[2024-01-24 14:14:46,986] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:46,988] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:46,989] [INFO] DQC Reference Directory: /var/lib/cwl/stg487aace4-309a-4f0e-b4f5-4778b50c6b9f/dqc_reference
[2024-01-24 14:14:49,422] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:49,424] [INFO] Task started: Prodigal
[2024-01-24 14:14:49,424] [INFO] Running command: gunzip -c /var/lib/cwl/stgc52263c5-6615-42bc-9104-319b92d2b09d/GCF_004564375.1_ASM456437v1_genomic.fna.gz | prodigal -d GCF_004564375.1_ASM456437v1_genomic.fna/cds.fna -a GCF_004564375.1_ASM456437v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:01,416] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:01,417] [INFO] Task started: HMMsearch
[2024-01-24 14:15:01,417] [INFO] Running command: hmmsearch --tblout GCF_004564375.1_ASM456437v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg487aace4-309a-4f0e-b4f5-4778b50c6b9f/dqc_reference/reference_markers.hmm GCF_004564375.1_ASM456437v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:01,717] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:01,719] [INFO] Found 6/6 markers.
[2024-01-24 14:15:01,756] [INFO] Query marker FASTA was written to GCF_004564375.1_ASM456437v1_genomic.fna/markers.fasta
[2024-01-24 14:15:01,757] [INFO] Task started: Blastn
[2024-01-24 14:15:01,757] [INFO] Running command: blastn -query GCF_004564375.1_ASM456437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg487aace4-309a-4f0e-b4f5-4778b50c6b9f/dqc_reference/reference_markers.fasta -out GCF_004564375.1_ASM456437v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:03,026] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:03,029] [INFO] Selected 22 target genomes.
[2024-01-24 14:15:03,029] [INFO] Target genome list was writen to GCF_004564375.1_ASM456437v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:03,047] [INFO] Task started: fastANI
[2024-01-24 14:15:03,047] [INFO] Running command: fastANI --query /var/lib/cwl/stgc52263c5-6615-42bc-9104-319b92d2b09d/GCF_004564375.1_ASM456437v1_genomic.fna.gz --refList GCF_004564375.1_ASM456437v1_genomic.fna/target_genomes.txt --output GCF_004564375.1_ASM456437v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:24,483] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:24,484] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg487aace4-309a-4f0e-b4f5-4778b50c6b9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:24,485] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg487aace4-309a-4f0e-b4f5-4778b50c6b9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:24,508] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:24,508] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:24,509] [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 euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	100.0	1339	1339	95	conclusive
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	82.6523	781	1339	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	81.7757	740	1339	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	81.5889	736	1339	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	81.4216	774	1339	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	81.2848	747	1339	95	below_threshold
Nocardioides sediminis	strain=KCTC 19271	GCA_003047295.1	433648	433648	type	True	81.2771	728	1339	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	81.0933	702	1339	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	81.0291	748	1339	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.9071	716	1339	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	80.8667	706	1339	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	80.8621	752	1339	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	80.7275	709	1339	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	80.6759	701	1339	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	80.6657	692	1339	95	below_threshold
Nocardioides dokdonensis	strain=FR1436	GCA_001653335.1	450734	450734	type	True	80.5793	672	1339	95	below_threshold
Nocardioides anomalus	strain=HKS04	GCA_011046535.1	2712223	2712223	type	True	80.5284	729	1339	95	below_threshold
Nocardioides islandensis	strain=KCTC 19275	GCA_015352455.1	433663	433663	type	True	80.4538	709	1339	95	below_threshold
Nocardioides stalactiti	strain=1.0914	GCA_014180715.1	2755356	2755356	type	True	80.2549	586	1339	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	80.062	580	1339	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	79.9024	596	1339	95	below_threshold
Nocardioides immobilis	strain=CCTCC AB 2017083	GCA_003515065.1	2049295	2049295	type	True	79.7813	672	1339	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:24,510] [INFO] DFAST Taxonomy check result was written to GCF_004564375.1_ASM456437v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:24,511] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:24,511] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:24,511] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg487aace4-309a-4f0e-b4f5-4778b50c6b9f/dqc_reference/checkm_data
[2024-01-24 14:15:24,512] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:24,553] [INFO] Task started: CheckM
[2024-01-24 14:15:24,553] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004564375.1_ASM456437v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004564375.1_ASM456437v1_genomic.fna/checkm_input GCF_004564375.1_ASM456437v1_genomic.fna/checkm_result
[2024-01-24 14:16:26,988] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:26,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:27,010] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:27,011] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:27,011] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004564375.1_ASM456437v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:27,011] [INFO] Task started: Blastn
[2024-01-24 14:16:27,012] [INFO] Running command: blastn -query GCF_004564375.1_ASM456437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg487aace4-309a-4f0e-b4f5-4778b50c6b9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004564375.1_ASM456437v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:28,968] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:28,973] [INFO] Selected 23 target genomes.
[2024-01-24 14:16:28,973] [INFO] Target genome list was writen to GCF_004564375.1_ASM456437v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:28,994] [INFO] Task started: fastANI
[2024-01-24 14:16:28,995] [INFO] Running command: fastANI --query /var/lib/cwl/stgc52263c5-6615-42bc-9104-319b92d2b09d/GCF_004564375.1_ASM456437v1_genomic.fna.gz --refList GCF_004564375.1_ASM456437v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004564375.1_ASM456437v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:51,386] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:51,409] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:51,410] [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_004564375.1	s__Nocardioides euryhalodurans	100.0	1339	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014138045.1	s__Nocardioides ginsengisegetis	81.7816	739	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCF_014212315.1	s__Nocardioides luti	81.566	739	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013466985.1	s__Nocardioides ungokensis	81.4855	769	1339	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	81.3175	743	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177455.1	s__Nocardioides sp013177455	81.3048	731	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_002117935.1	s__Nocardioides sp002117935	81.3032	712	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003047295.1	s__Nocardioides sediminis	81.2402	733	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003047265.1	s__Nocardioides terrigena	81.2364	749	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	95.44	95.44	0.86	0.86	2	-
GCF_011250565.1	s__Nocardioides sp011250565	81.2301	677	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805925.1	s__Nocardioides sp902805925	81.1649	603	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924665.1	s__Nocardioides sp016924665	81.0488	725	1339	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	80.8791	740	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004519545.1	s__Nocardioides guangzhouensis	80.8699	751	1339	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	80.8167	674	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.92	98.92	0.96	0.96	2	-
GCF_003076135.1	s__Nocardioides gansuensis	80.7985	674	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620645.1	s__Nocardioides sp000620645	80.7803	701	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409425.1	s__Nocardioides perillae	80.7099	690	1339	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	80.7077	711	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653335.1	s__Nocardioides dokdonensis	80.5576	678	1339	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	80.4294	712	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729525.1	s__Nocardioides sp002729525	80.4073	642	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018459925.1	s__Nocardioides aquaticus	80.2274	694	1339	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 14:16:51,411] [INFO] GTDB search result was written to GCF_004564375.1_ASM456437v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:51,412] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:51,416] [INFO] DFAST_QC result json was written to GCF_004564375.1_ASM456437v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:51,416] [INFO] DFAST_QC completed!
[2024-01-24 14:16:51,417] [INFO] Total running time: 0h2m4s