[2023-06-19 02:25:54,448] [INFO] DFAST_QC pipeline started.
[2023-06-19 02:25:54,453] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 02:25:54,453] [INFO] DQC Reference Directory: /var/lib/cwl/stg320b591f-384e-4bb0-8c19-11c81539b90f/dqc_reference
[2023-06-19 02:25:55,952] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 02:25:55,953] [INFO] Task started: Prodigal
[2023-06-19 02:25:55,953] [INFO] Running command: gunzip -c /var/lib/cwl/stg43ac7311-9faa-492e-8ce8-949510cd56d8/GCA_014359555.1_ASM1435955v1_genomic.fna.gz | prodigal -d GCA_014359555.1_ASM1435955v1_genomic.fna/cds.fna -a GCA_014359555.1_ASM1435955v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 02:26:02,473] [INFO] Task succeeded: Prodigal
[2023-06-19 02:26:02,474] [INFO] Task started: HMMsearch
[2023-06-19 02:26:02,474] [INFO] Running command: hmmsearch --tblout GCA_014359555.1_ASM1435955v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg320b591f-384e-4bb0-8c19-11c81539b90f/dqc_reference/reference_markers.hmm GCA_014359555.1_ASM1435955v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 02:26:02,736] [INFO] Task succeeded: HMMsearch
[2023-06-19 02:26:02,737] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg43ac7311-9faa-492e-8ce8-949510cd56d8/GCA_014359555.1_ASM1435955v1_genomic.fna.gz]
[2023-06-19 02:26:02,766] [INFO] Query marker FASTA was written to GCA_014359555.1_ASM1435955v1_genomic.fna/markers.fasta
[2023-06-19 02:26:02,767] [INFO] Task started: Blastn
[2023-06-19 02:26:02,767] [INFO] Running command: blastn -query GCA_014359555.1_ASM1435955v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg320b591f-384e-4bb0-8c19-11c81539b90f/dqc_reference/reference_markers.fasta -out GCA_014359555.1_ASM1435955v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:26:03,473] [INFO] Task succeeded: Blastn
[2023-06-19 02:26:03,478] [INFO] Selected 25 target genomes.
[2023-06-19 02:26:03,478] [INFO] Target genome list was writen to GCA_014359555.1_ASM1435955v1_genomic.fna/target_genomes.txt
[2023-06-19 02:26:03,485] [INFO] Task started: fastANI
[2023-06-19 02:26:03,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg43ac7311-9faa-492e-8ce8-949510cd56d8/GCA_014359555.1_ASM1435955v1_genomic.fna.gz --refList GCA_014359555.1_ASM1435955v1_genomic.fna/target_genomes.txt --output GCA_014359555.1_ASM1435955v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 02:26:17,238] [INFO] Task succeeded: fastANI
[2023-06-19 02:26:17,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg320b591f-384e-4bb0-8c19-11c81539b90f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 02:26:17,240] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg320b591f-384e-4bb0-8c19-11c81539b90f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 02:26:17,253] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 02:26:17,253] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 02:26:17,253] [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
Pusillimonas maritima	strain=17-4A	GCA_003576595.1	2026239	2026239	type	True	83.1775	345	464	95	below_threshold
Pusillimonas minor	strain=YC-7-48	GCA_014237865.1	2697024	2697024	type	True	78.0203	121	464	95	below_threshold
Pusillimonas noertemannii	strain=DSM 10065	GCA_003545825.1	305977	305977	type	True	77.3133	67	464	95	below_threshold
Pusillimonas noertemannii	strain=DSM 10065	GCA_003096595.1	305977	305977	type	True	77.2923	67	464	95	below_threshold
Pusillimonas ginsengisoli	strain=KCTC 22046	GCA_004153455.1	453575	453575	type	True	77.2397	51	464	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_013416545.1	645616	645616	type	True	77.069	79	464	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	77.0361	78	464	95	below_threshold
Eoetvoesia caeni	strain=DSM 25520	GCA_003315175.1	645616	645616	type	True	76.95	79	464	95	below_threshold
Parapusillimonas granuli	strain=DSM 18079	GCA_014202705.1	380911	380911	type	True	76.6132	67	464	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	76.5319	67	464	95	below_threshold
Paracandidimonas soli	strain=DSM 100048	GCA_004342005.1	1917182	1917182	type	True	76.1913	51	464	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 02:26:17,255] [INFO] DFAST Taxonomy check result was written to GCA_014359555.1_ASM1435955v1_genomic.fna/tc_result.tsv
[2023-06-19 02:26:17,256] [INFO] ===== Taxonomy check completed =====
[2023-06-19 02:26:17,256] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 02:26:17,256] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg320b591f-384e-4bb0-8c19-11c81539b90f/dqc_reference/checkm_data
[2023-06-19 02:26:17,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 02:26:17,287] [INFO] Task started: CheckM
[2023-06-19 02:26:17,287] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014359555.1_ASM1435955v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014359555.1_ASM1435955v1_genomic.fna/checkm_input GCA_014359555.1_ASM1435955v1_genomic.fna/checkm_result
[2023-06-19 02:26:42,984] [INFO] Task succeeded: CheckM
[2023-06-19 02:26:42,985] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.94%
Contamintation: 5.15%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2023-06-19 02:26:43,017] [INFO] ===== Completeness check finished =====
[2023-06-19 02:26:43,017] [INFO] ===== Start GTDB Search =====
[2023-06-19 02:26:43,017] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014359555.1_ASM1435955v1_genomic.fna/markers.fasta)
[2023-06-19 02:26:43,018] [INFO] Task started: Blastn
[2023-06-19 02:26:43,018] [INFO] Running command: blastn -query GCA_014359555.1_ASM1435955v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg320b591f-384e-4bb0-8c19-11c81539b90f/dqc_reference/reference_markers_gtdb.fasta -out GCA_014359555.1_ASM1435955v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:26:44,180] [INFO] Task succeeded: Blastn
[2023-06-19 02:26:44,186] [INFO] Selected 16 target genomes.
[2023-06-19 02:26:44,186] [INFO] Target genome list was writen to GCA_014359555.1_ASM1435955v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 02:26:44,197] [INFO] Task started: fastANI
[2023-06-19 02:26:44,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg43ac7311-9faa-492e-8ce8-949510cd56d8/GCA_014359555.1_ASM1435955v1_genomic.fna.gz --refList GCA_014359555.1_ASM1435955v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014359555.1_ASM1435955v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 02:26:54,110] [INFO] Task succeeded: fastANI
[2023-06-19 02:26:54,129] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 02:26:54,130] [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_003576595.1	s__Pusillimonas_A maritima	83.1956	344	464	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	96.55	95.88	0.88	0.85	8	-
GCF_011388195.1	s__Pusillimonas_A sp011388195	82.5131	359	464	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002384935.1	s__Pusillimonas_A sp002384935	81.9733	303	464	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	98.90	98.23	0.90	0.79	9	-
GCA_002694155.1	s__Pusillimonas_A sp002694155	81.7947	183	464	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014237865.1	s__Pusillimonas_A sp014237865	78.0203	121	464	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002236805.1	s__Pusillimonas_A sp002236805	77.3872	115	464	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	98.07	98.07	0.83	0.83	2	-
GCF_004153455.1	s__Pusillimonas_B ginsengisoli	77.2397	51	464	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000209655.1	s__Pusillimonas_C sp000209655	77.0413	70	464	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012744285.1	s__Pusillimonas_A sp012744285	76.8789	77	464	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339425.1	s__Candidimonas_A sp004339425	76.7984	63	464	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 02:26:54,132] [INFO] GTDB search result was written to GCA_014359555.1_ASM1435955v1_genomic.fna/result_gtdb.tsv
[2023-06-19 02:26:54,133] [INFO] ===== GTDB Search completed =====
[2023-06-19 02:26:54,138] [INFO] DFAST_QC result json was written to GCA_014359555.1_ASM1435955v1_genomic.fna/dqc_result.json
[2023-06-19 02:26:54,138] [INFO] DFAST_QC completed!
[2023-06-19 02:26:54,138] [INFO] Total running time: 0h0m60s