[2024-01-24 11:43:41,197] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:41,199] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:41,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ba07813-1437-4d94-a9ba-b111485c176e/dqc_reference
[2024-01-24 11:43:42,947] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:42,949] [INFO] Task started: Prodigal
[2024-01-24 11:43:42,949] [INFO] Running command: gunzip -c /var/lib/cwl/stgb568a41b-bb97-43a4-aa2b-9a9c52d02a4b/GCF_024832295.1_ASM2483229v1_genomic.fna.gz | prodigal -d GCF_024832295.1_ASM2483229v1_genomic.fna/cds.fna -a GCF_024832295.1_ASM2483229v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:54,195] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:54,196] [INFO] Task started: HMMsearch
[2024-01-24 11:43:54,196] [INFO] Running command: hmmsearch --tblout GCF_024832295.1_ASM2483229v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ba07813-1437-4d94-a9ba-b111485c176e/dqc_reference/reference_markers.hmm GCF_024832295.1_ASM2483229v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:54,528] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:54,530] [INFO] Found 6/6 markers.
[2024-01-24 11:43:54,575] [INFO] Query marker FASTA was written to GCF_024832295.1_ASM2483229v1_genomic.fna/markers.fasta
[2024-01-24 11:43:54,577] [INFO] Task started: Blastn
[2024-01-24 11:43:54,578] [INFO] Running command: blastn -query GCF_024832295.1_ASM2483229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ba07813-1437-4d94-a9ba-b111485c176e/dqc_reference/reference_markers.fasta -out GCF_024832295.1_ASM2483229v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:55,704] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:55,708] [INFO] Selected 19 target genomes.
[2024-01-24 11:43:55,708] [INFO] Target genome list was writen to GCF_024832295.1_ASM2483229v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:55,721] [INFO] Task started: fastANI
[2024-01-24 11:43:55,721] [INFO] Running command: fastANI --query /var/lib/cwl/stgb568a41b-bb97-43a4-aa2b-9a9c52d02a4b/GCF_024832295.1_ASM2483229v1_genomic.fna.gz --refList GCF_024832295.1_ASM2483229v1_genomic.fna/target_genomes.txt --output GCF_024832295.1_ASM2483229v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:16,142] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:16,142] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ba07813-1437-4d94-a9ba-b111485c176e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:16,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ba07813-1437-4d94-a9ba-b111485c176e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:16,158] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:44:16,158] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:16,158] [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
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	100.0	1205	1211	95	conclusive
Xylophilus ampelinus	strain=CECT 7646	GCA_003217575.1	54067	54067	type	True	99.9958	1209	1211	95	conclusive
Xylophilus rhododendri	strain=KACC 21265	GCA_009906855.1	2697032	2697032	type	True	82.4534	738	1211	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	81.4732	703	1211	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	80.7654	643	1211	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.7417	636	1211	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	80.6381	675	1211	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.5102	545	1211	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.4234	578	1211	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	80.3367	621	1211	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	80.3307	608	1211	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	80.1358	537	1211	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	80.0247	532	1211	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	79.9724	623	1211	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	79.9714	537	1211	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	79.8397	504	1211	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.3905	533	1211	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	79.2526	456	1211	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	78.8313	531	1211	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:16,160] [INFO] DFAST Taxonomy check result was written to GCF_024832295.1_ASM2483229v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:16,161] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:16,161] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:16,161] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ba07813-1437-4d94-a9ba-b111485c176e/dqc_reference/checkm_data
[2024-01-24 11:44:16,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:16,206] [INFO] Task started: CheckM
[2024-01-24 11:44:16,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024832295.1_ASM2483229v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024832295.1_ASM2483229v1_genomic.fna/checkm_input GCF_024832295.1_ASM2483229v1_genomic.fna/checkm_result
[2024-01-24 11:44:54,509] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:54,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:54,531] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:54,532] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:54,532] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024832295.1_ASM2483229v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:54,532] [INFO] Task started: Blastn
[2024-01-24 11:44:54,533] [INFO] Running command: blastn -query GCF_024832295.1_ASM2483229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ba07813-1437-4d94-a9ba-b111485c176e/dqc_reference/reference_markers_gtdb.fasta -out GCF_024832295.1_ASM2483229v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:56,697] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:56,700] [INFO] Selected 13 target genomes.
[2024-01-24 11:44:56,701] [INFO] Target genome list was writen to GCF_024832295.1_ASM2483229v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:56,710] [INFO] Task started: fastANI
[2024-01-24 11:44:56,710] [INFO] Running command: fastANI --query /var/lib/cwl/stgb568a41b-bb97-43a4-aa2b-9a9c52d02a4b/GCF_024832295.1_ASM2483229v1_genomic.fna.gz --refList GCF_024832295.1_ASM2483229v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024832295.1_ASM2483229v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:10,189] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:10,206] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:10,206] [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
GCF_003217575.1	s__Xylophilus ampelinus	99.9958	1209	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001421705.1	s__Xylophilus sp001421705	92.7943	999	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428875.1	s__Xylophilus sp016428875	83.6258	736	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009906855.1	s__Xylophilus rhododendri	82.4762	736	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014170375.1	s__Variovorax sp014170375	81.8167	728	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113035.1	s__Acidovorax_A wautersii	81.5255	698	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103645.1	s__Oryzisolibacter propanilivorax	80.8903	574	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oryzisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932145.1	s__Giesbergeria sp012932145	80.7286	540	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.72	98.72	0.89	0.89	2	-
GCF_003604195.1	s__Giesbergeria lacusdiani	80.6589	570	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011388215.1	s__Hydrogenophaga sp011388215	80.4697	549	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.06	99.06	0.95	0.95	2	-
GCA_003208485.1	s__Acidovorax sp003208485	80.3646	640	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002434305.1	s__Pulveribacter sp002434305	80.2867	566	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pulveribacter	95.0	97.39	97.21	0.93	0.92	3	-
GCA_001724785.1	s__Giesbergeria sp001724785	79.8558	402	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:10,208] [INFO] GTDB search result was written to GCF_024832295.1_ASM2483229v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:10,209] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:10,213] [INFO] DFAST_QC result json was written to GCF_024832295.1_ASM2483229v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:10,214] [INFO] DFAST_QC completed!
[2024-01-24 11:45:10,214] [INFO] Total running time: 0h1m29s