[2023-03-18 09:15:00,469] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:15:00,469] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:15:00,469] [INFO] DQC Reference Directory: /var/lib/cwl/stg71bcadf7-15e2-4162-bc94-805a3a6f6b3a/dqc_reference
[2023-03-18 09:15:02,030] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:15:02,030] [INFO] Task started: Prodigal
[2023-03-18 09:15:02,031] [INFO] Running command: cat /var/lib/cwl/stgaa502184-5227-44c2-8b71-d45d8b9cf5a5/OceanDNA-b35150.fa | prodigal -d OceanDNA-b35150/cds.fna -a OceanDNA-b35150/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:15:19,940] [INFO] Task succeeded: Prodigal
[2023-03-18 09:15:19,940] [INFO] Task started: HMMsearch
[2023-03-18 09:15:19,940] [INFO] Running command: hmmsearch --tblout OceanDNA-b35150/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71bcadf7-15e2-4162-bc94-805a3a6f6b3a/dqc_reference/reference_markers.hmm OceanDNA-b35150/protein.faa > /dev/null
[2023-03-18 09:15:20,143] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:15:20,143] [INFO] Found 6/6 markers.
[2023-03-18 09:15:20,162] [INFO] Query marker FASTA was written to OceanDNA-b35150/markers.fasta
[2023-03-18 09:15:20,164] [INFO] Task started: Blastn
[2023-03-18 09:15:20,164] [INFO] Running command: blastn -query OceanDNA-b35150/markers.fasta -db /var/lib/cwl/stg71bcadf7-15e2-4162-bc94-805a3a6f6b3a/dqc_reference/reference_markers.fasta -out OceanDNA-b35150/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:15:20,919] [INFO] Task succeeded: Blastn
[2023-03-18 09:15:20,920] [INFO] Selected 15 target genomes.
[2023-03-18 09:15:20,920] [INFO] Target genome list was writen to OceanDNA-b35150/target_genomes.txt
[2023-03-18 09:15:20,929] [INFO] Task started: fastANI
[2023-03-18 09:15:20,929] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa502184-5227-44c2-8b71-d45d8b9cf5a5/OceanDNA-b35150.fa --refList OceanDNA-b35150/target_genomes.txt --output OceanDNA-b35150/fastani_result.tsv --threads 1
[2023-03-18 09:15:32,538] [INFO] Task succeeded: fastANI
[2023-03-18 09:15:32,539] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71bcadf7-15e2-4162-bc94-805a3a6f6b3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:15:32,539] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71bcadf7-15e2-4162-bc94-805a3a6f6b3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:15:32,548] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:15:32,548] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:15:32,548] [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
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	86.9227	848	988	95	below_threshold
Erwinia aphidicola	strain=JCM 21238	GCA_014773485.1	68334	68334	type	True	86.8222	853	988	95	below_threshold
Erwinia persicina	strain=NBRC 102418	GCA_001571305.1	55211	55211	type	True	82.7618	740	988	95	below_threshold
Erwinia pyrifoliae	strain=DSM 12163	GCA_000026985.1	79967	79967	type	True	81.2976	580	988	95	below_threshold
Erwinia tasmaniensis	strain=Et1/99	GCA_000026185.1	338565	338565	type	True	81.2181	598	988	95	below_threshold
Erwinia amylovora	strain=ATCC 15580	GCA_017161565.1	552	552	type	True	81.1419	566	988	95	below_threshold
Erwinia amylovora	strain=NBRC 12687	GCA_000696075.1	552	552	type	True	81.1099	563	988	95	below_threshold
Erwinia amylovora	strain=type strain: CFBP 1232	GCA_000367625.2	552	552	type	True	81.0628	562	988	95	below_threshold
Erwinia piriflorinigrans	strain=CFBP 5888	GCA_001050515.1	665097	665097	type	True	80.9706	577	988	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	80.1814	530	988	95	below_threshold
Pantoea eucalypti	strain=LMG 24197	GCA_009646115.1	470933	470933	type	True	79.9133	470	988	95	below_threshold
Pantoea eucalypti	strain=LMG 24197	GCA_006494355.1	470933	470933	type	True	79.8226	473	988	95	below_threshold
Pantoea agglomerans	strain=NBRC 102470	GCA_001598475.1	549	549	suspected-type	True	79.4121	498	988	95	below_threshold
Pantoea agglomerans	strain=FDAARGOS 1447	GCA_019048385.1	549	549	suspected-type	True	79.3959	517	988	95	below_threshold
Pantoea conspicua	strain=LMG 24534	GCA_002095315.1	472705	472705	type	True	79.2671	490	988	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:15:32,549] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35150/tc_result.tsv
[2023-03-18 09:15:32,549] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:15:32,549] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:15:32,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71bcadf7-15e2-4162-bc94-805a3a6f6b3a/dqc_reference/checkm_data
[2023-03-18 09:15:32,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:15:32,554] [INFO] Task started: CheckM
[2023-03-18 09:15:32,554] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35150/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35150/checkm_input OceanDNA-b35150/checkm_result
[2023-03-18 09:16:18,735] [INFO] Task succeeded: CheckM
[2023-03-18 09:16:18,735] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:16:18,738] [INFO] ===== Completeness check finished =====
[2023-03-18 09:16:18,738] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:16:18,738] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35150/markers.fasta)
[2023-03-18 09:16:18,738] [INFO] Task started: Blastn
[2023-03-18 09:16:18,738] [INFO] Running command: blastn -query OceanDNA-b35150/markers.fasta -db /var/lib/cwl/stg71bcadf7-15e2-4162-bc94-805a3a6f6b3a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35150/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:16:19,774] [INFO] Task succeeded: Blastn
[2023-03-18 09:16:19,775] [INFO] Selected 15 target genomes.
[2023-03-18 09:16:19,775] [INFO] Target genome list was writen to OceanDNA-b35150/target_genomes_gtdb.txt
[2023-03-18 09:16:20,064] [INFO] Task started: fastANI
[2023-03-18 09:16:20,065] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa502184-5227-44c2-8b71-d45d8b9cf5a5/OceanDNA-b35150.fa --refList OceanDNA-b35150/target_genomes_gtdb.txt --output OceanDNA-b35150/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:16:32,520] [INFO] Task succeeded: fastANI
[2023-03-18 09:16:32,529] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:16:32,529] [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_014773485.1	s__Erwinia aphidicola	86.8396	852	988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.08	98.09	0.88	0.85	7	-
GCF_001756855.1	s__Erwinia dacicola	86.0649	282	988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.47	98.24	0.66	0.61	4	-
GCF_014838825.1	s__Erwinia persicina_A	82.8166	729	988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.46	99.46	0.97	0.97	2	-
GCF_001571305.1	s__Erwinia persicina	82.7541	741	988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.41	99.25	0.96	0.94	13	-
GCF_012271765.1	s__Erwinia rhapontici	82.74	728	988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.76	96.56	0.93	0.92	9	-
GCF_009738185.1	s__Erwinia sp009738185	82.4332	705	988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.50	99.50	0.98	0.98	2	-
GCF_018141005.1	s__Erwinia sp001422605	81.5927	645	988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.39	98.36	0.92	0.92	3	-
GCF_016909495.1	s__Erwinia coffeiphila	81.5517	662	988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	96.75	96.67	0.88	0.87	4	-
GCF_000026185.1	s__Erwinia tasmaniensis	81.1965	600	988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017161565.1	s__Erwinia amylovora	81.1313	567	988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.73	98.13	0.99	0.95	141	-
GCF_009646115.1	s__Pantoea eucalypti	79.9249	469	988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.21	98.96	0.95	0.93	16	-
GCF_004792415.1	s__Pantoea vagans	79.5044	509	988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.00	95.86	0.91	0.88	14	-
GCF_001598475.1	s__Pantoea agglomerans	79.4117	498	988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.21	96.93	0.94	0.88	124	-
GCF_900115075.1	s__Pantoea sp900115075	79.3569	506	988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	96.06	96.06	0.92	0.92	2	-
GCF_013415305.1	s__Pantoea sp002419935	79.3065	483	988	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.92	98.92	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-18 09:16:32,530] [INFO] GTDB search result was written to OceanDNA-b35150/result_gtdb.tsv
[2023-03-18 09:16:32,530] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:16:32,532] [INFO] DFAST_QC result json was written to OceanDNA-b35150/dqc_result.json
[2023-03-18 09:16:32,532] [INFO] DFAST_QC completed!
[2023-03-18 09:16:32,532] [INFO] Total running time: 0h1m32s