[2024-01-24 12:30:05,380] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:05,383] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:05,383] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfee93a1-480c-4efd-84f9-dd3f85accaf2/dqc_reference
[2024-01-24 12:30:07,247] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:07,248] [INFO] Task started: Prodigal
[2024-01-24 12:30:07,248] [INFO] Running command: gunzip -c /var/lib/cwl/stg602e34f5-ba6c-48f6-a0df-4d298ff5c718/GCF_013870575.1_ASM1387057v1_genomic.fna.gz | prodigal -d GCF_013870575.1_ASM1387057v1_genomic.fna/cds.fna -a GCF_013870575.1_ASM1387057v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:19,622] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:19,623] [INFO] Task started: HMMsearch
[2024-01-24 12:30:19,623] [INFO] Running command: hmmsearch --tblout GCF_013870575.1_ASM1387057v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfee93a1-480c-4efd-84f9-dd3f85accaf2/dqc_reference/reference_markers.hmm GCF_013870575.1_ASM1387057v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:19,921] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:19,922] [INFO] Found 6/6 markers.
[2024-01-24 12:30:19,985] [INFO] Query marker FASTA was written to GCF_013870575.1_ASM1387057v1_genomic.fna/markers.fasta
[2024-01-24 12:30:19,985] [INFO] Task started: Blastn
[2024-01-24 12:30:19,985] [INFO] Running command: blastn -query GCF_013870575.1_ASM1387057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfee93a1-480c-4efd-84f9-dd3f85accaf2/dqc_reference/reference_markers.fasta -out GCF_013870575.1_ASM1387057v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:21,224] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:21,226] [INFO] Selected 9 target genomes.
[2024-01-24 12:30:21,226] [INFO] Target genome list was writen to GCF_013870575.1_ASM1387057v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:21,229] [INFO] Task started: fastANI
[2024-01-24 12:30:21,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg602e34f5-ba6c-48f6-a0df-4d298ff5c718/GCF_013870575.1_ASM1387057v1_genomic.fna.gz --refList GCF_013870575.1_ASM1387057v1_genomic.fna/target_genomes.txt --output GCF_013870575.1_ASM1387057v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:34,368] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:34,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfee93a1-480c-4efd-84f9-dd3f85accaf2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:34,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfee93a1-480c-4efd-84f9-dd3f85accaf2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:34,376] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:34,376] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:34,376] [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
Pseudonocardia pini	strain=CAP47R	GCA_013870575.1	2758030	2758030	type	True	100.0	1358	1389	95	conclusive
Pseudonocardia oroxyli	strain=CGMCC 4.3143	GCA_900102195.1	366584	366584	type	True	84.8462	880	1389	95	below_threshold
Pseudonocardia terrae	strain=RS11V-5	GCA_021343995.1	2905831	2905831	type	True	83.7597	894	1389	95	below_threshold
Pseudonocardia kujensis	strain=KCTC 29062	GCA_021283305.1	1128675	1128675	type	True	83.5694	904	1389	95	below_threshold
Pseudonocardia dioxanivorans	strain=CB1190	GCA_000196675.2	240495	240495	type	True	79.7385	684	1389	95	below_threshold
Pseudonocardia oceani	strain=KRD185	GCA_019263585.2	2792013	2792013	type	True	79.5688	729	1389	95	below_threshold
Pseudonocardia endophytica	strain=DSM 44969	GCA_004339565.1	401976	401976	type	True	79.3649	708	1389	95	below_threshold
Pseudonocardia parietis	strain=DSM 45256	GCA_017876315.1	570936	570936	type	True	79.285	690	1389	95	below_threshold
Lentzea nigeriaca	strain=DSM 45680	GCA_016907955.1	1128665	1128665	type	True	77.6815	421	1389	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:34,377] [INFO] DFAST Taxonomy check result was written to GCF_013870575.1_ASM1387057v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:34,378] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:34,378] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:34,378] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfee93a1-480c-4efd-84f9-dd3f85accaf2/dqc_reference/checkm_data
[2024-01-24 12:30:34,379] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:34,436] [INFO] Task started: CheckM
[2024-01-24 12:30:34,436] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013870575.1_ASM1387057v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013870575.1_ASM1387057v1_genomic.fna/checkm_input GCF_013870575.1_ASM1387057v1_genomic.fna/checkm_result
[2024-01-24 12:31:15,431] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:15,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:15,447] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:15,447] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:15,447] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013870575.1_ASM1387057v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:15,448] [INFO] Task started: Blastn
[2024-01-24 12:31:15,448] [INFO] Running command: blastn -query GCF_013870575.1_ASM1387057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfee93a1-480c-4efd-84f9-dd3f85accaf2/dqc_reference/reference_markers_gtdb.fasta -out GCF_013870575.1_ASM1387057v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:17,423] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:17,425] [INFO] Selected 19 target genomes.
[2024-01-24 12:31:17,425] [INFO] Target genome list was writen to GCF_013870575.1_ASM1387057v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:17,440] [INFO] Task started: fastANI
[2024-01-24 12:31:17,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg602e34f5-ba6c-48f6-a0df-4d298ff5c718/GCF_013870575.1_ASM1387057v1_genomic.fna.gz --refList GCF_013870575.1_ASM1387057v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013870575.1_ASM1387057v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:42,125] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:42,137] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:31:42,137] [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_900102195.1	s__Pseudonocardia oroxyli	84.885	877	1389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717175.1	s__Pseudonocardia autotrophica_A	83.8427	937	1389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263595.1	s__Pseudonocardia sp019263595	80.1066	659	1389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217185.1	s__Pseudonocardia sediminis	80.081	676	1389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911875.1	s__Pseudonocardia bannensis	79.9102	598	1389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002583555.1	s__Pseudonocardia sp002583555	79.8962	667	1389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989085.1	s__Pseudonocardia sulfidoxydans	79.8891	667	1389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539565.1	s__Pseudonocardia hydrocarbonoxydans	79.7848	659	1389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196675.1	s__Pseudonocardia dioxanivorans	79.7654	680	1389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	98.76	98.74	0.91	0.91	3	-
GCA_019263705.1	s__Pseudonocardia sp019263705	79.729	705	1389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.99	99.99	1.00	1.00	2	-
GCA_001725415.1	s__Pseudonocardia sp001725415	79.7123	680	1389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	97.90	95.81	0.91	0.83	3	-
GCA_019263585.1	s__Pseudonocardia sp019263585	79.5958	725	1389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.90	99.65	0.98	0.94	5	-
GCF_014267175.1	s__Pseudonocardia sp014267175	79.5369	639	1389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339565.1	s__Pseudonocardia endophytica	79.3681	708	1389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876315.1	s__Pseudonocardia parietis	79.3145	685	1389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911925.1	s__Pseudonocardia xinjiangensis	79.2303	641	1389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907955.1	s__Lentzea nigeriaca	77.6595	424	1389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003269295.1	s__Lentzea atacamensis	77.6256	408	1389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	98.63	98.63	0.90	0.90	2	-
GCF_000974445.1	s__Lentzea aerocolonigenes	77.5521	454	1389	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:42,139] [INFO] GTDB search result was written to GCF_013870575.1_ASM1387057v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:42,139] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:42,144] [INFO] DFAST_QC result json was written to GCF_013870575.1_ASM1387057v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:42,144] [INFO] DFAST_QC completed!
[2024-01-24 12:31:42,144] [INFO] Total running time: 0h1m37s