[2023-03-16 07:49:28,868] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:49:28,868] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:49:28,868] [INFO] DQC Reference Directory: /var/lib/cwl/stg1805c7f9-59d8-4a0b-b53e-3e3f33e1041a/dqc_reference
[2023-03-16 07:49:29,955] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:49:29,955] [INFO] Task started: Prodigal
[2023-03-16 07:49:29,955] [INFO] Running command: cat /var/lib/cwl/stg5520d1f8-25ef-488a-b497-ac8418df0d0a/OceanDNA-b33512.fa | prodigal -d OceanDNA-b33512/cds.fna -a OceanDNA-b33512/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:49:58,498] [INFO] Task succeeded: Prodigal
[2023-03-16 07:49:58,499] [INFO] Task started: HMMsearch
[2023-03-16 07:49:58,499] [INFO] Running command: hmmsearch --tblout OceanDNA-b33512/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1805c7f9-59d8-4a0b-b53e-3e3f33e1041a/dqc_reference/reference_markers.hmm OceanDNA-b33512/protein.faa > /dev/null
[2023-03-16 07:49:58,747] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:49:58,747] [INFO] Found 6/6 markers.
[2023-03-16 07:49:58,786] [INFO] Query marker FASTA was written to OceanDNA-b33512/markers.fasta
[2023-03-16 07:49:58,786] [INFO] Task started: Blastn
[2023-03-16 07:49:58,786] [INFO] Running command: blastn -query OceanDNA-b33512/markers.fasta -db /var/lib/cwl/stg1805c7f9-59d8-4a0b-b53e-3e3f33e1041a/dqc_reference/reference_markers.fasta -out OceanDNA-b33512/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:49:59,568] [INFO] Task succeeded: Blastn
[2023-03-16 07:49:59,571] [INFO] Selected 10 target genomes.
[2023-03-16 07:49:59,572] [INFO] Target genome list was writen to OceanDNA-b33512/target_genomes.txt
[2023-03-16 07:49:59,578] [INFO] Task started: fastANI
[2023-03-16 07:49:59,578] [INFO] Running command: fastANI --query /var/lib/cwl/stg5520d1f8-25ef-488a-b497-ac8418df0d0a/OceanDNA-b33512.fa --refList OceanDNA-b33512/target_genomes.txt --output OceanDNA-b33512/fastani_result.tsv --threads 1
[2023-03-16 07:50:11,012] [INFO] Task succeeded: fastANI
[2023-03-16 07:50:11,012] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1805c7f9-59d8-4a0b-b53e-3e3f33e1041a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:50:11,013] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1805c7f9-59d8-4a0b-b53e-3e3f33e1041a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:50:11,020] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2023-03-16 07:50:11,020] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 07:50:11,020] [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
Ralstonia pickettii	strain=FDAARGOS_1535	GCA_020341455.1	329	329	type	True	99.1017	1321	1425	95	conclusive
Ralstonia pickettii	strain=K-288	GCA_016466415.2	329	329	type	True	99.0813	1285	1425	95	conclusive
Ralstonia pickettii	strain=ATCC 27511	GCA_000743455.1	329	329	type	True	99.0739	1287	1425	95	conclusive
Ralstonia pickettii	strain=NBRC 102503	GCA_001544155.1	329	329	type	True	99.0692	1279	1425	95	conclusive
Ralstonia pickettii	strain=NCTC11149	GCA_900455835.1	329	329	type	True	99.0403	1289	1425	95	conclusive
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	84.5471	862	1425	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	84.4485	887	1425	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	78.3457	450	1425	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	78.3205	449	1425	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	77.8878	390	1425	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:50:11,020] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33512/tc_result.tsv
[2023-03-16 07:50:11,020] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:50:11,020] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:50:11,020] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1805c7f9-59d8-4a0b-b53e-3e3f33e1041a/dqc_reference/checkm_data
[2023-03-16 07:50:11,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:50:11,028] [INFO] Task started: CheckM
[2023-03-16 07:50:11,028] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33512/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33512/checkm_input OceanDNA-b33512/checkm_result
[2023-03-16 07:51:22,917] [INFO] Task succeeded: CheckM
[2023-03-16 07:51:22,917] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.06%
Contamintation: 10.42%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 07:51:22,945] [INFO] ===== Completeness check finished =====
[2023-03-16 07:51:22,945] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:51:22,945] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33512/markers.fasta)
[2023-03-16 07:51:22,946] [INFO] Task started: Blastn
[2023-03-16 07:51:22,946] [INFO] Running command: blastn -query OceanDNA-b33512/markers.fasta -db /var/lib/cwl/stg1805c7f9-59d8-4a0b-b53e-3e3f33e1041a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33512/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:51:24,326] [INFO] Task succeeded: Blastn
[2023-03-16 07:51:24,330] [INFO] Selected 8 target genomes.
[2023-03-16 07:51:24,330] [INFO] Target genome list was writen to OceanDNA-b33512/target_genomes_gtdb.txt
[2023-03-16 07:51:24,340] [INFO] Task started: fastANI
[2023-03-16 07:51:24,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg5520d1f8-25ef-488a-b497-ac8418df0d0a/OceanDNA-b33512.fa --refList OceanDNA-b33512/target_genomes_gtdb.txt --output OceanDNA-b33512/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:51:34,042] [INFO] Task succeeded: fastANI
[2023-03-16 07:51:34,047] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-16 07:51:34,047] [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_016466415.1	s__Ralstonia pickettii	99.0813	1285	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	97.89	95.45	0.93	0.86	44	inconclusive
GCF_000020205.1	s__Ralstonia pickettii_B	95.1206	1236	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	98.08	96.31	0.87	0.83	22	inconclusive
GCF_000620465.1	s__Ralstonia sp000620465	92.6021	1155	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	96.59	96.59	0.94	0.94	2	-
GCF_007997035.1	s__Ralstonia sp007997035	92.0796	1081	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115545.1	s__Ralstonia sp900115545	91.5247	1149	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	98.84	98.84	0.97	0.97	2	-
GCF_000607165.1	s__Ralstonia pickettii_A	91.3858	1196	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	99.13	99.13	0.91	0.91	2	-
GCA_000955795.1	s__Ralstonia sp000955795	91.1647	1160	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000801955.1	s__Ralstonia sp000801955	86.9697	1063	1425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ralstonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:51:34,049] [INFO] GTDB search result was written to OceanDNA-b33512/result_gtdb.tsv
[2023-03-16 07:51:34,049] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:51:34,050] [INFO] DFAST_QC result json was written to OceanDNA-b33512/dqc_result.json
[2023-03-16 07:51:34,050] [INFO] DFAST_QC completed!
[2023-03-16 07:51:34,050] [INFO] Total running time: 0h2m5s