[2024-01-24 13:56:13,274] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:13,276] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:13,276] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ec7d60a-9853-46e5-9027-0bb93e6a04f8/dqc_reference
[2024-01-24 13:56:14,567] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:14,568] [INFO] Task started: Prodigal
[2024-01-24 13:56:14,569] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa71db01-da99-44f6-86e0-7d9d132bbec6/GCF_014652235.1_ASM1465223v1_genomic.fna.gz | prodigal -d GCF_014652235.1_ASM1465223v1_genomic.fna/cds.fna -a GCF_014652235.1_ASM1465223v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:38,765] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:38,766] [INFO] Task started: HMMsearch
[2024-01-24 13:56:38,766] [INFO] Running command: hmmsearch --tblout GCF_014652235.1_ASM1465223v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ec7d60a-9853-46e5-9027-0bb93e6a04f8/dqc_reference/reference_markers.hmm GCF_014652235.1_ASM1465223v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:39,114] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:39,116] [INFO] Found 6/6 markers.
[2024-01-24 13:56:39,175] [INFO] Query marker FASTA was written to GCF_014652235.1_ASM1465223v1_genomic.fna/markers.fasta
[2024-01-24 13:56:39,175] [INFO] Task started: Blastn
[2024-01-24 13:56:39,176] [INFO] Running command: blastn -query GCF_014652235.1_ASM1465223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ec7d60a-9853-46e5-9027-0bb93e6a04f8/dqc_reference/reference_markers.fasta -out GCF_014652235.1_ASM1465223v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:40,265] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:40,268] [INFO] Selected 21 target genomes.
[2024-01-24 13:56:40,269] [INFO] Target genome list was writen to GCF_014652235.1_ASM1465223v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:40,280] [INFO] Task started: fastANI
[2024-01-24 13:56:40,281] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa71db01-da99-44f6-86e0-7d9d132bbec6/GCF_014652235.1_ASM1465223v1_genomic.fna.gz --refList GCF_014652235.1_ASM1465223v1_genomic.fna/target_genomes.txt --output GCF_014652235.1_ASM1465223v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:08,080] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:08,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ec7d60a-9853-46e5-9027-0bb93e6a04f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:08,082] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ec7d60a-9853-46e5-9027-0bb93e6a04f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:08,104] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:08,104] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:08,104] [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
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	100.0	2323	2328	95	conclusive
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	90.3085	1841	2328	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	81.3424	833	2328	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	81.1909	1078	2328	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	81.1391	1072	2328	95	below_threshold
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	81.1013	1087	2328	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	81.0998	769	2328	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.9099	845	2328	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	80.8961	439	2328	95	below_threshold
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	80.7533	644	2328	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.6704	834	2328	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	80.6645	861	2328	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	80.6087	879	2328	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	80.6069	850	2328	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.517	929	2328	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	80.4811	892	2328	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	80.3752	776	2328	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	80.2665	697	2328	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	80.2008	750	2328	95	below_threshold
Xylophilus rhododendri	strain=KACC 21265	GCA_009906855.1	2697032	2697032	type	True	80.1557	951	2328	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.7761	777	2328	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:08,106] [INFO] DFAST Taxonomy check result was written to GCF_014652235.1_ASM1465223v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:08,107] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:08,107] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:08,108] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ec7d60a-9853-46e5-9027-0bb93e6a04f8/dqc_reference/checkm_data
[2024-01-24 13:57:08,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:08,182] [INFO] Task started: CheckM
[2024-01-24 13:57:08,182] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652235.1_ASM1465223v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652235.1_ASM1465223v1_genomic.fna/checkm_input GCF_014652235.1_ASM1465223v1_genomic.fna/checkm_result
[2024-01-24 13:59:48,617] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:48,618] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:48,641] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:48,642] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:48,643] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652235.1_ASM1465223v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:48,643] [INFO] Task started: Blastn
[2024-01-24 13:59:48,643] [INFO] Running command: blastn -query GCF_014652235.1_ASM1465223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ec7d60a-9853-46e5-9027-0bb93e6a04f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652235.1_ASM1465223v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:50,892] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:50,896] [INFO] Selected 5 target genomes.
[2024-01-24 13:59:50,897] [INFO] Target genome list was writen to GCF_014652235.1_ASM1465223v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:50,903] [INFO] Task started: fastANI
[2024-01-24 13:59:50,903] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa71db01-da99-44f6-86e0-7d9d132bbec6/GCF_014652235.1_ASM1465223v1_genomic.fna.gz --refList GCF_014652235.1_ASM1465223v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652235.1_ASM1465223v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:03,728] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:03,738] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:03,739] [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_014652235.1	s__Pseudorhodoferax aquiterrae	100.0	2323	2328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007677875.1	s__Pseudorhodoferax boronicumulans_A	93.9211	1752	2328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422365.1	s__Pseudorhodoferax sp001422365	91.9526	1875	2328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	98.81	98.81	0.87	0.87	3	-
GCF_003337555.1	s__Pseudorhodoferax soli	90.317	1840	2328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422445.1	s__Pseudorhodoferax sp001422445	89.9512	1665	2328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:03,741] [INFO] GTDB search result was written to GCF_014652235.1_ASM1465223v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:03,741] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:03,745] [INFO] DFAST_QC result json was written to GCF_014652235.1_ASM1465223v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:03,746] [INFO] DFAST_QC completed!
[2024-01-24 14:00:03,746] [INFO] Total running time: 0h3m50s