[2023-06-29 20:24:41,792] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:24:41,795] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:24:41,795] [INFO] DQC Reference Directory: /var/lib/cwl/stg0111f96d-18da-41b6-9af9-9486048f32d1/dqc_reference
[2023-06-29 20:24:43,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:24:43,271] [INFO] Task started: Prodigal
[2023-06-29 20:24:43,272] [INFO] Running command: gunzip -c /var/lib/cwl/stg19857bbf-b70a-44d4-a183-0ee786b57ce7/GCA_023417315.1_ASM2341731v1_genomic.fna.gz | prodigal -d GCA_023417315.1_ASM2341731v1_genomic.fna/cds.fna -a GCA_023417315.1_ASM2341731v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:25:00,954] [INFO] Task succeeded: Prodigal
[2023-06-29 20:25:00,954] [INFO] Task started: HMMsearch
[2023-06-29 20:25:00,954] [INFO] Running command: hmmsearch --tblout GCA_023417315.1_ASM2341731v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0111f96d-18da-41b6-9af9-9486048f32d1/dqc_reference/reference_markers.hmm GCA_023417315.1_ASM2341731v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:25:01,309] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:25:01,311] [INFO] Found 6/6 markers.
[2023-06-29 20:25:01,364] [INFO] Query marker FASTA was written to GCA_023417315.1_ASM2341731v1_genomic.fna/markers.fasta
[2023-06-29 20:25:01,364] [INFO] Task started: Blastn
[2023-06-29 20:25:01,364] [INFO] Running command: blastn -query GCA_023417315.1_ASM2341731v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0111f96d-18da-41b6-9af9-9486048f32d1/dqc_reference/reference_markers.fasta -out GCA_023417315.1_ASM2341731v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:25:02,178] [INFO] Task succeeded: Blastn
[2023-06-29 20:25:02,187] [INFO] Selected 22 target genomes.
[2023-06-29 20:25:02,187] [INFO] Target genome list was writen to GCA_023417315.1_ASM2341731v1_genomic.fna/target_genomes.txt
[2023-06-29 20:25:02,188] [INFO] Task started: fastANI
[2023-06-29 20:25:02,189] [INFO] Running command: fastANI --query /var/lib/cwl/stg19857bbf-b70a-44d4-a183-0ee786b57ce7/GCA_023417315.1_ASM2341731v1_genomic.fna.gz --refList GCA_023417315.1_ASM2341731v1_genomic.fna/target_genomes.txt --output GCA_023417315.1_ASM2341731v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:25:19,496] [INFO] Task succeeded: fastANI
[2023-06-29 20:25:19,497] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0111f96d-18da-41b6-9af9-9486048f32d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:25:19,498] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0111f96d-18da-41b6-9af9-9486048f32d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:25:19,512] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:25:19,512] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 20:25:19,512] [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	77.6433	347	1887	95	below_threshold
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	77.4688	360	1887	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	77.3766	365	1887	95	below_threshold
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	77.2981	337	1887	95	below_threshold
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	77.2899	358	1887	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	77.2116	337	1887	95	below_threshold
Steroidobacter denitrificans	strain=DSM 18526	GCA_001579945.1	465721	465721	type	True	76.644	141	1887	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	75.6119	53	1887	95	below_threshold
Usitatibacter palustris	strain=Swamp67	GCA_013003985.1	2732487	2732487	type	True	75.4746	51	1887	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	75.3468	53	1887	95	below_threshold
Burkholderia cepacia	strain=NBRC 14074	GCA_001528845.1	292	292	type	True	75.253	98	1887	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 20:25:19,514] [INFO] DFAST Taxonomy check result was written to GCA_023417315.1_ASM2341731v1_genomic.fna/tc_result.tsv
[2023-06-29 20:25:19,515] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:25:19,515] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:25:19,515] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0111f96d-18da-41b6-9af9-9486048f32d1/dqc_reference/checkm_data
[2023-06-29 20:25:19,516] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:25:19,570] [INFO] Task started: CheckM
[2023-06-29 20:25:19,570] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023417315.1_ASM2341731v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023417315.1_ASM2341731v1_genomic.fna/checkm_input GCA_023417315.1_ASM2341731v1_genomic.fna/checkm_result
[2023-06-29 20:26:11,442] [INFO] Task succeeded: CheckM
[2023-06-29 20:26:11,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:26:11,469] [INFO] ===== Completeness check finished =====
[2023-06-29 20:26:11,469] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:26:11,470] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023417315.1_ASM2341731v1_genomic.fna/markers.fasta)
[2023-06-29 20:26:11,470] [INFO] Task started: Blastn
[2023-06-29 20:26:11,470] [INFO] Running command: blastn -query GCA_023417315.1_ASM2341731v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0111f96d-18da-41b6-9af9-9486048f32d1/dqc_reference/reference_markers_gtdb.fasta -out GCA_023417315.1_ASM2341731v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:26:12,705] [INFO] Task succeeded: Blastn
[2023-06-29 20:26:12,709] [INFO] Selected 16 target genomes.
[2023-06-29 20:26:12,710] [INFO] Target genome list was writen to GCA_023417315.1_ASM2341731v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:26:12,712] [INFO] Task started: fastANI
[2023-06-29 20:26:12,712] [INFO] Running command: fastANI --query /var/lib/cwl/stg19857bbf-b70a-44d4-a183-0ee786b57ce7/GCA_023417315.1_ASM2341731v1_genomic.fna.gz --refList GCA_023417315.1_ASM2341731v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023417315.1_ASM2341731v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:26:24,757] [INFO] Task succeeded: fastANI
[2023-06-29 20:26:24,774] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 20:26:24,774] [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_012516015.1	s__JAAYXG01 sp012516015	78.643	409	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__JAAYXG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577615.1	s__JAAYXG01 sp017577615	77.73	428	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__JAAYXG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202975.1	s__Povalibacter uvarum	77.6168	350	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Povalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009932555.1	s__Steroidobacter_A agaridevorans	77.4688	360	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	99.33	99.33	0.96	0.96	2	-
GCF_004138335.1	s__Steroidobacter_A agariperforans	77.367	367	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016801985.1	s__Steroidobacter_A sp016801985	77.3155	335	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242495.1	s__ZC4RG39 sp003242495	76.9931	194	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG39	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790065.1	s__Steroidobacter_A sp016790065	76.7995	237	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903898785.1	s__CAIUGU01 sp903898785	76.7147	114	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIUGU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001579945.1	s__Steroidobacter denitrificans	76.6443	142	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704655.1	s__RPQJ01 sp016704655	76.6227	138	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	98.97	98.97	0.93	0.93	2	-
GCA_003819815.1	s__RPQJ01 sp003819815	76.0336	112	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005877705.1	s__13-2-20CM-66-19 sp005877705	75.8381	65	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	97.92	97.92	0.70	0.70	2	-
GCF_013003985.1	s__Usitatibacter palustris	75.4532	52	1887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__Usitatibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 20:26:24,776] [INFO] GTDB search result was written to GCA_023417315.1_ASM2341731v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:26:24,777] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:26:24,780] [INFO] DFAST_QC result json was written to GCA_023417315.1_ASM2341731v1_genomic.fna/dqc_result.json
[2023-06-29 20:26:24,781] [INFO] DFAST_QC completed!
[2023-06-29 20:26:24,781] [INFO] Total running time: 0h1m43s