[2024-01-24 13:46:03,795] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:03,798] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:03,798] [INFO] DQC Reference Directory: /var/lib/cwl/stg7802d5b7-1654-499b-b192-e066bfe4cd81/dqc_reference
[2024-01-24 13:46:05,156] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:05,156] [INFO] Task started: Prodigal
[2024-01-24 13:46:05,157] [INFO] Running command: gunzip -c /var/lib/cwl/stg410f8bdf-4700-4da3-b73e-37748b32cb3e/GCF_003574835.2_ASM357483v2_genomic.fna.gz | prodigal -d GCF_003574835.2_ASM357483v2_genomic.fna/cds.fna -a GCF_003574835.2_ASM357483v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:23,753] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:23,753] [INFO] Task started: HMMsearch
[2024-01-24 13:46:23,753] [INFO] Running command: hmmsearch --tblout GCF_003574835.2_ASM357483v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7802d5b7-1654-499b-b192-e066bfe4cd81/dqc_reference/reference_markers.hmm GCF_003574835.2_ASM357483v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:24,055] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:24,057] [INFO] Found 6/6 markers.
[2024-01-24 13:46:24,111] [INFO] Query marker FASTA was written to GCF_003574835.2_ASM357483v2_genomic.fna/markers.fasta
[2024-01-24 13:46:24,111] [INFO] Task started: Blastn
[2024-01-24 13:46:24,112] [INFO] Running command: blastn -query GCF_003574835.2_ASM357483v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg7802d5b7-1654-499b-b192-e066bfe4cd81/dqc_reference/reference_markers.fasta -out GCF_003574835.2_ASM357483v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:25,320] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:25,323] [INFO] Selected 11 target genomes.
[2024-01-24 13:46:25,324] [INFO] Target genome list was writen to GCF_003574835.2_ASM357483v2_genomic.fna/target_genomes.txt
[2024-01-24 13:46:25,330] [INFO] Task started: fastANI
[2024-01-24 13:46:25,330] [INFO] Running command: fastANI --query /var/lib/cwl/stg410f8bdf-4700-4da3-b73e-37748b32cb3e/GCF_003574835.2_ASM357483v2_genomic.fna.gz --refList GCF_003574835.2_ASM357483v2_genomic.fna/target_genomes.txt --output GCF_003574835.2_ASM357483v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:40,276] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:40,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7802d5b7-1654-499b-b192-e066bfe4cd81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:40,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7802d5b7-1654-499b-b192-e066bfe4cd81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:40,287] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:46:40,287] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:40,287] [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
Thermobifida halotolerans	strain=DSM 44931	GCA_003574835.2	483545	483545	type	True	100.0	1833	1834	95	conclusive
Thermobifida halotolerans	strain=YIM 90462	GCA_001660385.1	483545	483545	type	True	99.9317	1774	1834	95	conclusive
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	88.7207	1321	1834	95	below_threshold
Thermobifida cellulosilytica	strain=TB100	GCA_001517975.1	144786	144786	type	True	88.0585	1201	1834	95	below_threshold
Thermobifida fusca	strain=NBRC 14071	GCA_001592045.1	2021	2021	type	True	83.1704	938	1834	95	below_threshold
Nocardiopsis mwathae	strain=DSM 46659	GCA_014201195.1	1472723	1472723	type	True	80.1271	800	1834	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	80.0431	787	1834	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	79.8991	781	1834	95	below_threshold
Nocardiopsis composta	strain=DSM 44551	GCA_014200805.1	157465	157465	type	True	79.7488	904	1834	95	below_threshold
Nocardiopsis lucentensis	strain=DSM 44048	GCA_000341125.1	53441	53441	type	True	79.5983	596	1834	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	79.4733	741	1834	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:40,291] [INFO] DFAST Taxonomy check result was written to GCF_003574835.2_ASM357483v2_genomic.fna/tc_result.tsv
[2024-01-24 13:46:40,291] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:40,291] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:40,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7802d5b7-1654-499b-b192-e066bfe4cd81/dqc_reference/checkm_data
[2024-01-24 13:46:40,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:40,358] [INFO] Task started: CheckM
[2024-01-24 13:46:40,358] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003574835.2_ASM357483v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003574835.2_ASM357483v2_genomic.fna/checkm_input GCF_003574835.2_ASM357483v2_genomic.fna/checkm_result
[2024-01-24 13:47:48,697] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:48,698] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:48,715] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:48,716] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:48,716] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003574835.2_ASM357483v2_genomic.fna/markers.fasta)
[2024-01-24 13:47:48,716] [INFO] Task started: Blastn
[2024-01-24 13:47:48,716] [INFO] Running command: blastn -query GCF_003574835.2_ASM357483v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg7802d5b7-1654-499b-b192-e066bfe4cd81/dqc_reference/reference_markers_gtdb.fasta -out GCF_003574835.2_ASM357483v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:50,414] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:50,417] [INFO] Selected 16 target genomes.
[2024-01-24 13:47:50,417] [INFO] Target genome list was writen to GCF_003574835.2_ASM357483v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:50,459] [INFO] Task started: fastANI
[2024-01-24 13:47:50,459] [INFO] Running command: fastANI --query /var/lib/cwl/stg410f8bdf-4700-4da3-b73e-37748b32cb3e/GCF_003574835.2_ASM357483v2_genomic.fna.gz --refList GCF_003574835.2_ASM357483v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003574835.2_ASM357483v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:07,917] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:07,929] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:07,929] [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_001660385.1	s__Thermobifida halotolerans	99.9317	1774	1834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida	95.0	99.91	99.91	0.97	0.97	2	conclusive
GCF_001517975.1	s__Thermobifida cellulosilytica	88.0493	1202	1834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363075.1	s__Actinorugispora endophytica	84.4037	1090	1834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinorugispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592045.1	s__Thermobifida fusca	83.1821	937	1834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida	95.0	99.75	99.61	0.97	0.95	9	-
GCF_013408795.1	s__Spinactinospora alkalitolerans	81.3163	987	1834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spinactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167435.1	s__Marinactinospora thermotolerans	80.6242	833	1834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Marinactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552555.1	s__Nocardiopsis_B trehalosi	80.28	845	1834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201195.1	s__Nocardiopsis_C mwathae	80.1569	799	1834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009728995.1	s__Streptomonospora sp009728995	80.0615	840	1834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341105.1	s__Nocardiopsis_A potens	79.7941	859	1834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000515115.1	s__Nocardiopsis sp000515115	79.6574	659	1834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341125.1	s__Nocardiopsis lucentensis	79.6422	591	1834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019244295.1	s__Pseudonocardia sp019244295	76.155	125	1834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:07,931] [INFO] GTDB search result was written to GCF_003574835.2_ASM357483v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:07,931] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:07,937] [INFO] DFAST_QC result json was written to GCF_003574835.2_ASM357483v2_genomic.fna/dqc_result.json
[2024-01-24 13:48:07,937] [INFO] DFAST_QC completed!
[2024-01-24 13:48:07,937] [INFO] Total running time: 0h2m4s