[2024-01-25 19:43:50,377] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:50,379] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:50,380] [INFO] DQC Reference Directory: /var/lib/cwl/stgefda1660-479a-4ea7-9a27-81aa35182be1/dqc_reference
[2024-01-25 19:43:51,492] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:51,493] [INFO] Task started: Prodigal
[2024-01-25 19:43:51,493] [INFO] Running command: gunzip -c /var/lib/cwl/stg098afe0d-d472-49da-ab14-265ac6ca7837/GCF_001592045.1_ASM159204v1_genomic.fna.gz | prodigal -d GCF_001592045.1_ASM159204v1_genomic.fna/cds.fna -a GCF_001592045.1_ASM159204v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:44:00,953] [INFO] Task succeeded: Prodigal
[2024-01-25 19:44:00,953] [INFO] Task started: HMMsearch
[2024-01-25 19:44:00,953] [INFO] Running command: hmmsearch --tblout GCF_001592045.1_ASM159204v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefda1660-479a-4ea7-9a27-81aa35182be1/dqc_reference/reference_markers.hmm GCF_001592045.1_ASM159204v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:44:01,180] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:44:01,181] [INFO] Found 6/6 markers.
[2024-01-25 19:44:01,216] [INFO] Query marker FASTA was written to GCF_001592045.1_ASM159204v1_genomic.fna/markers.fasta
[2024-01-25 19:44:01,216] [INFO] Task started: Blastn
[2024-01-25 19:44:01,216] [INFO] Running command: blastn -query GCF_001592045.1_ASM159204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefda1660-479a-4ea7-9a27-81aa35182be1/dqc_reference/reference_markers.fasta -out GCF_001592045.1_ASM159204v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:02,241] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:02,244] [INFO] Selected 8 target genomes.
[2024-01-25 19:44:02,244] [INFO] Target genome list was writen to GCF_001592045.1_ASM159204v1_genomic.fna/target_genomes.txt
[2024-01-25 19:44:02,253] [INFO] Task started: fastANI
[2024-01-25 19:44:02,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg098afe0d-d472-49da-ab14-265ac6ca7837/GCF_001592045.1_ASM159204v1_genomic.fna.gz --refList GCF_001592045.1_ASM159204v1_genomic.fna/target_genomes.txt --output GCF_001592045.1_ASM159204v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:11,803] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:11,803] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefda1660-479a-4ea7-9a27-81aa35182be1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:11,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefda1660-479a-4ea7-9a27-81aa35182be1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:11,810] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:44:11,810] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:44:11,811] [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 fusca	strain=NBRC 14071	GCA_001592045.1	2021	2021	type	True	100.0	1165	1171	95	conclusive
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	84.9048	1027	1171	95	below_threshold
Thermobifida cellulosilytica	strain=TB100	GCA_001517975.1	144786	144786	type	True	84.1682	964	1171	95	below_threshold
Thermobifida halotolerans	strain=DSM 44931	GCA_003574835.2	483545	483545	type	True	83.3283	941	1171	95	below_threshold
Thermobifida halotolerans	strain=YIM 90462	GCA_001660385.1	483545	483545	type	True	83.2215	950	1171	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	78.5836	466	1171	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	78.4695	443	1171	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	77.0716	326	1171	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:11,812] [INFO] DFAST Taxonomy check result was written to GCF_001592045.1_ASM159204v1_genomic.fna/tc_result.tsv
[2024-01-25 19:44:11,812] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:11,813] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:11,813] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefda1660-479a-4ea7-9a27-81aa35182be1/dqc_reference/checkm_data
[2024-01-25 19:44:11,814] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:11,852] [INFO] Task started: CheckM
[2024-01-25 19:44:11,852] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001592045.1_ASM159204v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001592045.1_ASM159204v1_genomic.fna/checkm_input GCF_001592045.1_ASM159204v1_genomic.fna/checkm_result
[2024-01-25 19:44:42,108] [INFO] Task succeeded: CheckM
[2024-01-25 19:44:42,109] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:44:42,124] [INFO] ===== Completeness check finished =====
[2024-01-25 19:44:42,124] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:44:42,124] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001592045.1_ASM159204v1_genomic.fna/markers.fasta)
[2024-01-25 19:44:42,125] [INFO] Task started: Blastn
[2024-01-25 19:44:42,125] [INFO] Running command: blastn -query GCF_001592045.1_ASM159204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefda1660-479a-4ea7-9a27-81aa35182be1/dqc_reference/reference_markers_gtdb.fasta -out GCF_001592045.1_ASM159204v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:43,702] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:43,705] [INFO] Selected 12 target genomes.
[2024-01-25 19:44:43,705] [INFO] Target genome list was writen to GCF_001592045.1_ASM159204v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:44:43,718] [INFO] Task started: fastANI
[2024-01-25 19:44:43,719] [INFO] Running command: fastANI --query /var/lib/cwl/stg098afe0d-d472-49da-ab14-265ac6ca7837/GCF_001592045.1_ASM159204v1_genomic.fna.gz --refList GCF_001592045.1_ASM159204v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001592045.1_ASM159204v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:44:56,868] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:56,876] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:44:56,876] [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_001592045.1	s__Thermobifida fusca	100.0	1165	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida	95.0	99.75	99.61	0.97	0.95	9	conclusive
GCF_001517975.1	s__Thermobifida cellulosilytica	84.1682	964	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001660385.1	s__Thermobifida halotolerans	83.2262	949	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida	95.0	99.91	99.91	0.97	0.97	2	-
GCF_004363075.1	s__Actinorugispora endophytica	80.5222	725	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinorugispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408795.1	s__Spinactinospora alkalitolerans	79.6053	597	1171	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	79.3466	513	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Marinactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336425.1	s__Marinitenerispora sediminis	79.1515	501	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Marinitenerispora	95.0	99.95	99.94	0.96	0.96	3	-
GCF_000341105.1	s__Nocardiopsis_A potens	79.0311	514	1171	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_014201195.1	s__Nocardiopsis_C mwathae	78.9995	491	1171	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_001552555.1	s__Nocardiopsis_B trehalosi	78.8458	539	1171	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_001905145.1	s__Nocardiopsis sp001905145	78.8458	471	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386285.1	s__Nocardiopsis sp003386285	78.5163	450	1171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:44:56,878] [INFO] GTDB search result was written to GCF_001592045.1_ASM159204v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:44:56,878] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:44:56,881] [INFO] DFAST_QC result json was written to GCF_001592045.1_ASM159204v1_genomic.fna/dqc_result.json
[2024-01-25 19:44:56,881] [INFO] DFAST_QC completed!
[2024-01-25 19:44:56,881] [INFO] Total running time: 0h1m7s