[2023-03-15 21:48:07,256] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:48:07,259] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:48:07,259] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5d80221-9505-45d1-a701-54d5b259ae93/dqc_reference
[2023-03-15 21:48:08,883] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:48:08,883] [INFO] Task started: Prodigal
[2023-03-15 21:48:08,883] [INFO] Running command: cat /var/lib/cwl/stg4cb1b154-8c4c-4eca-affc-b4f373fa84b5/OceanDNA-b33607.fa | prodigal -d OceanDNA-b33607/cds.fna -a OceanDNA-b33607/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:48:33,174] [INFO] Task succeeded: Prodigal
[2023-03-15 21:48:33,174] [INFO] Task started: HMMsearch
[2023-03-15 21:48:33,174] [INFO] Running command: hmmsearch --tblout OceanDNA-b33607/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5d80221-9505-45d1-a701-54d5b259ae93/dqc_reference/reference_markers.hmm OceanDNA-b33607/protein.faa > /dev/null
[2023-03-15 21:48:33,407] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:48:33,408] [INFO] Found 6/6 markers.
[2023-03-15 21:48:33,440] [INFO] Query marker FASTA was written to OceanDNA-b33607/markers.fasta
[2023-03-15 21:48:33,440] [INFO] Task started: Blastn
[2023-03-15 21:48:33,440] [INFO] Running command: blastn -query OceanDNA-b33607/markers.fasta -db /var/lib/cwl/stgc5d80221-9505-45d1-a701-54d5b259ae93/dqc_reference/reference_markers.fasta -out OceanDNA-b33607/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:34,436] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:34,437] [INFO] Selected 16 target genomes.
[2023-03-15 21:48:34,437] [INFO] Target genome list was writen to OceanDNA-b33607/target_genomes.txt
[2023-03-15 21:48:34,449] [INFO] Task started: fastANI
[2023-03-15 21:48:34,449] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cb1b154-8c4c-4eca-affc-b4f373fa84b5/OceanDNA-b33607.fa --refList OceanDNA-b33607/target_genomes.txt --output OceanDNA-b33607/fastani_result.tsv --threads 1
[2023-03-15 21:48:51,897] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:51,898] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5d80221-9505-45d1-a701-54d5b259ae93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:48:51,898] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5d80221-9505-45d1-a701-54d5b259ae93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:48:51,908] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:48:51,908] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:48:51,908] [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
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	83.6525	731	1215	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	83.534	701	1215	95	below_threshold
Variovorax gossypii	strain=DSM 100435	GCA_003965815.1	1679495	1679495	type	True	83.2946	609	1215	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	83.2524	715	1215	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	83.2427	719	1215	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	83.0776	645	1215	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	81.8621	693	1215	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	81.3724	665	1215	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	81.3627	506	1215	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	81.256	479	1215	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	81.1865	532	1215	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	81.0194	489	1215	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.9221	549	1215	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	80.8368	455	1215	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	80.6909	455	1215	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.6496	468	1215	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:48:51,908] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33607/tc_result.tsv
[2023-03-15 21:48:51,908] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:48:51,908] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:48:51,908] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5d80221-9505-45d1-a701-54d5b259ae93/dqc_reference/checkm_data
[2023-03-15 21:48:51,909] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:48:51,915] [INFO] Task started: CheckM
[2023-03-15 21:48:51,915] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33607/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33607/checkm_input OceanDNA-b33607/checkm_result
[2023-03-15 21:49:53,778] [INFO] Task succeeded: CheckM
[2023-03-15 21:49:53,779] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:49:53,782] [INFO] ===== Completeness check finished =====
[2023-03-15 21:49:53,782] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:49:53,782] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33607/markers.fasta)
[2023-03-15 21:49:53,783] [INFO] Task started: Blastn
[2023-03-15 21:49:53,783] [INFO] Running command: blastn -query OceanDNA-b33607/markers.fasta -db /var/lib/cwl/stgc5d80221-9505-45d1-a701-54d5b259ae93/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33607/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:49:55,883] [INFO] Task succeeded: Blastn
[2023-03-15 21:49:55,884] [INFO] Selected 11 target genomes.
[2023-03-15 21:49:55,884] [INFO] Target genome list was writen to OceanDNA-b33607/target_genomes_gtdb.txt
[2023-03-15 21:49:55,928] [INFO] Task started: fastANI
[2023-03-15 21:49:55,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cb1b154-8c4c-4eca-affc-b4f373fa84b5/OceanDNA-b33607.fa --refList OceanDNA-b33607/target_genomes_gtdb.txt --output OceanDNA-b33607/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:50:09,627] [INFO] Task succeeded: fastANI
[2023-03-15 21:50:09,634] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:50:09,635] [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_901875635.1	s__ALPHA2B sp901875635	99.5636	1095	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	99.68	99.68	0.89	0.89	2	conclusive
GCA_005503065.1	s__ALPHA2B sp005503065	93.3744	988	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241185.1	s__ALPHA2B sp018241185	92.1803	815	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003671765.1	s__ALPHA2B sp003671765	91.7369	889	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745855.1	s__Xenophilus azovorans	86.6037	775	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xenophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016806145.1	s__Variovorax sp900115375	83.8038	774	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	96.08	95.68	0.83	0.79	13	-
GCF_014170375.1	s__Variovorax sp014170375	83.4549	730	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952185.1	s__Variovorax sp003952185	83.3108	713	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	99.99	99.98	0.99	0.99	3	-
GCF_009765735.1	s__Variovorax sp009765735	82.3486	673	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090195.1	s__Variovorax sp900090195	82.1338	645	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744285.1	s__Variovorax sp017744285	81.465	431	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:50:09,635] [INFO] GTDB search result was written to OceanDNA-b33607/result_gtdb.tsv
[2023-03-15 21:50:09,635] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:50:09,636] [INFO] DFAST_QC result json was written to OceanDNA-b33607/dqc_result.json
[2023-03-15 21:50:09,637] [INFO] DFAST_QC completed!
[2023-03-15 21:50:09,637] [INFO] Total running time: 0h2m2s