[2024-01-24 13:32:18,193] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:18,195] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:18,195] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4558e4e-46fd-4111-8475-28abfa783905/dqc_reference
[2024-01-24 13:32:19,636] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:19,637] [INFO] Task started: Prodigal
[2024-01-24 13:32:19,637] [INFO] Running command: gunzip -c /var/lib/cwl/stg650447c6-edff-459f-94a0-3c3cf1a2c7dc/GCF_003217575.1_ASM321757v1_genomic.fna.gz | prodigal -d GCF_003217575.1_ASM321757v1_genomic.fna/cds.fna -a GCF_003217575.1_ASM321757v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:31,457] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:31,457] [INFO] Task started: HMMsearch
[2024-01-24 13:32:31,457] [INFO] Running command: hmmsearch --tblout GCF_003217575.1_ASM321757v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4558e4e-46fd-4111-8475-28abfa783905/dqc_reference/reference_markers.hmm GCF_003217575.1_ASM321757v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:31,743] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:31,744] [INFO] Found 6/6 markers.
[2024-01-24 13:32:31,776] [INFO] Query marker FASTA was written to GCF_003217575.1_ASM321757v1_genomic.fna/markers.fasta
[2024-01-24 13:32:31,776] [INFO] Task started: Blastn
[2024-01-24 13:32:31,777] [INFO] Running command: blastn -query GCF_003217575.1_ASM321757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4558e4e-46fd-4111-8475-28abfa783905/dqc_reference/reference_markers.fasta -out GCF_003217575.1_ASM321757v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:32,912] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:32,921] [INFO] Selected 19 target genomes.
[2024-01-24 13:32:32,922] [INFO] Target genome list was writen to GCF_003217575.1_ASM321757v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:32,930] [INFO] Task started: fastANI
[2024-01-24 13:32:32,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg650447c6-edff-459f-94a0-3c3cf1a2c7dc/GCF_003217575.1_ASM321757v1_genomic.fna.gz --refList GCF_003217575.1_ASM321757v1_genomic.fna/target_genomes.txt --output GCF_003217575.1_ASM321757v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:54,860] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:54,860] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4558e4e-46fd-4111-8475-28abfa783905/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:54,861] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4558e4e-46fd-4111-8475-28abfa783905/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:54,876] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:54,876] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:54,877] [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=CECT 7646	GCA_003217575.1	54067	54067	type	True	100.0	1209	1212	95	conclusive
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	99.9925	1198	1212	95	conclusive
Xylophilus rhododendri	strain=KACC 21265	GCA_009906855.1	2697032	2697032	type	True	82.4488	740	1212	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	81.5314	709	1212	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	80.7158	646	1212	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.6985	638	1212	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	80.6089	673	1212	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	80.3702	606	1212	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.35	553	1212	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.3433	576	1212	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	80.2381	629	1212	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	80.0952	539	1212	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	80.064	603	1212	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	80.0479	529	1212	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	79.9407	494	1212	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	79.9374	550	1212	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.5406	529	1212	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	79.2404	458	1212	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	78.7967	544	1212	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:54,880] [INFO] DFAST Taxonomy check result was written to GCF_003217575.1_ASM321757v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:54,881] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:54,881] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:54,881] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4558e4e-46fd-4111-8475-28abfa783905/dqc_reference/checkm_data
[2024-01-24 13:32:54,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:54,925] [INFO] Task started: CheckM
[2024-01-24 13:32:54,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003217575.1_ASM321757v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003217575.1_ASM321757v1_genomic.fna/checkm_input GCF_003217575.1_ASM321757v1_genomic.fna/checkm_result
[2024-01-24 13:33:34,691] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:34,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:34,715] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:34,716] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:34,716] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003217575.1_ASM321757v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:34,716] [INFO] Task started: Blastn
[2024-01-24 13:33:34,717] [INFO] Running command: blastn -query GCF_003217575.1_ASM321757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4558e4e-46fd-4111-8475-28abfa783905/dqc_reference/reference_markers_gtdb.fasta -out GCF_003217575.1_ASM321757v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:36,967] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:36,974] [INFO] Selected 13 target genomes.
[2024-01-24 13:33:36,974] [INFO] Target genome list was writen to GCF_003217575.1_ASM321757v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:37,252] [INFO] Task started: fastANI
[2024-01-24 13:33:37,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg650447c6-edff-459f-94a0-3c3cf1a2c7dc/GCF_003217575.1_ASM321757v1_genomic.fna.gz --refList GCF_003217575.1_ASM321757v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003217575.1_ASM321757v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:50,457] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:50,474] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:50,475] [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	100.0	1209	1212	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	92.9156	991	1212	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	83.7134	731	1212	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	82.4088	744	1212	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	81.9471	720	1212	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	81.5579	707	1212	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	80.8285	578	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oryzisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003604195.1	s__Giesbergeria lacusdiani	80.7038	561	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932145.1	s__Giesbergeria sp012932145	80.567	551	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.72	98.72	0.89	0.89	2	-
GCA_003208485.1	s__Acidovorax sp003208485	80.4266	631	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011388215.1	s__Hydrogenophaga sp011388215	80.3616	552	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.06	99.06	0.95	0.95	2	-
GCA_002434305.1	s__Pulveribacter sp002434305	80.1569	568	1212	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	79.812	409	1212	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 13:33:50,477] [INFO] GTDB search result was written to GCF_003217575.1_ASM321757v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:50,478] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:50,482] [INFO] DFAST_QC result json was written to GCF_003217575.1_ASM321757v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:50,483] [INFO] DFAST_QC completed!
[2024-01-24 13:33:50,483] [INFO] Total running time: 0h1m32s