[2023-03-14 14:16:15,382] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:16:15,382] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:16:15,382] [INFO] DQC Reference Directory: /var/lib/cwl/stgb99edd97-3933-4999-a7b7-d7496b5a9924/dqc_reference
[2023-03-14 14:16:16,460] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:16:16,460] [INFO] Task started: Prodigal
[2023-03-14 14:16:16,461] [INFO] Running command: cat /var/lib/cwl/stg27d2684c-978f-4345-a550-5ba9358b10dd/OceanDNA-b40439.fa | prodigal -d OceanDNA-b40439/cds.fna -a OceanDNA-b40439/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:16:51,084] [INFO] Task succeeded: Prodigal
[2023-03-14 14:16:51,084] [INFO] Task started: HMMsearch
[2023-03-14 14:16:51,084] [INFO] Running command: hmmsearch --tblout OceanDNA-b40439/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb99edd97-3933-4999-a7b7-d7496b5a9924/dqc_reference/reference_markers.hmm OceanDNA-b40439/protein.faa > /dev/null
[2023-03-14 14:16:51,560] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:16:51,561] [INFO] Found 6/6 markers.
[2023-03-14 14:16:51,598] [INFO] Query marker FASTA was written to OceanDNA-b40439/markers.fasta
[2023-03-14 14:16:51,598] [INFO] Task started: Blastn
[2023-03-14 14:16:51,598] [INFO] Running command: blastn -query OceanDNA-b40439/markers.fasta -db /var/lib/cwl/stgb99edd97-3933-4999-a7b7-d7496b5a9924/dqc_reference/reference_markers.fasta -out OceanDNA-b40439/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:16:52,515] [INFO] Task succeeded: Blastn
[2023-03-14 14:16:52,516] [INFO] Selected 24 target genomes.
[2023-03-14 14:16:52,517] [INFO] Target genome list was writen to OceanDNA-b40439/target_genomes.txt
[2023-03-14 14:16:52,546] [INFO] Task started: fastANI
[2023-03-14 14:16:52,546] [INFO] Running command: fastANI --query /var/lib/cwl/stg27d2684c-978f-4345-a550-5ba9358b10dd/OceanDNA-b40439.fa --refList OceanDNA-b40439/target_genomes.txt --output OceanDNA-b40439/fastani_result.tsv --threads 1
[2023-03-14 14:17:11,525] [INFO] Task succeeded: fastANI
[2023-03-14 14:17:11,525] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb99edd97-3933-4999-a7b7-d7496b5a9924/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:17:11,526] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb99edd97-3933-4999-a7b7-d7496b5a9924/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:17:11,537] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:17:11,537] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 14:17:11,537] [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
Pseudohongiella acticola	strain=KCTC 42131	GCA_001758195.1	1524254	1524254	type	True	81.1079	739	1211	95	below_threshold
Pseudohongiella nitratireducens	strain=CGMCC 1.15425	GCA_014642795.1	1768907	1768907	type	True	78.039	169	1211	95	below_threshold
Pseudohongiella nitratireducens	strain=SCS-49	GCA_001642735.1	1768907	1768907	type	True	77.8399	168	1211	95	below_threshold
Pseudohongiella spirulinae	strain=KCTC 32221	GCA_001444425.1	1249552	1249552	type	True	77.6509	277	1211	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.0689	62	1211	95	below_threshold
Pseudomonas farsensis	strain=SWRI107	GCA_014268805.2	2745492	2745492	type	True	75.9391	62	1211	95	below_threshold
Pseudomonas furukawaii	strain=KF707	GCA_000262065.3	1149133	1149133	type	True	75.9176	75	1211	95	below_threshold
Pseudomonas furukawaii	strain=KF707	GCA_002355475.1	1149133	1149133	type	True	75.9089	75	1211	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	75.8321	63	1211	95	below_threshold
Stutzerimonas xanthomarina	strain=DSM 18231	GCA_900129835.1	271420	271420	suspected-type	True	75.7304	53	1211	95	below_threshold
Stutzerimonas xanthomarina	strain=DSM 18231	GCA_024328335.1	271420	271420	suspected-type	True	75.6848	51	1211	95	below_threshold
Pseudomonas chengduensis	strain=MBR	GCA_017905455.1	489632	489632	type	True	75.6439	80	1211	95	below_threshold
Pseudomonas chengduensis	strain=DSM 26382	GCA_012986985.1	489632	489632	type	True	75.6421	78	1211	95	below_threshold
Alcanivorax sediminis	strain=PA15-N-34	GCA_009601165.1	2663008	2663008	type	True	75.6274	61	1211	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.6149	87	1211	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	75.5614	66	1211	95	below_threshold
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	75.5482	82	1211	95	below_threshold
Pseudomonas umsongensis	strain=DSM 16611	GCA_002236105.1	198618	198618	type	True	75.5465	55	1211	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	75.3905	54	1211	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 14:17:11,538] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40439/tc_result.tsv
[2023-03-14 14:17:11,541] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:17:11,541] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:17:11,541] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb99edd97-3933-4999-a7b7-d7496b5a9924/dqc_reference/checkm_data
[2023-03-14 14:17:11,542] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:17:11,555] [INFO] Task started: CheckM
[2023-03-14 14:17:11,555] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40439/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40439/checkm_input OceanDNA-b40439/checkm_result
[2023-03-14 14:18:19,863] [INFO] Task succeeded: CheckM
[2023-03-14 14:18:19,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:18:19,866] [INFO] ===== Completeness check finished =====
[2023-03-14 14:18:19,866] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:18:19,867] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40439/markers.fasta)
[2023-03-14 14:18:19,868] [INFO] Task started: Blastn
[2023-03-14 14:18:19,868] [INFO] Running command: blastn -query OceanDNA-b40439/markers.fasta -db /var/lib/cwl/stgb99edd97-3933-4999-a7b7-d7496b5a9924/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40439/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:18:21,023] [INFO] Task succeeded: Blastn
[2023-03-14 14:18:21,024] [INFO] Selected 11 target genomes.
[2023-03-14 14:18:21,024] [INFO] Target genome list was writen to OceanDNA-b40439/target_genomes_gtdb.txt
[2023-03-14 14:18:21,088] [INFO] Task started: fastANI
[2023-03-14 14:18:21,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg27d2684c-978f-4345-a550-5ba9358b10dd/OceanDNA-b40439.fa --refList OceanDNA-b40439/target_genomes_gtdb.txt --output OceanDNA-b40439/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:18:28,479] [INFO] Task succeeded: fastANI
[2023-03-14 14:18:28,485] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:18:28,486] [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
GCA_002711845.1	s__Pseudohongiella sp002711845	83.3069	904	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.97	99.97	0.98	0.98	2	-
GCA_011050365.1	s__Pseudohongiella sp011050365	81.9965	810	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001758195.1	s__Pseudohongiella acticola	81.0906	741	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354805.1	s__Pseudohongiella sp002354805	78.605	310	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.49	99.10	0.99	0.98	3	-
GCA_002706685.1	s__Pseudohongiella sp002706685	78.2108	318	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.93	99.90	0.98	0.96	5	-
GCF_001642735.1	s__Pseudohongiella nitratireducens	77.8804	166	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.60	98.82	0.97	0.93	4	-
GCF_001444425.1	s__Pseudohongiella spirulinae	77.6362	279	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004535785.1	s__Pseudohongiella sp004535785	77.1632	210	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002803095.1	s__Pseudomonas_E sp002803095	75.7192	79	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.6432	99.96	99.96	0.99	0.99	2	-
GCF_019061305.1	s__Marinobacterium sp019061305	75.2481	54	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:18:28,486] [INFO] GTDB search result was written to OceanDNA-b40439/result_gtdb.tsv
[2023-03-14 14:18:28,486] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:18:28,488] [INFO] DFAST_QC result json was written to OceanDNA-b40439/dqc_result.json
[2023-03-14 14:18:28,488] [INFO] DFAST_QC completed!
[2023-03-14 14:18:28,488] [INFO] Total running time: 0h2m13s