[2024-01-25 18:59:50,714] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:59:50,716] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:59:50,717] [INFO] DQC Reference Directory: /var/lib/cwl/stg9736a2d7-579e-4ffa-aa46-61feb2f5a9e1/dqc_reference
[2024-01-25 18:59:51,843] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:59:51,844] [INFO] Task started: Prodigal
[2024-01-25 18:59:51,844] [INFO] Running command: gunzip -c /var/lib/cwl/stge8058c89-c0df-4048-afc1-4b75724192c2/GCF_003337555.1_ASM333755v1_genomic.fna.gz | prodigal -d GCF_003337555.1_ASM333755v1_genomic.fna/cds.fna -a GCF_003337555.1_ASM333755v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:00:16,418] [INFO] Task succeeded: Prodigal
[2024-01-25 19:00:16,418] [INFO] Task started: HMMsearch
[2024-01-25 19:00:16,418] [INFO] Running command: hmmsearch --tblout GCF_003337555.1_ASM333755v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9736a2d7-579e-4ffa-aa46-61feb2f5a9e1/dqc_reference/reference_markers.hmm GCF_003337555.1_ASM333755v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:00:16,731] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:00:16,732] [INFO] Found 6/6 markers.
[2024-01-25 19:00:16,795] [INFO] Query marker FASTA was written to GCF_003337555.1_ASM333755v1_genomic.fna/markers.fasta
[2024-01-25 19:00:16,795] [INFO] Task started: Blastn
[2024-01-25 19:00:16,795] [INFO] Running command: blastn -query GCF_003337555.1_ASM333755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9736a2d7-579e-4ffa-aa46-61feb2f5a9e1/dqc_reference/reference_markers.fasta -out GCF_003337555.1_ASM333755v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:17,841] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:17,843] [INFO] Selected 21 target genomes.
[2024-01-25 19:00:17,844] [INFO] Target genome list was writen to GCF_003337555.1_ASM333755v1_genomic.fna/target_genomes.txt
[2024-01-25 19:00:17,849] [INFO] Task started: fastANI
[2024-01-25 19:00:17,849] [INFO] Running command: fastANI --query /var/lib/cwl/stge8058c89-c0df-4048-afc1-4b75724192c2/GCF_003337555.1_ASM333755v1_genomic.fna.gz --refList GCF_003337555.1_ASM333755v1_genomic.fna/target_genomes.txt --output GCF_003337555.1_ASM333755v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:00:45,851] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:45,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9736a2d7-579e-4ffa-aa46-61feb2f5a9e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:00:45,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9736a2d7-579e-4ffa-aa46-61feb2f5a9e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:00:45,864] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:00:45,864] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:00:45,864] [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 soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	100.0	2705	2706	95	conclusive
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	90.2411	1866	2706	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	81.0447	1070	2706	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	80.9416	1078	2706	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	80.8345	964	2706	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	80.7166	1091	2706	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.4394	833	2706	95	below_threshold
Xylophilus ampelinus	strain=CECT 7646	GCA_003217575.1	54067	54067	type	True	80.3999	684	2706	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.3918	913	2706	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	80.2672	690	2706	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	80.194	873	2706	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	80.0663	883	2706	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	80.0242	760	2706	95	below_threshold
Acidovorax konjaci	strain=DSM 7481	GCA_900112675.1	32040	32040	type	True	79.9255	817	2706	95	below_threshold
Xylophilus rhododendri	strain=KACC 21265	GCA_009906855.1	2697032	2697032	type	True	79.9131	971	2706	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	79.8526	907	2706	95	below_threshold
Malikia granosa	strain=P1	GCA_002980595.1	263067	263067	type	True	79.592	591	2706	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	79.5649	1042	2706	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.507	800	2706	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	79.3228	786	2706	95	below_threshold
Malikia spinosa	strain=83	GCA_002980625.1	86180	86180	type	True	79.2088	574	2706	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:00:45,866] [INFO] DFAST Taxonomy check result was written to GCF_003337555.1_ASM333755v1_genomic.fna/tc_result.tsv
[2024-01-25 19:00:45,866] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:00:45,866] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:00:45,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9736a2d7-579e-4ffa-aa46-61feb2f5a9e1/dqc_reference/checkm_data
[2024-01-25 19:00:45,867] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:00:45,941] [INFO] Task started: CheckM
[2024-01-25 19:00:45,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003337555.1_ASM333755v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003337555.1_ASM333755v1_genomic.fna/checkm_input GCF_003337555.1_ASM333755v1_genomic.fna/checkm_result
[2024-01-25 19:04:51,960] [INFO] Task succeeded: CheckM
[2024-01-25 19:04:51,962] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:04:51,985] [INFO] ===== Completeness check finished =====
[2024-01-25 19:04:51,985] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:04:51,986] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003337555.1_ASM333755v1_genomic.fna/markers.fasta)
[2024-01-25 19:04:51,986] [INFO] Task started: Blastn
[2024-01-25 19:04:51,986] [INFO] Running command: blastn -query GCF_003337555.1_ASM333755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9736a2d7-579e-4ffa-aa46-61feb2f5a9e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_003337555.1_ASM333755v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:54,273] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:54,275] [INFO] Selected 6 target genomes.
[2024-01-25 19:04:54,276] [INFO] Target genome list was writen to GCF_003337555.1_ASM333755v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:04:54,280] [INFO] Task started: fastANI
[2024-01-25 19:04:54,280] [INFO] Running command: fastANI --query /var/lib/cwl/stge8058c89-c0df-4048-afc1-4b75724192c2/GCF_003337555.1_ASM333755v1_genomic.fna.gz --refList GCF_003337555.1_ASM333755v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003337555.1_ASM333755v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:05:09,007] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:09,012] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:05:09,012] [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_003337555.1	s__Pseudorhodoferax soli	100.0	2705	2706	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_001422365.1	s__Pseudorhodoferax sp001422365	91.408	1893	2706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	98.81	98.81	0.87	0.87	3	-
GCF_014652235.1	s__Pseudorhodoferax aquiterrae	90.225	1868	2706	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	90.1955	1708	2706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007677875.1	s__Pseudorhodoferax boronicumulans_A	89.8211	1749	2706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422405.1	s__Pseudorhodoferax sp001422405	85.1485	1491	2706	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:05:09,014] [INFO] GTDB search result was written to GCF_003337555.1_ASM333755v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:05:09,014] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:05:09,017] [INFO] DFAST_QC result json was written to GCF_003337555.1_ASM333755v1_genomic.fna/dqc_result.json
[2024-01-25 19:05:09,017] [INFO] DFAST_QC completed!
[2024-01-25 19:05:09,017] [INFO] Total running time: 0h5m18s