[2024-01-25 17:51:05,460] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:05,461] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:05,461] [INFO] DQC Reference Directory: /var/lib/cwl/stg48fe2ef8-ddb9-421f-84fd-b41fdee0d08c/dqc_reference
[2024-01-25 17:51:06,566] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:06,566] [INFO] Task started: Prodigal
[2024-01-25 17:51:06,567] [INFO] Running command: gunzip -c /var/lib/cwl/stg1290c695-edff-4bdb-a6df-0c13cddcd7a1/GCF_030410375.1_ASM3041037v1_genomic.fna.gz | prodigal -d GCF_030410375.1_ASM3041037v1_genomic.fna/cds.fna -a GCF_030410375.1_ASM3041037v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:51:15,107] [INFO] Task succeeded: Prodigal
[2024-01-25 17:51:15,108] [INFO] Task started: HMMsearch
[2024-01-25 17:51:15,108] [INFO] Running command: hmmsearch --tblout GCF_030410375.1_ASM3041037v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48fe2ef8-ddb9-421f-84fd-b41fdee0d08c/dqc_reference/reference_markers.hmm GCF_030410375.1_ASM3041037v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:51:15,319] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:51:15,320] [INFO] Found 6/6 markers.
[2024-01-25 17:51:15,348] [INFO] Query marker FASTA was written to GCF_030410375.1_ASM3041037v1_genomic.fna/markers.fasta
[2024-01-25 17:51:15,348] [INFO] Task started: Blastn
[2024-01-25 17:51:15,348] [INFO] Running command: blastn -query GCF_030410375.1_ASM3041037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48fe2ef8-ddb9-421f-84fd-b41fdee0d08c/dqc_reference/reference_markers.fasta -out GCF_030410375.1_ASM3041037v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:16,012] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:16,014] [INFO] Selected 28 target genomes.
[2024-01-25 17:51:16,015] [INFO] Target genome list was writen to GCF_030410375.1_ASM3041037v1_genomic.fna/target_genomes.txt
[2024-01-25 17:51:16,029] [INFO] Task started: fastANI
[2024-01-25 17:51:16,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg1290c695-edff-4bdb-a6df-0c13cddcd7a1/GCF_030410375.1_ASM3041037v1_genomic.fna.gz --refList GCF_030410375.1_ASM3041037v1_genomic.fna/target_genomes.txt --output GCF_030410375.1_ASM3041037v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:34,430] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:34,430] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48fe2ef8-ddb9-421f-84fd-b41fdee0d08c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:34,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48fe2ef8-ddb9-421f-84fd-b41fdee0d08c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:34,439] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:51:34,440] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:51:34,440] [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
Zwartia hollandica	strain=LF4-65	GCA_019923725.1	324606	324606	type	True	78.2405	171	1053	95	below_threshold
Sheuella amnicola	strain=NBD-18	GCA_010499255.1	2707330	2707330	type	True	77.9792	133	1053	95	below_threshold
Orrella marina	strain=HZ20	GCA_003058465.1	2163011	2163011	type	True	77.6818	55	1053	95	below_threshold
Jezberella montanilacus	strain=MWH-P2sevCIIIb	GCA_003003055.1	323426	323426	type	True	77.6676	88	1053	95	below_threshold
Achromobacter piechaudii	strain=LMG 1873	GCA_902859685.1	72556	72556	type	True	77.1231	63	1053	95	below_threshold
Achromobacter aestuarii	strain=KS-M25	GCA_009866805.1	2511204	2511204	type	True	76.9067	70	1053	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	76.8098	63	1053	95	below_threshold
Bordetella holmesii	strain=NCTC12912	GCA_900445775.1	35814	35814	type	True	76.7313	69	1053	95	below_threshold
Bordetella holmesii	strain=FDAARGOS_1539	GCA_020735985.1	35814	35814	type	True	76.7313	69	1053	95	below_threshold
Achromobacter piechaudii	strain=NBRC 102461	GCA_001571245.1	72556	72556	type	True	76.7004	62	1053	95	below_threshold
Pusillimonas harenae	strain=DSM 25667	GCA_013416515.1	657015	657015	type	True	76.6892	51	1053	95	below_threshold
Pusillimonas ginsengisoli	strain=KCTC 22046	GCA_004153455.1	453575	453575	type	True	76.4444	57	1053	95	below_threshold
Corticimicrobacter populi	strain=3d-2-2	GCA_003123725.1	2175229	2175229	type	True	76.3851	57	1053	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:34,442] [INFO] DFAST Taxonomy check result was written to GCF_030410375.1_ASM3041037v1_genomic.fna/tc_result.tsv
[2024-01-25 17:51:34,442] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:34,442] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:34,442] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48fe2ef8-ddb9-421f-84fd-b41fdee0d08c/dqc_reference/checkm_data
[2024-01-25 17:51:34,443] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:34,478] [INFO] Task started: CheckM
[2024-01-25 17:51:34,478] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030410375.1_ASM3041037v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030410375.1_ASM3041037v1_genomic.fna/checkm_input GCF_030410375.1_ASM3041037v1_genomic.fna/checkm_result
[2024-01-25 17:52:04,093] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:04,094] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:04,117] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:04,117] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:04,118] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030410375.1_ASM3041037v1_genomic.fna/markers.fasta)
[2024-01-25 17:52:04,119] [INFO] Task started: Blastn
[2024-01-25 17:52:04,119] [INFO] Running command: blastn -query GCF_030410375.1_ASM3041037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48fe2ef8-ddb9-421f-84fd-b41fdee0d08c/dqc_reference/reference_markers_gtdb.fasta -out GCF_030410375.1_ASM3041037v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:05,423] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:05,427] [INFO] Selected 29 target genomes.
[2024-01-25 17:52:05,427] [INFO] Target genome list was writen to GCF_030410375.1_ASM3041037v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:05,452] [INFO] Task started: fastANI
[2024-01-25 17:52:05,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg1290c695-edff-4bdb-a6df-0c13cddcd7a1/GCF_030410375.1_ASM3041037v1_genomic.fna.gz --refList GCF_030410375.1_ASM3041037v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030410375.1_ASM3041037v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:52:25,227] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:25,238] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:52:25,238] [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_002292845.1	s__NBD-18 sp002292845	79.292	350	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010499255.1	s__NBD-18 sp003507735	77.9792	133	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.47	99.47	0.95	0.95	2	-
GCA_003003055.1	s__NBD-18 sp003003055	77.6676	88	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.26	99.12	0.90	0.84	10	-
GCA_903821335.1	s__NBD-18 sp903821335	77.4852	130	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.43	99.29	0.86	0.84	5	-
GCA_903958565.1	s__NBD-18 sp903958565	77.4005	160	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.16	98.92	0.86	0.85	5	-
GCA_013205565.1	s__NBD-18 sp013205565	77.3028	128	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903929925.1	s__NBD-18 sp903929925	77.1395	135	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903847325.1	s__NBD-18 sp903847325	77.1175	145	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859705.1	s__Achromobacter deleyi	77.025	64	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.99	97.40	0.95	0.91	5	-
GCA_903903735.1	s__NBD-18 sp903903735	76.9809	115	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900445835.1	s__Bordetella avium	76.9228	64	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.81	99.47	0.98	0.95	26	-
GCA_903894155.1	s__NBD-18 sp903894155	76.8965	99	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.08	98.85	0.85	0.83	4	-
GCA_903932425.1	s__NBD-18 sp903932425	76.8166	117	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903924715.1	s__NBD-18 sp903924715	76.7803	93	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000612485.1	s__Bordetella holmesii	76.6353	72	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.96	99.94	1.00	0.99	92	-
GCF_003123725.1	s__Corticimicrobacter populi	76.4185	56	1053	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Corticimicrobacter	95.0	96.49	96.49	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:52:25,240] [INFO] GTDB search result was written to GCF_030410375.1_ASM3041037v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:52:25,241] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:52:25,246] [INFO] DFAST_QC result json was written to GCF_030410375.1_ASM3041037v1_genomic.fna/dqc_result.json
[2024-01-25 17:52:25,246] [INFO] DFAST_QC completed!
[2024-01-25 17:52:25,246] [INFO] Total running time: 0h1m20s