[2024-01-24 10:57:13,408] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:13,410] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:13,410] [INFO] DQC Reference Directory: /var/lib/cwl/stged4b32f1-e5de-4954-acce-ab4dd4744e50/dqc_reference
[2024-01-24 10:57:14,758] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,759] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,759] [INFO] Running command: gunzip -c /var/lib/cwl/stgf24fe3c9-5052-4737-855e-d9d145d27c45/GCF_008124835.1_ASM812483v1_genomic.fna.gz | prodigal -d GCF_008124835.1_ASM812483v1_genomic.fna/cds.fna -a GCF_008124835.1_ASM812483v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:26,880] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:26,881] [INFO] Task started: HMMsearch
[2024-01-24 10:57:26,881] [INFO] Running command: hmmsearch --tblout GCF_008124835.1_ASM812483v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged4b32f1-e5de-4954-acce-ab4dd4744e50/dqc_reference/reference_markers.hmm GCF_008124835.1_ASM812483v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:27,203] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:27,204] [INFO] Found 6/6 markers.
[2024-01-24 10:57:27,270] [INFO] Query marker FASTA was written to GCF_008124835.1_ASM812483v1_genomic.fna/markers.fasta
[2024-01-24 10:57:27,271] [INFO] Task started: Blastn
[2024-01-24 10:57:27,271] [INFO] Running command: blastn -query GCF_008124835.1_ASM812483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged4b32f1-e5de-4954-acce-ab4dd4744e50/dqc_reference/reference_markers.fasta -out GCF_008124835.1_ASM812483v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:28,698] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:28,702] [INFO] Selected 15 target genomes.
[2024-01-24 10:57:28,703] [INFO] Target genome list was writen to GCF_008124835.1_ASM812483v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:28,726] [INFO] Task started: fastANI
[2024-01-24 10:57:28,727] [INFO] Running command: fastANI --query /var/lib/cwl/stgf24fe3c9-5052-4737-855e-d9d145d27c45/GCF_008124835.1_ASM812483v1_genomic.fna.gz --refList GCF_008124835.1_ASM812483v1_genomic.fna/target_genomes.txt --output GCF_008124835.1_ASM812483v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:48,957] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:48,957] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged4b32f1-e5de-4954-acce-ab4dd4744e50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:48,957] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged4b32f1-e5de-4954-acce-ab4dd4744e50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:48,970] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:48,970] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:48,970] [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
Blastococcus xanthinilyticus	strain=DSM 46842	GCA_008124835.1	1564164	1564164	type	True	100.0	1515	1518	95	conclusive
Blastococcus saxobsidens	strain=DSM 44509	GCA_004217455.1	138336	138336	type	True	85.1112	1046	1518	95	below_threshold
Blastococcus saxobsidens	strain=DSM 44509	GCA_002938435.1	138336	138336	type	True	85.0343	1038	1518	95	below_threshold
Blastococcus atacamensis	strain=P6	GCA_002938425.1	2070508	2070508	type	True	84.7105	916	1518	95	below_threshold
Blastococcus aggregatus	strain=DSM 4725	GCA_900221005.1	38502	38502	type	True	83.7428	944	1518	95	below_threshold
Geodermatophilus chilensis	strain=B12	GCA_002802985.1	2035835	2035835	type	True	83.0606	909	1518	95	below_threshold
Geodermatophilus sabuli	strain=DSM 46844	GCA_900215145.1	1564158	1564158	type	True	83.0492	948	1518	95	below_threshold
Geodermatophilus bullaregiensis	strain=DSM 46841	GCA_016907675.1	1564160	1564160	type	True	83.0249	962	1518	95	below_threshold
Geodermatophilus sabuli	strain=CECT 8820	GCA_014191795.1	1564158	1564158	type	True	83.0125	945	1518	95	below_threshold
Geodermatophilus nigrescens	strain=DSM 45408	GCA_900129495.1	1070870	1070870	type	True	83.0005	997	1518	95	below_threshold
Geodermatophilus normandii	strain=DSM 45417	GCA_003182485.1	1137989	1137989	type	True	82.8841	952	1518	95	below_threshold
Geodermatophilus saharensis	strain=DSM 45423	GCA_900188205.1	1137994	1137994	type	True	82.8704	960	1518	95	below_threshold
Modestobacter roseus	strain=DSM 45764	GCA_007994135.1	1181884	1181884	type	True	82.4482	910	1518	95	below_threshold
Modestobacter muralis	strain=DSM 100205	GCA_010686625.1	1608614	1608614	type	True	81.9122	845	1518	95	below_threshold
Modestobacter muralis	strain=DSM 100205	GCA_010682105.1	1608614	1608614	type	True	81.858	822	1518	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:48,972] [INFO] DFAST Taxonomy check result was written to GCF_008124835.1_ASM812483v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:48,972] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:48,972] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:48,973] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged4b32f1-e5de-4954-acce-ab4dd4744e50/dqc_reference/checkm_data
[2024-01-24 10:57:48,974] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:49,017] [INFO] Task started: CheckM
[2024-01-24 10:57:49,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008124835.1_ASM812483v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008124835.1_ASM812483v1_genomic.fna/checkm_input GCF_008124835.1_ASM812483v1_genomic.fna/checkm_result
[2024-01-24 10:58:48,133] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:48,135] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:48,152] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:48,152] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:48,153] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008124835.1_ASM812483v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:48,153] [INFO] Task started: Blastn
[2024-01-24 10:58:48,153] [INFO] Running command: blastn -query GCF_008124835.1_ASM812483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged4b32f1-e5de-4954-acce-ab4dd4744e50/dqc_reference/reference_markers_gtdb.fasta -out GCF_008124835.1_ASM812483v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:50,253] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:50,258] [INFO] Selected 17 target genomes.
[2024-01-24 10:58:50,258] [INFO] Target genome list was writen to GCF_008124835.1_ASM812483v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:50,275] [INFO] Task started: fastANI
[2024-01-24 10:58:50,275] [INFO] Running command: fastANI --query /var/lib/cwl/stgf24fe3c9-5052-4737-855e-d9d145d27c45/GCF_008124835.1_ASM812483v1_genomic.fna.gz --refList GCF_008124835.1_ASM812483v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008124835.1_ASM812483v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:10,094] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:10,124] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:10,125] [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_008124835.1	s__Blastococcus xanthinilyticus	100.0	1515	1518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900109665.1	s__Blastococcus sp900109665	86.253	1088	1518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284015.1	s__Blastococcus saxobsidens_A	86.2246	1056	1518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010682065.1	s__Blastococcus saxobsidens_B	85.4283	959	1518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004571075.1	s__Blastococcus sp004571075	85.1847	971	1518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003319095.1	s__Blastococcus sp003319095	85.1145	995	1518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002938425.1	s__Blastococcus atacamensis	84.7102	916	1518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003319175.1	s__Blastococcus sp003319175	84.6767	956	1518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112815.1	s__Blastococcus sp900112815	83.8798	1013	1518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900221005.1	s__Blastococcus aggregatus	83.7435	944	1518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900102115.1	s__Blastococcus sp900102115	83.74	933	1518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410015.1	s__Blastococcus sp013410015	83.5912	987	1518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000582785.1	s__Blastococcus massiliensis	83.5587	905	1518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900230285.1	s__Blastococcus sp900230285	83.3862	996	1518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570385.1	s__Blastococcus sp004570385	82.7565	901	1518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994135.1	s__Modestobacter roseus	82.4158	914	1518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	99.87	99.87	0.97	0.97	2	-
GCF_010682105.1	s__Modestobacter muralis	81.918	815	1518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:10,129] [INFO] GTDB search result was written to GCF_008124835.1_ASM812483v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:10,130] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:10,137] [INFO] DFAST_QC result json was written to GCF_008124835.1_ASM812483v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:10,138] [INFO] DFAST_QC completed!
[2024-01-24 10:59:10,138] [INFO] Total running time: 0h1m57s