[2024-01-24 11:18:04,590] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:18:04,592] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:18:04,592] [INFO] DQC Reference Directory: /var/lib/cwl/stg3eb83524-4599-4395-ab72-bfff9f035ab7/dqc_reference
[2024-01-24 11:18:05,784] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:18:05,785] [INFO] Task started: Prodigal
[2024-01-24 11:18:05,785] [INFO] Running command: gunzip -c /var/lib/cwl/stg3dafe10d-e636-478e-8fa1-746db45c1a1f/GCF_015339545.1_ASM1533954v1_genomic.fna.gz | prodigal -d GCF_015339545.1_ASM1533954v1_genomic.fna/cds.fna -a GCF_015339545.1_ASM1533954v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:18:17,943] [INFO] Task succeeded: Prodigal
[2024-01-24 11:18:17,944] [INFO] Task started: HMMsearch
[2024-01-24 11:18:17,944] [INFO] Running command: hmmsearch --tblout GCF_015339545.1_ASM1533954v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3eb83524-4599-4395-ab72-bfff9f035ab7/dqc_reference/reference_markers.hmm GCF_015339545.1_ASM1533954v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:18:18,213] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:18:18,215] [INFO] Found 6/6 markers.
[2024-01-24 11:18:18,255] [INFO] Query marker FASTA was written to GCF_015339545.1_ASM1533954v1_genomic.fna/markers.fasta
[2024-01-24 11:18:18,255] [INFO] Task started: Blastn
[2024-01-24 11:18:18,256] [INFO] Running command: blastn -query GCF_015339545.1_ASM1533954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3eb83524-4599-4395-ab72-bfff9f035ab7/dqc_reference/reference_markers.fasta -out GCF_015339545.1_ASM1533954v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:18:19,536] [INFO] Task succeeded: Blastn
[2024-01-24 11:18:19,540] [INFO] Selected 12 target genomes.
[2024-01-24 11:18:19,541] [INFO] Target genome list was writen to GCF_015339545.1_ASM1533954v1_genomic.fna/target_genomes.txt
[2024-01-24 11:18:19,547] [INFO] Task started: fastANI
[2024-01-24 11:18:19,547] [INFO] Running command: fastANI --query /var/lib/cwl/stg3dafe10d-e636-478e-8fa1-746db45c1a1f/GCF_015339545.1_ASM1533954v1_genomic.fna.gz --refList GCF_015339545.1_ASM1533954v1_genomic.fna/target_genomes.txt --output GCF_015339545.1_ASM1533954v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:18:34,240] [INFO] Task succeeded: fastANI
[2024-01-24 11:18:34,241] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3eb83524-4599-4395-ab72-bfff9f035ab7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:18:34,241] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3eb83524-4599-4395-ab72-bfff9f035ab7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:18:34,260] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:18:34,260] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:18:34,261] [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 salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	100.0	1452	1455	95	conclusive
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	100.0	1449	1455	95	conclusive
Nocardioides salarius	strain=DSM 18239	GCA_016907435.1	374513	374513	type	True	99.9981	1453	1455	95	conclusive
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	90.5385	1151	1455	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	90.471	1162	1455	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	81.9733	878	1455	95	below_threshold
Nocardioides acrostichi	strain=CBS4Y-1	GCA_015319165.1	2784339	2784339	type	True	81.4788	793	1455	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	81.2374	764	1455	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.8177	698	1455	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	80.7044	759	1455	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	80.3232	754	1455	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	80.0928	664	1455	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:18:34,263] [INFO] DFAST Taxonomy check result was written to GCF_015339545.1_ASM1533954v1_genomic.fna/tc_result.tsv
[2024-01-24 11:18:34,263] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:18:34,264] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:18:34,264] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3eb83524-4599-4395-ab72-bfff9f035ab7/dqc_reference/checkm_data
[2024-01-24 11:18:34,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:18:34,308] [INFO] Task started: CheckM
[2024-01-24 11:18:34,308] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015339545.1_ASM1533954v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015339545.1_ASM1533954v1_genomic.fna/checkm_input GCF_015339545.1_ASM1533954v1_genomic.fna/checkm_result
[2024-01-24 11:19:36,249] [INFO] Task succeeded: CheckM
[2024-01-24 11:19:36,251] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:19:36,273] [INFO] ===== Completeness check finished =====
[2024-01-24 11:19:36,274] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:19:36,274] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015339545.1_ASM1533954v1_genomic.fna/markers.fasta)
[2024-01-24 11:19:36,274] [INFO] Task started: Blastn
[2024-01-24 11:19:36,275] [INFO] Running command: blastn -query GCF_015339545.1_ASM1533954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3eb83524-4599-4395-ab72-bfff9f035ab7/dqc_reference/reference_markers_gtdb.fasta -out GCF_015339545.1_ASM1533954v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:19:38,358] [INFO] Task succeeded: Blastn
[2024-01-24 11:19:38,363] [INFO] Selected 16 target genomes.
[2024-01-24 11:19:38,363] [INFO] Target genome list was writen to GCF_015339545.1_ASM1533954v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:19:38,376] [INFO] Task started: fastANI
[2024-01-24 11:19:38,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg3dafe10d-e636-478e-8fa1-746db45c1a1f/GCF_015339545.1_ASM1533954v1_genomic.fna.gz --refList GCF_015339545.1_ASM1533954v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015339545.1_ASM1533954v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:19:55,827] [INFO] Task succeeded: fastANI
[2024-01-24 11:19:55,845] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:19:55,845] [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_016907435.1	s__Nocardioides salarius	99.9981	1453	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_013466785.1	s__Nocardioides marinisabuli	90.4902	1160	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001653335.1	s__Nocardioides dokdonensis	87.4666	1115	1455	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	83.3444	871	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCA_001627335.1	s__Nocardioides sp001627335	83.2857	804	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	96.50	0.91	0.88	12	-
GCF_013408145.1	s__Nocardioides marinus	83.2685	913	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.85	95.82	0.82	0.73	3	-
GCF_013177455.1	s__Nocardioides sp013177455	82.3452	870	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_013155365.1	s__Nocardioides sp013155365	82.1153	819	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003660455.1	s__Nocardioides ferulae	81.9882	876	1455	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	81.5879	802	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506435.1	s__Nocardioides sp902506435	81.5727	778	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319165.1	s__Nocardioides acrostichi	81.5017	791	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003047295.1	s__Nocardioides sediminis	81.1727	739	1455	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	81.0729	789	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735675.1	s__Nocardioides sp016735675	80.8828	734	1455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014108865.1	s__Nocardioides sp014108865	79.5833	624	1455	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 11:19:55,847] [INFO] GTDB search result was written to GCF_015339545.1_ASM1533954v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:19:55,847] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:19:55,851] [INFO] DFAST_QC result json was written to GCF_015339545.1_ASM1533954v1_genomic.fna/dqc_result.json
[2024-01-24 11:19:55,851] [INFO] DFAST_QC completed!
[2024-01-24 11:19:55,851] [INFO] Total running time: 0h1m51s