[2023-06-30 00:55:34,594] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:55:34,603] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:55:34,603] [INFO] DQC Reference Directory: /var/lib/cwl/stgb56fdf8c-2204-479d-bc09-cdad60b6653c/dqc_reference
[2023-06-30 00:55:35,978] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:55:35,978] [INFO] Task started: Prodigal
[2023-06-30 00:55:35,979] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ab2e505-751b-46b9-a228-22a3e9cd8968/GCA_024643255.1_ASM2464325v1_genomic.fna.gz | prodigal -d GCA_024643255.1_ASM2464325v1_genomic.fna/cds.fna -a GCA_024643255.1_ASM2464325v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:55:46,727] [INFO] Task succeeded: Prodigal
[2023-06-30 00:55:46,727] [INFO] Task started: HMMsearch
[2023-06-30 00:55:46,727] [INFO] Running command: hmmsearch --tblout GCA_024643255.1_ASM2464325v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb56fdf8c-2204-479d-bc09-cdad60b6653c/dqc_reference/reference_markers.hmm GCA_024643255.1_ASM2464325v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:55:47,018] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:55:47,020] [INFO] Found 6/6 markers.
[2023-06-30 00:55:47,055] [INFO] Query marker FASTA was written to GCA_024643255.1_ASM2464325v1_genomic.fna/markers.fasta
[2023-06-30 00:55:47,056] [INFO] Task started: Blastn
[2023-06-30 00:55:47,056] [INFO] Running command: blastn -query GCA_024643255.1_ASM2464325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb56fdf8c-2204-479d-bc09-cdad60b6653c/dqc_reference/reference_markers.fasta -out GCA_024643255.1_ASM2464325v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:55:47,955] [INFO] Task succeeded: Blastn
[2023-06-30 00:55:47,960] [INFO] Selected 15 target genomes.
[2023-06-30 00:55:47,960] [INFO] Target genome list was writen to GCA_024643255.1_ASM2464325v1_genomic.fna/target_genomes.txt
[2023-06-30 00:55:47,962] [INFO] Task started: fastANI
[2023-06-30 00:55:47,963] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ab2e505-751b-46b9-a228-22a3e9cd8968/GCA_024643255.1_ASM2464325v1_genomic.fna.gz --refList GCA_024643255.1_ASM2464325v1_genomic.fna/target_genomes.txt --output GCA_024643255.1_ASM2464325v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:56:00,024] [INFO] Task succeeded: fastANI
[2023-06-30 00:56:00,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb56fdf8c-2204-479d-bc09-cdad60b6653c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:56:00,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb56fdf8c-2204-479d-bc09-cdad60b6653c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:56:00,039] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:56:00,040] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 00:56:00,040] [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
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	78.3979	504	1140	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	78.3655	427	1140	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	77.8578	431	1140	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	77.6259	402	1140	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.6345	186	1140	95	below_threshold
Phycicoccus endophyticus	strain=IP6SC6	GCA_011326735.1	1690220	1690220	type	True	75.4615	109	1140	95	below_threshold
Phycicoccus endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	75.4419	111	1140	95	below_threshold
Demequina salsinemoris	strain=NBRC 105323	GCA_000974805.1	577470	577470	type	True	75.3021	78	1140	95	below_threshold
Catellatospora chokoriensis	strain=2-25(1)	GCA_011297315.1	310353	310353	type	True	75.2456	176	1140	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	75.2397	119	1140	95	below_threshold
Saccharopolyspora rhizosphaerae	strain=H219	GCA_003931915.1	2492662	2492662	type	True	75.1954	109	1140	95	below_threshold
Klenkia marina	strain=DSM 45722	GCA_900101025.1	1960309	1960309	type	True	75.1835	138	1140	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	75.0274	238	1140	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_000421645.1	182270	182270	type	True	74.9306	73	1140	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_001463825.1	182270	182270	type	True	74.8962	73	1140	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 00:56:00,042] [INFO] DFAST Taxonomy check result was written to GCA_024643255.1_ASM2464325v1_genomic.fna/tc_result.tsv
[2023-06-30 00:56:00,043] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:56:00,043] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:56:00,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb56fdf8c-2204-479d-bc09-cdad60b6653c/dqc_reference/checkm_data
[2023-06-30 00:56:00,045] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:56:00,089] [INFO] Task started: CheckM
[2023-06-30 00:56:00,089] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024643255.1_ASM2464325v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024643255.1_ASM2464325v1_genomic.fna/checkm_input GCA_024643255.1_ASM2464325v1_genomic.fna/checkm_result
[2023-06-30 00:57:04,324] [INFO] Task succeeded: CheckM
[2023-06-30 00:57:04,325] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 00:57:04,347] [INFO] ===== Completeness check finished =====
[2023-06-30 00:57:04,347] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:57:04,348] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024643255.1_ASM2464325v1_genomic.fna/markers.fasta)
[2023-06-30 00:57:04,348] [INFO] Task started: Blastn
[2023-06-30 00:57:04,348] [INFO] Running command: blastn -query GCA_024643255.1_ASM2464325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb56fdf8c-2204-479d-bc09-cdad60b6653c/dqc_reference/reference_markers_gtdb.fasta -out GCA_024643255.1_ASM2464325v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:57:05,624] [INFO] Task succeeded: Blastn
[2023-06-30 00:57:05,629] [INFO] Selected 14 target genomes.
[2023-06-30 00:57:05,630] [INFO] Target genome list was writen to GCA_024643255.1_ASM2464325v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:57:05,630] [INFO] Task started: fastANI
[2023-06-30 00:57:05,631] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ab2e505-751b-46b9-a228-22a3e9cd8968/GCA_024643255.1_ASM2464325v1_genomic.fna.gz --refList GCA_024643255.1_ASM2464325v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024643255.1_ASM2464325v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:57:14,204] [INFO] Task succeeded: fastANI
[2023-06-30 00:57:14,228] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 00:57:14,228] [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_013002175.1	s__Ilumatobacter_A sp013002175	78.9777	421	1140	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000348785.1	s__Ilumatobacter_A coccineus	78.4209	501	1140	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000350145.1	s__Ilumatobacter_A nonamiensis	78.3928	424	1140	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007122945.1	s__SKSP01 sp007122945	78.157	346	1140	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	99.05	99.05	0.83	0.83	2	-
GCA_007693335.1	s__SKSP01 sp007693335	78.0732	343	1140	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213745.1	s__JABSQH01 sp013213745	77.9916	383	1140	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JABSQH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009704985.1	s__VFMC01 sp009704985	77.8939	375	1140	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__VFMC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666235.1	s__Ilumatobacter_A sp018666235	77.7176	278	1140	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	99.79	99.78	0.94	0.93	4	-
GCA_010024485.1	s__Casp-actino5 sp010024485	77.6507	114	1140	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	98.53	98.53	0.77	0.77	2	-
GCF_003426815.1	s__Desertimonas flava	77.618	403	1140	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Desertimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_015767405.1	s__Sva-07 sp015767405	77.5732	257	1140	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Sva-07	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013815505.1	s__JACDHN01 sp013815505	77.3883	178	1140	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JACDHN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005787035.1	s__Casp-actino8 sp005787035	76.1858	119	1140	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003155135.1	s__Bog-515 sp003155135	76.1158	107	1140	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-515	95.0	99.89	99.76	0.97	0.95	17	-
--------------------------------------------------------------------------------
[2023-06-30 00:57:14,231] [INFO] GTDB search result was written to GCA_024643255.1_ASM2464325v1_genomic.fna/result_gtdb.tsv
[2023-06-30 00:57:14,231] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:57:14,235] [INFO] DFAST_QC result json was written to GCA_024643255.1_ASM2464325v1_genomic.fna/dqc_result.json
[2023-06-30 00:57:14,235] [INFO] DFAST_QC completed!
[2023-06-30 00:57:14,236] [INFO] Total running time: 0h1m40s