:09,273] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 23:37:09,273] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 23:37:09,273] [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 cynanchi	strain=SB3-45	GCA_008761635.1	2558918	2558918	type	True	82.3066	727	1049	95	below_threshold
Nocardioides islandensis	strain=KCTC 19275	GCA_015352455.1	433663	433663	type	True	80.0662	592	1049	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	79.9387	565	1049	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	79.8623	511	1049	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	79.7418	521	1049	95	below_threshold
Nocardioides agariphilus	strain=KCTC 19276	GCA_015352445.1	433664	433664	type	True	79.7295	530	1049	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	79.5626	572	1049	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	79.5283	537	1049	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	79.5	521	1049	95	below_threshold
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	79.4931	529	1049	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	79.3576	539	1049	95	below_threshold
Nocardioides anomalus	strain=HKS04	GCA_011046535.1	2712223	2712223	type	True	79.3438	568	1049	95	below_threshold
Nocardioides gansuensis	strain=WSJ-1	GCA_003076135.1	2138300	2138300	type	True	79.328	439	1049	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	79.2784	539	1049	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	79.248	469	1049	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	79.2303	516	1049	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	79.2185	545	1049	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	79.1799	503	1049	95	below_threshold
Nocardioides rubriscoriae	strain=DSM 23986	GCA_008087085.1	642762	642762	type	True	79.1358	511	1049	95	below_threshold
Nocardioides eburneiflavus	strain=MMS17-SY213	GCA_004785795.1	2518372	2518372	type	True	79.1286	507	1049	95	below_threshold
Nocardioides humi	strain=DCY24	GCA_006494775.1	449461	449461	type	True	78.8379	522	1049	95	below_threshold
Marmoricola scoriae	strain=DSM 22127	GCA_900104965.1	642780	642780	type	True	78.8307	467	1049	95	below_threshold
Geodermatophilus daqingensis	strain=DSM 104001	GCA_013408985.1	2026353	2026353	type	True	76.8455	329	1049	95	below_threshold
Geodermatophilus obscurus	strain=DSM 43160	GCA_000025345.1	1861	1861	type	True	76.489	288	1049	95	below_threshold
Modestobacter altitudinis	strain=1G4	GCA_005930475.1	2213158	2213158	type	True	76.4238	282	1049	95	below_threshold
Geodermatophilus poikilotrophus	strain=DSM 44209	GCA_900111455.1	1333667	1333667	type	True	76.3649	289	1049	95	below_threshold
Goekera deserti	strain=CPCC 205119	GCA_010685995.1	2497753	2497753	type	True	76.3167	273	1049	95	below_threshold
Micromonospora sagamiensis	strain=DSM 43912	GCA_007829995.1	47875	47875	type	True	76.3146	259	1049	95	below_threshold
Micromonospora sagamiensis	strain=JCM 3310	GCA_014680085.1	47875	47875	type	True	76.3015	261	1049	95	below_threshold
Micromonospora rifamycinica	strain=DSM 44983	GCA_900090265.1	291594	291594	type	True	76.1281	293	1049	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 23:37:09,278] [INFO] DFAST Taxonomy check result was written to GCA_025928855.1_ASM2592885v1_genomic.fna/tc_result.tsv
[2023-06-30 23:37:09,278] [INFO] ===== Taxonomy check completed =====
[2023-06-30 23:37:09,279] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 23:37:09,279] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0aff2b03-6986-4923-a964-81160a5d52cd/dqc_reference/checkm_data
[2023-06-30 23:37:09,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 23:37:09,321] [INFO] Task started: CheckM
[2023-06-30 23:37:09,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025928855.1_ASM2592885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025928855.1_ASM2592885v1_genomic.fna/checkm_input GCA_025928855.1_ASM2592885v1_genomic.fna/checkm_result
[2023-06-30 23:37:53,014] [INFO] Task succeeded: CheckM
[2023-06-30 23:37:53,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.65%
Contamintation: 5.61%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 23:37:53,040] [INFO] ===== Completeness check finished =====
[2023-06-30 23:37:53,040] [INFO] ===== Start GTDB Search =====
[2023-06-30 23:37:53,041] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025928855.1_ASM2592885v1_genomic.fna/markers.fasta)
[2023-06-30 23:37:53,041] [INFO] Task started: Blastn
[2023-06-30 23:37:53,041] [INFO] Running command: blastn -query GCA_025928855.1_ASM2592885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0aff2b03-6986-4923-a964-81160a5d52cd/dqc_reference/reference_markers_gtdb.fasta -out GCA_025928855.1_ASM2592885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 23:37:54,841] [INFO] Task succeeded: Blastn
[2023-06-30 23:37:54,846] [INFO] Selected 25 target genomes.
[2023-06-30 23:37:54,846] [INFO] Target genome list was writen to GCA_025928855.1_ASM2592885v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 23:37:54,853] [INFO] Task started: fastANI
[2023-06-30 23:37:54,853] [INFO] Running command: fastANI --query /var/lib/cwl/stgd60d513e-5aa8-41af-a0dd-d9d35a791356/GCA_025928855.1_ASM2592885v1_genomic.fna.gz --refList GCA_025928855.1_ASM2592885v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025928855.1_ASM2592885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 23:38:15,195] [INFO] Task succeeded: fastANI
[2023-06-30 23:38:15,219] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 23:38:15,219] [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_017354415.1	s__Nocardioides sp017354415	82.4906	637	1049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008761635.1	s__Nocardioides cynanchi	82.3246	725	1049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015352455.1	s__Nocardioides islandensis	80.0575	593	1049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103935.1	s__Nocardioides szechwanensis	79.7393	522	1049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCA_902805925.1	s__Nocardioides sp902805925	79.6091	430	1049	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	79.5024	540	1049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015024225.1	s__Nocardioides sp015024225	79.4949	521	1049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	97.48	0.91	0.91	2	-
GCF_004564375.1	s__Nocardioides euryhalodurans	79.4759	532	1049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425175.1	s__Nocardioides sp001425175	79.4155	583	1049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003633575.1	s__Nocardioides sp003633575	79.3686	515	1049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011046535.1	s__Nocardioides anomalus	79.3424	568	1049	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	79.3388	497	1049	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	79.3139	534	1049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101465.1	s__Nocardioides lianchengensis	79.2555	539	1049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900105585.1	s__Nocardioides exalbidus	79.1846	502	1049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009701885.1	s__Nocardioides sp009701885	79.1646	445	1049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008087085.1	s__Nocardioides rubriscoriae	79.1318	511	1049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006494775.1	s__Nocardioides humi	78.8692	518	1049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104965.1	s__Marmoricola scoriae	78.8425	467	1049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001429555.1	s__Nocardioides sp001429555	78.3298	403	1049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003319115.1	s__Geodermatophilus sp003319115	76.5121	284	1049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003428645.1	s__Geodermatophilus sp003428645	76.5102	301	1049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000306785.1	s__Modestobacter marinus_A	76.4886	318	1049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000620205.1	s__Modestobacter sp000620205	76.4784	280	1049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005930475.1	s__Modestobacter altitudinis	76.4372	280	1049	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 23:38:15,222] [INFO] GTDB search result was written to GCA_025928855.1_ASM2592885v1_genomic.fna/result_gtdb.tsv
[2023-06-30 23:38:15,222] [INFO] ===== GTDB Search completed =====
[2023-06-30 23:38:15,228] [INFO] DFAST_QC result json was written to GCA_025928855.1_ASM2592885v1_genomic.fna/dqc_result.json
[2023-06-30 23:38:15,228] [INFO] DFAST_QC completed!
[2023-06-30 23:38:15,228] [INFO] Total running time: 0h1m42s