[2023-03-18 03:09:35,395] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:09:35,395] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:09:35,395] [INFO] DQC Reference Directory: /var/lib/cwl/stg5887d4cc-fd2e-4390-a196-8a8689496ede/dqc_reference
[2023-03-18 03:09:36,570] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:09:36,571] [INFO] Task started: Prodigal
[2023-03-18 03:09:36,571] [INFO] Running command: cat /var/lib/cwl/stg08b01bca-8f43-4112-b884-c827758c10a1/OceanDNA-b33391.fa | prodigal -d OceanDNA-b33391/cds.fna -a OceanDNA-b33391/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:10:08,171] [INFO] Task succeeded: Prodigal
[2023-03-18 03:10:08,171] [INFO] Task started: HMMsearch
[2023-03-18 03:10:08,171] [INFO] Running command: hmmsearch --tblout OceanDNA-b33391/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5887d4cc-fd2e-4390-a196-8a8689496ede/dqc_reference/reference_markers.hmm OceanDNA-b33391/protein.faa > /dev/null
[2023-03-18 03:10:08,530] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:10:08,531] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg08b01bca-8f43-4112-b884-c827758c10a1/OceanDNA-b33391.fa]
[2023-03-18 03:10:08,575] [INFO] Query marker FASTA was written to OceanDNA-b33391/markers.fasta
[2023-03-18 03:10:08,576] [INFO] Task started: Blastn
[2023-03-18 03:10:08,576] [INFO] Running command: blastn -query OceanDNA-b33391/markers.fasta -db /var/lib/cwl/stg5887d4cc-fd2e-4390-a196-8a8689496ede/dqc_reference/reference_markers.fasta -out OceanDNA-b33391/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:10:09,349] [INFO] Task succeeded: Blastn
[2023-03-18 03:10:09,350] [INFO] Selected 12 target genomes.
[2023-03-18 03:10:09,350] [INFO] Target genome list was writen to OceanDNA-b33391/target_genomes.txt
[2023-03-18 03:10:09,359] [INFO] Task started: fastANI
[2023-03-18 03:10:09,359] [INFO] Running command: fastANI --query /var/lib/cwl/stg08b01bca-8f43-4112-b884-c827758c10a1/OceanDNA-b33391.fa --refList OceanDNA-b33391/target_genomes.txt --output OceanDNA-b33391/fastani_result.tsv --threads 1
[2023-03-18 03:10:28,836] [INFO] Task succeeded: fastANI
[2023-03-18 03:10:28,836] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5887d4cc-fd2e-4390-a196-8a8689496ede/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:10:28,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5887d4cc-fd2e-4390-a196-8a8689496ede/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:10:28,844] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2023-03-18 03:10:28,844] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-03-18 03:10:28,844] [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
Paraburkholderia fungorum	strain=ATCC BAA-463	GCA_000961515.1	134537	134537	suspected-type	True	98.3405	1330	1522	95	inconclusive
Paraburkholderia fungorum	strain=LMG 16225	GCA_902833645.1	134537	134537	suspected-type	True	97.9167	1282	1522	95	inconclusive
Paraburkholderia fungorum	strain=NBRC 102489	GCA_000685055.1	134537	134537	type	True	97.802	1238	1522	95	inconclusive
Paraburkholderia agricolaris	strain=BaQS159	GCA_009455635.1	2152888	2152888	type	True	95.4959	1093	1522	95	inconclusive
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	88.864	975	1522	95	below_threshold
Paraburkholderia elongata	strain=5N	GCA_013177735.1	2675747	2675747	type	True	88.8571	992	1522	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	88.6754	1030	1522	95	below_threshold
Paraburkholderia solitsugae	strain=1N	GCA_013177695.1	2675748	2675748	type	True	88.4151	1008	1522	95	below_threshold
Paraburkholderia caffeinilytica	strain=CF1	GCA_003368325.1	1761016	1761016	type	True	88.3962	937	1522	95	below_threshold
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	88.3621	1016	1522	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	83.0177	725	1522	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	82.7294	758	1522	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:10:28,844] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33391/tc_result.tsv
[2023-03-18 03:10:28,844] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:10:28,844] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:10:28,845] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5887d4cc-fd2e-4390-a196-8a8689496ede/dqc_reference/checkm_data
[2023-03-18 03:10:28,845] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:10:28,854] [INFO] Task started: CheckM
[2023-03-18 03:10:28,854] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33391/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33391/checkm_input OceanDNA-b33391/checkm_result
[2023-03-18 03:11:44,275] [INFO] Task succeeded: CheckM
[2023-03-18 03:11:44,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.82%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:11:44,280] [INFO] ===== Completeness check finished =====
[2023-03-18 03:11:44,280] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:11:44,280] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33391/markers.fasta)
[2023-03-18 03:11:44,280] [INFO] Task started: Blastn
[2023-03-18 03:11:44,280] [INFO] Running command: blastn -query OceanDNA-b33391/markers.fasta -db /var/lib/cwl/stg5887d4cc-fd2e-4390-a196-8a8689496ede/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33391/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:11:45,677] [INFO] Task succeeded: Blastn
[2023-03-18 03:11:45,678] [INFO] Selected 14 target genomes.
[2023-03-18 03:11:45,678] [INFO] Target genome list was writen to OceanDNA-b33391/target_genomes_gtdb.txt
[2023-03-18 03:11:45,688] [INFO] Task started: fastANI
[2023-03-18 03:11:45,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg08b01bca-8f43-4112-b884-c827758c10a1/OceanDNA-b33391.fa --refList OceanDNA-b33391/target_genomes_gtdb.txt --output OceanDNA-b33391/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:12:07,873] [INFO] Task succeeded: fastANI
[2023-03-18 03:12:07,881] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:12:07,882] [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_902833645.1	s__Paraburkholderia fungorum	97.9026	1283	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.62	95.59	0.90	0.75	14	conclusive
GCF_003610895.1	s__Paraburkholderia fungorum_B	89.829	1097	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927345.1	s__Paraburkholderia sp012927345	89.1158	1065	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905220975.1	s__Paraburkholderia sp905220975	88.8889	973	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177735.1	s__Paraburkholderia sp013177735	88.8721	990	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001634365.1	s__Paraburkholderia sp001634365	88.8012	883	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116445.1	s__Paraburkholderia aspalathi	88.7937	1050	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	96.47	95.19	0.81	0.72	20	-
GCF_900142905.1	s__Paraburkholderia sp900142905	88.6578	1070	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.29	98.24	0.83	0.82	6	-
GCF_009690905.1	s__Paraburkholderia madseniana	88.6304	1050	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.82	98.82	0.85	0.85	2	-
GCF_905220835.1	s__Paraburkholderia sp905220835	88.5001	1005	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.73	99.56	0.96	0.94	13	-
GCF_003610295.1	s__Paraburkholderia sp003610295	88.4851	1015	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177695.1	s__Paraburkholderia sp013177695	88.4033	1009	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003368325.1	s__Paraburkholderia caffeinilytica	88.3778	939	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003353175.1	s__Paraburkholderia lacunae	85.6419	868	1522	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:12:07,882] [INFO] GTDB search result was written to OceanDNA-b33391/result_gtdb.tsv
[2023-03-18 03:12:07,882] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:12:07,883] [INFO] DFAST_QC result json was written to OceanDNA-b33391/dqc_result.json
[2023-03-18 03:12:07,884] [INFO] DFAST_QC completed!
[2023-03-18 03:12:07,884] [INFO] Total running time: 0h2m32s