[2024-01-24 14:28:18,194] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:18,199] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:18,199] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c8cb111-8c0d-46b0-ad80-ac590749ac5b/dqc_reference
[2024-01-24 14:28:20,483] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:20,484] [INFO] Task started: Prodigal
[2024-01-24 14:28:20,485] [INFO] Running command: gunzip -c /var/lib/cwl/stg523a2ac0-8144-4866-8065-5d8bac786fa3/GCF_009901565.1_ASM990156v1_genomic.fna.gz | prodigal -d GCF_009901565.1_ASM990156v1_genomic.fna/cds.fna -a GCF_009901565.1_ASM990156v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:45,451] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:45,451] [INFO] Task started: HMMsearch
[2024-01-24 14:28:45,451] [INFO] Running command: hmmsearch --tblout GCF_009901565.1_ASM990156v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c8cb111-8c0d-46b0-ad80-ac590749ac5b/dqc_reference/reference_markers.hmm GCF_009901565.1_ASM990156v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:45,864] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:45,865] [INFO] Found 6/6 markers.
[2024-01-24 14:28:45,943] [INFO] Query marker FASTA was written to GCF_009901565.1_ASM990156v1_genomic.fna/markers.fasta
[2024-01-24 14:28:45,943] [INFO] Task started: Blastn
[2024-01-24 14:28:45,943] [INFO] Running command: blastn -query GCF_009901565.1_ASM990156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c8cb111-8c0d-46b0-ad80-ac590749ac5b/dqc_reference/reference_markers.fasta -out GCF_009901565.1_ASM990156v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:47,374] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:47,378] [INFO] Selected 16 target genomes.
[2024-01-24 14:28:47,379] [INFO] Target genome list was writen to GCF_009901565.1_ASM990156v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:47,386] [INFO] Task started: fastANI
[2024-01-24 14:28:47,387] [INFO] Running command: fastANI --query /var/lib/cwl/stg523a2ac0-8144-4866-8065-5d8bac786fa3/GCF_009901565.1_ASM990156v1_genomic.fna.gz --refList GCF_009901565.1_ASM990156v1_genomic.fna/target_genomes.txt --output GCF_009901565.1_ASM990156v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:29:16,023] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:16,024] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c8cb111-8c0d-46b0-ad80-ac590749ac5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:29:16,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c8cb111-8c0d-46b0-ad80-ac590749ac5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:29:16,044] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:29:16,044] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:29:16,044] [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
Herbidospora solisilvae	strain=NEAU-GS84	GCA_009901565.1	2696284	2696284	type	True	100.0	2780	2781	95	conclusive
Herbidospora galbida	strain=NEAU-GS14	GCA_005233835.1	2575442	2575442	type	True	93.7144	2296	2781	95	below_threshold
Herbidospora sakaeratensis	strain=NBRC 102641	GCA_001570525.1	564415	564415	type	True	93.3717	2349	2781	95	below_threshold
Herbidospora cretacea	strain=NBRC 15474	GCA_001570605.1	28444	28444	type	True	90.4635	2211	2781	95	below_threshold
Herbidospora mongoliensis	strain=NBRC 105882	GCA_001570545.1	688067	688067	type	True	89.5817	2216	2781	95	below_threshold
Acrocarpospora catenulata	strain=H8750	GCA_018476525.1	2836182	2836182	type	True	81.0387	1490	2781	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.5883	1267	2781	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.512	871	2781	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	79.3273	1278	2781	95	below_threshold
Streptosporangium violaceochromogenes	strain=JCM 3281	GCA_014654615.1	46188	46188	type	True	79.2559	917	2781	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	78.8703	1284	2781	95	below_threshold
Bowdeniella nasicola	strain=DSM 19116	GCA_001907295.1	208480	208480	type	True	76.2005	127	2781	95	below_threshold
Isoptericola chiayiensis	strain=KCTC 19740	GCA_013149805.1	579446	579446	type	True	75.9581	412	2781	95	below_threshold
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	75.7865	308	2781	95	below_threshold
Agrococcus jenensis	strain=DSM 9580	GCA_003752465.1	46353	46353	type	True	75.7826	321	2781	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:29:16,046] [INFO] DFAST Taxonomy check result was written to GCF_009901565.1_ASM990156v1_genomic.fna/tc_result.tsv
[2024-01-24 14:29:16,047] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:29:16,047] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:29:16,047] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c8cb111-8c0d-46b0-ad80-ac590749ac5b/dqc_reference/checkm_data
[2024-01-24 14:29:16,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:29:16,126] [INFO] Task started: CheckM
[2024-01-24 14:29:16,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009901565.1_ASM990156v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009901565.1_ASM990156v1_genomic.fna/checkm_input GCF_009901565.1_ASM990156v1_genomic.fna/checkm_result
[2024-01-24 14:30:30,563] [INFO] Task succeeded: CheckM
[2024-01-24 14:30:30,564] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:30:30,587] [INFO] ===== Completeness check finished =====
[2024-01-24 14:30:30,587] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:30:30,587] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009901565.1_ASM990156v1_genomic.fna/markers.fasta)
[2024-01-24 14:30:30,588] [INFO] Task started: Blastn
[2024-01-24 14:30:30,588] [INFO] Running command: blastn -query GCF_009901565.1_ASM990156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c8cb111-8c0d-46b0-ad80-ac590749ac5b/dqc_reference/reference_markers_gtdb.fasta -out GCF_009901565.1_ASM990156v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:32,735] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:32,740] [INFO] Selected 10 target genomes.
[2024-01-24 14:30:32,741] [INFO] Target genome list was writen to GCF_009901565.1_ASM990156v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:30:32,751] [INFO] Task started: fastANI
[2024-01-24 14:30:32,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg523a2ac0-8144-4866-8065-5d8bac786fa3/GCF_009901565.1_ASM990156v1_genomic.fna.gz --refList GCF_009901565.1_ASM990156v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009901565.1_ASM990156v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:30:53,300] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:53,309] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:30:53,309] [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_009901565.1	s__Herbidospora solisilvae	100.0	2780	2781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	95.93	95.93	0.91	0.91	2	conclusive
GCF_001570565.1	s__Herbidospora yilanensis	94.5861	2229	2781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005233835.1	s__Herbidospora galbida	93.7235	2295	2781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570525.1	s__Herbidospora sakaeratensis	93.3687	2350	2781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570585.1	s__Herbidospora daliensis	92.9885	2368	2781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570605.1	s__Herbidospora cretacea	90.4467	2214	2781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002262875.1	s__Amycolatopsis antarctica	75.8683	465	2781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302295.1	s__Thauera sp017302295	74.9604	147	2781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853245.1	s__FEB-7 sp017853245	74.9527	54	2781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861105.1	s__VBCG01 sp016861105	74.8517	307	2781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:30:53,311] [INFO] GTDB search result was written to GCF_009901565.1_ASM990156v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:30:53,312] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:30:53,315] [INFO] DFAST_QC result json was written to GCF_009901565.1_ASM990156v1_genomic.fna/dqc_result.json
[2024-01-24 14:30:53,316] [INFO] DFAST_QC completed!
[2024-01-24 14:30:53,316] [INFO] Total running time: 0h2m35s