[2023-06-27 06:55:17,733] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:55:17,742] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:55:17,742] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c997e4e-0e86-4632-b194-609d9fcdccbe/dqc_reference
[2023-06-27 06:55:19,100] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:55:19,101] [INFO] Task started: Prodigal
[2023-06-27 06:55:19,101] [INFO] Running command: gunzip -c /var/lib/cwl/stg218a93ca-6bae-4e69-9dc4-ed5a4b8cb33f/GCA_002337405.1_ASM233740v1_genomic.fna.gz | prodigal -d GCA_002337405.1_ASM233740v1_genomic.fna/cds.fna -a GCA_002337405.1_ASM233740v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:55:29,867] [INFO] Task succeeded: Prodigal
[2023-06-27 06:55:29,868] [INFO] Task started: HMMsearch
[2023-06-27 06:55:29,868] [INFO] Running command: hmmsearch --tblout GCA_002337405.1_ASM233740v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c997e4e-0e86-4632-b194-609d9fcdccbe/dqc_reference/reference_markers.hmm GCA_002337405.1_ASM233740v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:55:30,174] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:55:30,175] [INFO] Found 6/6 markers.
[2023-06-27 06:55:30,209] [INFO] Query marker FASTA was written to GCA_002337405.1_ASM233740v1_genomic.fna/markers.fasta
[2023-06-27 06:55:30,209] [INFO] Task started: Blastn
[2023-06-27 06:55:30,209] [INFO] Running command: blastn -query GCA_002337405.1_ASM233740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c997e4e-0e86-4632-b194-609d9fcdccbe/dqc_reference/reference_markers.fasta -out GCA_002337405.1_ASM233740v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:55:30,955] [INFO] Task succeeded: Blastn
[2023-06-27 06:55:30,960] [INFO] Selected 24 target genomes.
[2023-06-27 06:55:30,961] [INFO] Target genome list was writen to GCA_002337405.1_ASM233740v1_genomic.fna/target_genomes.txt
[2023-06-27 06:55:30,971] [INFO] Task started: fastANI
[2023-06-27 06:55:30,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg218a93ca-6bae-4e69-9dc4-ed5a4b8cb33f/GCA_002337405.1_ASM233740v1_genomic.fna.gz --refList GCA_002337405.1_ASM233740v1_genomic.fna/target_genomes.txt --output GCA_002337405.1_ASM233740v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:55:46,424] [INFO] Task succeeded: fastANI
[2023-06-27 06:55:46,424] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c997e4e-0e86-4632-b194-609d9fcdccbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:55:46,424] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c997e4e-0e86-4632-b194-609d9fcdccbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:55:46,436] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 06:55:46,437] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 06:55:46,437] [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	83.7877	772	1094	95	below_threshold
Pusillimonas minor	strain=YC-7-48	GCA_014237865.1	2697024	2697024	type	True	77.7529	248	1094	95	below_threshold
Eoetvoesia caeni	strain=DSM 25520	GCA_003315175.1	645616	645616	type	True	77.7463	181	1094	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_013416545.1	645616	645616	type	True	77.7092	181	1094	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	77.6965	182	1094	95	below_threshold
Paracandidimonas soli	strain=DSM 100048	GCA_004342005.1	1917182	1917182	type	True	77.1647	104	1094	95	below_threshold
Paralcaligenes ureilyticus	strain=DSM 24591	GCA_004346225.1	627131	627131	type	True	77.0705	118	1094	95	below_threshold
Pusillimonas harenae	strain=DSM 25667	GCA_013416515.1	657015	657015	type	True	76.9598	131	1094	95	below_threshold
Castellaniella defragrans	strain=CCUG 39790	GCA_008801975.1	75697	75697	type	True	76.9365	89	1094	95	below_threshold
Pusillimonas harenae	strain=JCM 16917	GCA_004153685.1	657015	657015	type	True	76.8761	128	1094	95	below_threshold
Castellaniella defragrans	strain=DSM 12141	GCA_014203015.1	75697	75697	type	True	76.8028	90	1094	95	below_threshold
Advenella alkanexedens	strain=LAM0050	GCA_019132845.1	1481665	1481665	type	True	76.712	67	1094	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	76.6804	95	1094	95	below_threshold
Achromobacter spanius	strain=LMG 5911	GCA_902859605.1	217203	217203	suspected-type	True	76.5978	109	1094	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 06:55:46,439] [INFO] DFAST Taxonomy check result was written to GCA_002337405.1_ASM233740v1_genomic.fna/tc_result.tsv
[2023-06-27 06:55:46,439] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:55:46,439] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:55:46,440] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c997e4e-0e86-4632-b194-609d9fcdccbe/dqc_reference/checkm_data
[2023-06-27 06:55:46,441] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:55:46,481] [INFO] Task started: CheckM
[2023-06-27 06:55:46,481] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002337405.1_ASM233740v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002337405.1_ASM233740v1_genomic.fna/checkm_input GCA_002337405.1_ASM233740v1_genomic.fna/checkm_result
[2023-06-27 06:56:22,090] [INFO] Task succeeded: CheckM
[2023-06-27 06:56:22,091] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 06:56:22,111] [INFO] ===== Completeness check finished =====
[2023-06-27 06:56:22,112] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:56:22,112] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002337405.1_ASM233740v1_genomic.fna/markers.fasta)
[2023-06-27 06:56:22,113] [INFO] Task started: Blastn
[2023-06-27 06:56:22,113] [INFO] Running command: blastn -query GCA_002337405.1_ASM233740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c997e4e-0e86-4632-b194-609d9fcdccbe/dqc_reference/reference_markers_gtdb.fasta -out GCA_002337405.1_ASM233740v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:56:23,268] [INFO] Task succeeded: Blastn
[2023-06-27 06:56:23,272] [INFO] Selected 15 target genomes.
[2023-06-27 06:56:23,272] [INFO] Target genome list was writen to GCA_002337405.1_ASM233740v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:56:23,285] [INFO] Task started: fastANI
[2023-06-27 06:56:23,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg218a93ca-6bae-4e69-9dc4-ed5a4b8cb33f/GCA_002337405.1_ASM233740v1_genomic.fna.gz --refList GCA_002337405.1_ASM233740v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002337405.1_ASM233740v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:56:32,606] [INFO] Task succeeded: fastANI
[2023-06-27 06:56:32,621] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 06:56:32,621] [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
GCA_002384935.1	s__Pusillimonas_A sp002384935	99.9941	1072	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	98.90	98.23	0.90	0.79	9	conclusive
GCF_003576595.1	s__Pusillimonas_A maritima	83.7787	773	1094	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	83.2527	765	1094	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_002694155.1	s__Pusillimonas_A sp002694155	81.6797	293	1094	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_000209655.1	s__Pusillimonas_C sp000209655	79.2551	144	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014237865.1	s__Pusillimonas_A sp014237865	77.7657	247	1094	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	77.7339	227	1094	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_004022565.1	s__Pusillimonas_D thiosulfatoxidans	77.7173	129	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_D	95.0	97.98	97.65	0.84	0.81	3	-
GCF_002849655.1	s__Candidimonas_A sp002849655	77.6401	137	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346225.1	s__Paralcaligenes ureilyticus	77.0729	118	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paralcaligenes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012727555.1	s__JAAYGT01 sp012727555	76.9626	117	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAAYGT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004153685.1	s__Pusillimonas_C harenae	76.8761	128	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_C	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-27 06:56:32,623] [INFO] GTDB search result was written to GCA_002337405.1_ASM233740v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:56:32,624] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:56:32,627] [INFO] DFAST_QC result json was written to GCA_002337405.1_ASM233740v1_genomic.fna/dqc_result.json
[2023-06-27 06:56:32,628] [INFO] DFAST_QC completed!
[2023-06-27 06:56:32,628] [INFO] Total running time: 0h1m15s