[2023-06-29 20:02:39,235] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:02:39,239] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:02:39,239] [INFO] DQC Reference Directory: /var/lib/cwl/stg225683cc-126a-477e-9d29-b97e762b40e5/dqc_reference
[2023-06-29 20:02:40,742] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:02:40,743] [INFO] Task started: Prodigal
[2023-06-29 20:02:40,743] [INFO] Running command: gunzip -c /var/lib/cwl/stg094a00a2-9671-4fd3-9ab3-0510e07a8450/GCA_021780475.1_ASM2178047v1_genomic.fna.gz | prodigal -d GCA_021780475.1_ASM2178047v1_genomic.fna/cds.fna -a GCA_021780475.1_ASM2178047v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:02:49,633] [INFO] Task succeeded: Prodigal
[2023-06-29 20:02:49,633] [INFO] Task started: HMMsearch
[2023-06-29 20:02:49,634] [INFO] Running command: hmmsearch --tblout GCA_021780475.1_ASM2178047v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg225683cc-126a-477e-9d29-b97e762b40e5/dqc_reference/reference_markers.hmm GCA_021780475.1_ASM2178047v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:02:49,909] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:02:49,910] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg094a00a2-9671-4fd3-9ab3-0510e07a8450/GCA_021780475.1_ASM2178047v1_genomic.fna.gz]
[2023-06-29 20:02:49,941] [INFO] Query marker FASTA was written to GCA_021780475.1_ASM2178047v1_genomic.fna/markers.fasta
[2023-06-29 20:02:49,942] [INFO] Task started: Blastn
[2023-06-29 20:02:49,942] [INFO] Running command: blastn -query GCA_021780475.1_ASM2178047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg225683cc-126a-477e-9d29-b97e762b40e5/dqc_reference/reference_markers.fasta -out GCA_021780475.1_ASM2178047v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:02:50,752] [INFO] Task succeeded: Blastn
[2023-06-29 20:02:50,756] [INFO] Selected 27 target genomes.
[2023-06-29 20:02:50,756] [INFO] Target genome list was writen to GCA_021780475.1_ASM2178047v1_genomic.fna/target_genomes.txt
[2023-06-29 20:02:50,759] [INFO] Task started: fastANI
[2023-06-29 20:02:50,759] [INFO] Running command: fastANI --query /var/lib/cwl/stg094a00a2-9671-4fd3-9ab3-0510e07a8450/GCA_021780475.1_ASM2178047v1_genomic.fna.gz --refList GCA_021780475.1_ASM2178047v1_genomic.fna/target_genomes.txt --output GCA_021780475.1_ASM2178047v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:03:15,937] [INFO] Task succeeded: fastANI
[2023-06-29 20:03:15,938] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg225683cc-126a-477e-9d29-b97e762b40e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:03:15,938] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg225683cc-126a-477e-9d29-b97e762b40e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:03:15,961] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:03:15,961] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 20:03:15,962] [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
Povalibacter uvarum	strain=DSM 26723	GCA_014202975.1	732238	732238	type	True	76.9395	147	970	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	76.7042	123	970	95	below_threshold
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	76.5398	154	970	95	below_threshold
Thioalkalivibrio paradoxus	strain=ARh 1	GCA_000227685.3	108010	108010	type	True	76.4862	75	970	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	76.462	71	970	95	below_threshold
Rhodanobacter panaciterrae	strain=KCTC 22232	GCA_014651895.1	490572	490572	type	True	76.4557	67	970	95	below_threshold
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	76.4526	147	970	95	below_threshold
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	76.4329	134	970	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	76.4183	135	970	95	below_threshold
Thioalkalivibrio nitratireducens	strain=DSM 14787	GCA_000321415.2	186931	186931	type	True	76.2865	79	970	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	76.286	93	970	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	76.1432	57	970	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	76.1133	58	970	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	76.0969	125	970	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.0336	182	970	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	75.9765	130	970	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	75.9507	187	970	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	75.9025	97	970	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	75.6175	117	970	95	below_threshold
Burkholderia catarinensis	strain=89	GCA_001883705.2	1108140	1108140	type	True	75.5981	187	970	95	below_threshold
Burkholderia stabilis	strain=ATCC BAA-67	GCA_001742165.1	95485	95485	type	True	75.4349	173	970	95	below_threshold
Massilia glaciei	strain=B448-2	GCA_003011895.2	1524097	1524097	type	True	75.4282	117	970	95	below_threshold
Burkholderia cepacia	strain=NBRC 14074	GCA_001528845.1	292	292	type	True	75.3456	189	970	95	below_threshold
Cupriavidus plantarum	strain=LMG 26296	GCA_905397285.1	942865	942865	type	True	75.2912	117	970	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 20:03:15,964] [INFO] DFAST Taxonomy check result was written to GCA_021780475.1_ASM2178047v1_genomic.fna/tc_result.tsv
[2023-06-29 20:03:15,964] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:03:15,964] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:03:15,965] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg225683cc-126a-477e-9d29-b97e762b40e5/dqc_reference/checkm_data
[2023-06-29 20:03:15,965] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:03:16,004] [INFO] Task started: CheckM
[2023-06-29 20:03:16,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021780475.1_ASM2178047v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021780475.1_ASM2178047v1_genomic.fna/checkm_input GCA_021780475.1_ASM2178047v1_genomic.fna/checkm_result
[2023-06-29 20:03:46,625] [INFO] Task succeeded: CheckM
[2023-06-29 20:03:46,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:03:46,649] [INFO] ===== Completeness check finished =====
[2023-06-29 20:03:46,650] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:03:46,650] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021780475.1_ASM2178047v1_genomic.fna/markers.fasta)
[2023-06-29 20:03:46,650] [INFO] Task started: Blastn
[2023-06-29 20:03:46,651] [INFO] Running command: blastn -query GCA_021780475.1_ASM2178047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg225683cc-126a-477e-9d29-b97e762b40e5/dqc_reference/reference_markers_gtdb.fasta -out GCA_021780475.1_ASM2178047v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:03:47,960] [INFO] Task succeeded: Blastn
[2023-06-29 20:03:47,965] [INFO] Selected 16 target genomes.
[2023-06-29 20:03:47,965] [INFO] Target genome list was writen to GCA_021780475.1_ASM2178047v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:03:47,967] [INFO] Task started: fastANI
[2023-06-29 20:03:47,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg094a00a2-9671-4fd3-9ab3-0510e07a8450/GCA_021780475.1_ASM2178047v1_genomic.fna.gz --refList GCA_021780475.1_ASM2178047v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021780475.1_ASM2178047v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:03:58,066] [INFO] Task succeeded: fastANI
[2023-06-29 20:03:58,086] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 20:03:58,086] [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_013044085.1	s__JABEVI01 sp013044085	80.0445	328	970	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__JABEVI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003164785.1	s__Bog-1198 sp003164785	77.7509	231	970	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Bog-1198	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003137095.1	s__Bog-1198 sp003137095	77.6909	304	970	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Bog-1198	95.0	99.69	99.56	0.95	0.94	4	-
GCA_003134045.1	s__Bog-1198 sp003134045	77.6606	258	970	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Bog-1198	95.0	99.80	99.72	0.93	0.90	6	-
GCA_018240265.1	s__TMP-86 sp018240265	77.6598	155	970	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__TMP-86	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241525.1	s__SZAS-83 sp018241525	77.3085	327	970	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SZAS-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874295.1	s__SCUD01 sp016874295	77.2428	148	970	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SCUD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242685.1	s__ZC4RG24 sp003242685	77.1419	163	970	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003132425.1	s__Bog-1198 sp003132425	76.9381	191	970	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Bog-1198	95.0	99.87	99.87	0.94	0.94	2	-
GCA_003165495.1	s__Bog-1198 sp003165495	76.8209	157	970	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Bog-1198	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826575.1	s__CADEFQ01 sp902826575	76.6719	164	970	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CADEFQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242495.1	s__ZC4RG39 sp003242495	76.5199	114	970	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG39	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014138265.1	s__Dokdonella_A fugitiva_A	75.9526	195	970	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910705.1	s__Aromatoleum anaerobium	75.6417	112	970	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017880745.1	s__2-12-FULL-64-23 sp017880745	75.6003	61	970	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__2-12-FULL-64-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192435.1	s__Sulfuritalea sp016192435	75.4404	67	970	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 20:03:58,089] [INFO] GTDB search result was written to GCA_021780475.1_ASM2178047v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:03:58,090] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:03:58,094] [INFO] DFAST_QC result json was written to GCA_021780475.1_ASM2178047v1_genomic.fna/dqc_result.json
[2023-06-29 20:03:58,094] [INFO] DFAST_QC completed!
[2023-06-29 20:03:58,095] [INFO] Total running time: 0h1m19s