[2024-01-25 18:43:35,731] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:35,733] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:35,733] [INFO] DQC Reference Directory: /var/lib/cwl/stg5996a1f3-cd18-41a8-a2fc-5ac1355ae753/dqc_reference
[2024-01-25 18:43:36,896] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:36,897] [INFO] Task started: Prodigal
[2024-01-25 18:43:36,897] [INFO] Running command: gunzip -c /var/lib/cwl/stg34c74563-3ab3-402a-8485-b9f6527bbf1d/GCF_003633755.1_ASM363375v1_genomic.fna.gz | prodigal -d GCF_003633755.1_ASM363375v1_genomic.fna/cds.fna -a GCF_003633755.1_ASM363375v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:43:54,574] [INFO] Task succeeded: Prodigal
[2024-01-25 18:43:54,574] [INFO] Task started: HMMsearch
[2024-01-25 18:43:54,575] [INFO] Running command: hmmsearch --tblout GCF_003633755.1_ASM363375v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5996a1f3-cd18-41a8-a2fc-5ac1355ae753/dqc_reference/reference_markers.hmm GCF_003633755.1_ASM363375v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:43:54,870] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:43:54,871] [INFO] Found 6/6 markers.
[2024-01-25 18:43:54,926] [INFO] Query marker FASTA was written to GCF_003633755.1_ASM363375v1_genomic.fna/markers.fasta
[2024-01-25 18:43:54,926] [INFO] Task started: Blastn
[2024-01-25 18:43:54,926] [INFO] Running command: blastn -query GCF_003633755.1_ASM363375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5996a1f3-cd18-41a8-a2fc-5ac1355ae753/dqc_reference/reference_markers.fasta -out GCF_003633755.1_ASM363375v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:55,578] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:55,580] [INFO] Selected 8 target genomes.
[2024-01-25 18:43:55,580] [INFO] Target genome list was writen to GCF_003633755.1_ASM363375v1_genomic.fna/target_genomes.txt
[2024-01-25 18:43:55,584] [INFO] Task started: fastANI
[2024-01-25 18:43:55,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg34c74563-3ab3-402a-8485-b9f6527bbf1d/GCF_003633755.1_ASM363375v1_genomic.fna.gz --refList GCF_003633755.1_ASM363375v1_genomic.fna/target_genomes.txt --output GCF_003633755.1_ASM363375v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:44:07,663] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:07,663] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5996a1f3-cd18-41a8-a2fc-5ac1355ae753/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:44:07,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5996a1f3-cd18-41a8-a2fc-5ac1355ae753/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:44:07,670] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:44:07,670] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:44:07,670] [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
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	100.0	2377	2377	95	conclusive
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	77.1895	780	2377	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	77.135	906	2377	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	77.0803	935	2377	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	77.0483	746	2377	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	77.0396	779	2377	95	below_threshold
Patulibacter americanus	strain=DSM 16676	GCA_000420025.1	588672	588672	type	True	76.5484	651	2377	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	75.1191	443	2377	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:44:07,672] [INFO] DFAST Taxonomy check result was written to GCF_003633755.1_ASM363375v1_genomic.fna/tc_result.tsv
[2024-01-25 18:44:07,672] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:44:07,672] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:44:07,672] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5996a1f3-cd18-41a8-a2fc-5ac1355ae753/dqc_reference/checkm_data
[2024-01-25 18:44:07,673] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:44:07,737] [INFO] Task started: CheckM
[2024-01-25 18:44:07,737] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003633755.1_ASM363375v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003633755.1_ASM363375v1_genomic.fna/checkm_input GCF_003633755.1_ASM363375v1_genomic.fna/checkm_result
[2024-01-25 18:45:21,436] [INFO] Task succeeded: CheckM
[2024-01-25 18:45:21,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:45:21,463] [INFO] ===== Completeness check finished =====
[2024-01-25 18:45:21,463] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:45:21,464] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003633755.1_ASM363375v1_genomic.fna/markers.fasta)
[2024-01-25 18:45:21,464] [INFO] Task started: Blastn
[2024-01-25 18:45:21,464] [INFO] Running command: blastn -query GCF_003633755.1_ASM363375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5996a1f3-cd18-41a8-a2fc-5ac1355ae753/dqc_reference/reference_markers_gtdb.fasta -out GCF_003633755.1_ASM363375v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:22,577] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:22,580] [INFO] Selected 10 target genomes.
[2024-01-25 18:45:22,580] [INFO] Target genome list was writen to GCF_003633755.1_ASM363375v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:45:22,591] [INFO] Task started: fastANI
[2024-01-25 18:45:22,591] [INFO] Running command: fastANI --query /var/lib/cwl/stg34c74563-3ab3-402a-8485-b9f6527bbf1d/GCF_003633755.1_ASM363375v1_genomic.fna.gz --refList GCF_003633755.1_ASM363375v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003633755.1_ASM363375v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:45:39,644] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:39,651] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:45:39,651] [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_003633755.1	s__Solirubrobacter pauli	100.0	2377	2377	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Solirubrobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003344625.1	s__Solirubrobacter sp003344625	85.4593	1676	2377	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Solirubrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423665.1	s__Solirubrobacter soli	81.5893	1505	2377	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Solirubrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425945.1	s__Solirubrobacter sp000425945	80.4925	1188	2377	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Solirubrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268595.1	s__Conexibacter sp018268595	77.4016	660	2377	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806175.1	s__CADCVQ01 sp902806175	77.3496	573	2377	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__CADCVQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017084525.1	s__Baekduia sp017084525	77.2693	758	2377	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025265.1	s__Conexibacter woesei	77.0947	924	2377	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463765.1	s__SYBY01 sp016463765	77.0206	588	2377	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SYBY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000688095.1	s__Baekduia sp000688095	76.9649	903	2377	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:45:39,653] [INFO] GTDB search result was written to GCF_003633755.1_ASM363375v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:45:39,654] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:45:39,657] [INFO] DFAST_QC result json was written to GCF_003633755.1_ASM363375v1_genomic.fna/dqc_result.json
[2024-01-25 18:45:39,657] [INFO] DFAST_QC completed!
[2024-01-25 18:45:39,657] [INFO] Total running time: 0h2m4s