[2023-03-16 10:20:34,787] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:20:34,787] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:20:34,787] [INFO] DQC Reference Directory: /var/lib/cwl/stgf51b19b4-ea98-4208-bd04-5071693bc0f4/dqc_reference
[2023-03-16 10:20:35,926] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:20:35,926] [INFO] Task started: Prodigal
[2023-03-16 10:20:35,926] [INFO] Running command: cat /var/lib/cwl/stg80f5d25e-19a8-4b25-b809-1d9cb3344870/OceanDNA-b35156.fa | prodigal -d OceanDNA-b35156/cds.fna -a OceanDNA-b35156/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:21:01,070] [INFO] Task succeeded: Prodigal
[2023-03-16 10:21:01,071] [INFO] Task started: HMMsearch
[2023-03-16 10:21:01,071] [INFO] Running command: hmmsearch --tblout OceanDNA-b35156/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf51b19b4-ea98-4208-bd04-5071693bc0f4/dqc_reference/reference_markers.hmm OceanDNA-b35156/protein.faa > /dev/null
[2023-03-16 10:21:01,366] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:21:01,367] [INFO] Found 6/6 markers.
[2023-03-16 10:21:01,392] [INFO] Query marker FASTA was written to OceanDNA-b35156/markers.fasta
[2023-03-16 10:21:01,393] [INFO] Task started: Blastn
[2023-03-16 10:21:01,393] [INFO] Running command: blastn -query OceanDNA-b35156/markers.fasta -db /var/lib/cwl/stgf51b19b4-ea98-4208-bd04-5071693bc0f4/dqc_reference/reference_markers.fasta -out OceanDNA-b35156/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:21:02,223] [INFO] Task succeeded: Blastn
[2023-03-16 10:21:02,224] [INFO] Selected 12 target genomes.
[2023-03-16 10:21:02,224] [INFO] Target genome list was writen to OceanDNA-b35156/target_genomes.txt
[2023-03-16 10:21:02,232] [INFO] Task started: fastANI
[2023-03-16 10:21:02,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg80f5d25e-19a8-4b25-b809-1d9cb3344870/OceanDNA-b35156.fa --refList OceanDNA-b35156/target_genomes.txt --output OceanDNA-b35156/fastani_result.tsv --threads 1
[2023-03-16 10:21:14,530] [INFO] Task succeeded: fastANI
[2023-03-16 10:21:14,530] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf51b19b4-ea98-4208-bd04-5071693bc0f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:21:14,530] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf51b19b4-ea98-4208-bd04-5071693bc0f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:21:14,538] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:21:14,538] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:21:14,538] [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
Pantoea rodasii	strain=LMG 26273	GCA_002095465.1	1076549	1076549	type	True	89.4029	1182	1321	95	below_threshold
Pantoea rodasii	strain=DSM 26611	GCA_002811195.1	1076549	1076549	type	True	89.3918	1181	1321	95	below_threshold
Pantoea rwandensis	strain=LMG 26275	GCA_002095475.1	1076550	1076550	type	True	87.2426	1095	1321	95	below_threshold
Pantoea endophytica	strain=596	GCA_002858935.1	92488	92488	type	True	84.572	1074	1321	95	below_threshold
Pantoea dispersa	strain=CCUG 25232T	GCA_008692915.1	59814	59814	type	True	83.8208	971	1321	95	below_threshold
Pantoea dispersa	strain=DSM 30073	GCA_014155765.1	59814	59814	type	True	83.7615	993	1321	95	below_threshold
Pantoea wallisii	strain=LMG 26277	GCA_002095485.1	1076551	1076551	type	True	83.2908	919	1321	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	80.2126	743	1321	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	79.2363	597	1321	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	78.9386	618	1321	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	78.0109	400	1321	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	77.8222	369	1321	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:21:14,539] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35156/tc_result.tsv
[2023-03-16 10:21:14,539] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:21:14,539] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:21:14,539] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf51b19b4-ea98-4208-bd04-5071693bc0f4/dqc_reference/checkm_data
[2023-03-16 10:21:14,540] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:21:14,547] [INFO] Task started: CheckM
[2023-03-16 10:21:14,547] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35156/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35156/checkm_input OceanDNA-b35156/checkm_result
[2023-03-16 10:22:16,915] [INFO] Task succeeded: CheckM
[2023-03-16 10:22:16,916] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:22:16,919] [INFO] ===== Completeness check finished =====
[2023-03-16 10:22:16,919] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:22:16,919] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35156/markers.fasta)
[2023-03-16 10:22:16,920] [INFO] Task started: Blastn
[2023-03-16 10:22:16,921] [INFO] Running command: blastn -query OceanDNA-b35156/markers.fasta -db /var/lib/cwl/stgf51b19b4-ea98-4208-bd04-5071693bc0f4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35156/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:22:18,192] [INFO] Task succeeded: Blastn
[2023-03-16 10:22:18,193] [INFO] Selected 9 target genomes.
[2023-03-16 10:22:18,193] [INFO] Target genome list was writen to OceanDNA-b35156/target_genomes_gtdb.txt
[2023-03-16 10:22:18,199] [INFO] Task started: fastANI
[2023-03-16 10:22:18,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg80f5d25e-19a8-4b25-b809-1d9cb3344870/OceanDNA-b35156.fa --refList OceanDNA-b35156/target_genomes_gtdb.txt --output OceanDNA-b35156/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:22:28,951] [INFO] Task succeeded: fastANI
[2023-03-16 10:22:28,957] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:22:28,958] [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_000759475.1	s__Pantoea rwandensis_B	98.0355	1161	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.54	98.22	0.92	0.90	5	conclusive
GCF_000773965.1	s__Pantoea cancerogena_A	94.1281	1211	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	96.89	96.70	0.91	0.89	9	-
GCF_016625195.1	s__Pantoea sp016625195	92.0031	1205	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002095465.1	s__Pantoea rodasii	89.4029	1182	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.97	99.97	1.00	1.00	2	-
GCF_011752625.1	s__Pantoea sp011752625	87.6175	1128	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002095475.1	s__Pantoea rwandensis	87.2142	1098	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001506165.1	s__Pantoea vagans_C	86.5139	1088	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.95	97.99	0.91	0.89	3	-
GCF_002858935.1	s__Pantoea endophytica	84.5898	1071	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.84	95.24	0.93	0.88	7	-
GCF_900068835.1	s__Pantoea ludwigii_B	84.5761	1073	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.17	96.60	0.91	0.89	10	-
--------------------------------------------------------------------------------
[2023-03-16 10:22:28,958] [INFO] GTDB search result was written to OceanDNA-b35156/result_gtdb.tsv
[2023-03-16 10:22:28,958] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:22:28,960] [INFO] DFAST_QC result json was written to OceanDNA-b35156/dqc_result.json
[2023-03-16 10:22:28,960] [INFO] DFAST_QC completed!
[2023-03-16 10:22:28,960] [INFO] Total running time: 0h1m54s