[2023-03-18 00:21:54,211] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:21:54,212] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:21:54,212] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a626485-5ed2-43ad-8247-9bae6fd75aa9/dqc_reference
[2023-03-18 00:21:55,650] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:21:55,650] [INFO] Task started: Prodigal
[2023-03-18 00:21:55,651] [INFO] Running command: cat /var/lib/cwl/stg2861907d-9430-4ff1-a2a5-2657740106b0/OceanDNA-b35158.fa | prodigal -d OceanDNA-b35158/cds.fna -a OceanDNA-b35158/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:22:13,081] [INFO] Task succeeded: Prodigal
[2023-03-18 00:22:13,081] [INFO] Task started: HMMsearch
[2023-03-18 00:22:13,081] [INFO] Running command: hmmsearch --tblout OceanDNA-b35158/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a626485-5ed2-43ad-8247-9bae6fd75aa9/dqc_reference/reference_markers.hmm OceanDNA-b35158/protein.faa > /dev/null
[2023-03-18 00:22:13,278] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:22:13,279] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2861907d-9430-4ff1-a2a5-2657740106b0/OceanDNA-b35158.fa]
[2023-03-18 00:22:13,299] [INFO] Query marker FASTA was written to OceanDNA-b35158/markers.fasta
[2023-03-18 00:22:13,299] [INFO] Task started: Blastn
[2023-03-18 00:22:13,299] [INFO] Running command: blastn -query OceanDNA-b35158/markers.fasta -db /var/lib/cwl/stg2a626485-5ed2-43ad-8247-9bae6fd75aa9/dqc_reference/reference_markers.fasta -out OceanDNA-b35158/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:22:14,044] [INFO] Task succeeded: Blastn
[2023-03-18 00:22:14,045] [INFO] Selected 18 target genomes.
[2023-03-18 00:22:14,045] [INFO] Target genome list was writen to OceanDNA-b35158/target_genomes.txt
[2023-03-18 00:22:14,055] [INFO] Task started: fastANI
[2023-03-18 00:22:14,055] [INFO] Running command: fastANI --query /var/lib/cwl/stg2861907d-9430-4ff1-a2a5-2657740106b0/OceanDNA-b35158.fa --refList OceanDNA-b35158/target_genomes.txt --output OceanDNA-b35158/fastani_result.tsv --threads 1
[2023-03-18 00:22:28,047] [INFO] Task succeeded: fastANI
[2023-03-18 00:22:28,047] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a626485-5ed2-43ad-8247-9bae6fd75aa9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:22:28,047] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a626485-5ed2-43ad-8247-9bae6fd75aa9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:22:28,058] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:22:28,058] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:22:28,058] [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 dispersa	strain=CCUG 25232T	GCA_008692915.1	59814	59814	type	True	80.6382	504	962	95	below_threshold
Pantoea dispersa	strain=DSM 30073	GCA_014155765.1	59814	59814	type	True	80.5643	511	962	95	below_threshold
Pantoea rodasii	strain=DSM 26611	GCA_002811195.1	1076549	1076549	type	True	80.3608	515	962	95	below_threshold
Pantoea endophytica	strain=596	GCA_002858935.1	92488	92488	type	True	80.3288	516	962	95	below_threshold
Pantoea rodasii	strain=LMG 26273	GCA_002095465.1	1076549	1076549	type	True	80.3025	525	962	95	below_threshold
Pantoea rwandensis	strain=LMG 26275	GCA_002095475.1	1076550	1076550	type	True	80.2436	478	962	95	below_threshold
Pantoea cypripedii	strain=LMG 2657	GCA_002095535.1	55209	55209	type	True	80.2359	526	962	95	below_threshold
Pantoea wallisii	strain=LMG 26277	GCA_002095485.1	1076551	1076551	type	True	80.0636	476	962	95	below_threshold
Pantoea conspicua	strain=LMG 24534	GCA_002095315.1	472705	472705	type	True	80.0003	473	962	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	79.9265	462	962	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_002095375.1	470932	470932	type	True	79.9263	438	962	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_006494415.1	470932	470932	type	True	79.8899	463	962	95	below_threshold
Pantoea agglomerans	strain=NBRC 102470	GCA_001598475.1	549	549	suspected-type	True	79.7388	481	962	95	below_threshold
Pantoea agglomerans	strain=FDAARGOS 1447	GCA_019048385.1	549	549	suspected-type	True	79.725	495	962	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	79.1379	401	962	95	below_threshold
Erwinia iniecta	strain=B120	GCA_001267535.1	1560201	1560201	type	True	79.0543	401	962	95	below_threshold
Mixta calida	strain=DSM 22759	GCA_002953215.1	665913	665913	type	True	78.6264	361	962	95	below_threshold
Mixta calida	strain=LMG 25383	GCA_002095355.1	665913	665913	type	True	78.6221	337	962	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:22:28,059] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35158/tc_result.tsv
[2023-03-18 00:22:28,059] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:22:28,059] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:22:28,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a626485-5ed2-43ad-8247-9bae6fd75aa9/dqc_reference/checkm_data
[2023-03-18 00:22:28,060] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:22:28,064] [INFO] Task started: CheckM
[2023-03-18 00:22:28,064] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35158/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35158/checkm_input OceanDNA-b35158/checkm_result
[2023-03-18 00:23:13,274] [INFO] Task succeeded: CheckM
[2023-03-18 00:23:13,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:23:13,277] [INFO] ===== Completeness check finished =====
[2023-03-18 00:23:13,277] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:23:13,277] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35158/markers.fasta)
[2023-03-18 00:23:13,277] [INFO] Task started: Blastn
[2023-03-18 00:23:13,277] [INFO] Running command: blastn -query OceanDNA-b35158/markers.fasta -db /var/lib/cwl/stg2a626485-5ed2-43ad-8247-9bae6fd75aa9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35158/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:23:14,216] [INFO] Task succeeded: Blastn
[2023-03-18 00:23:14,216] [INFO] Selected 18 target genomes.
[2023-03-18 00:23:14,217] [INFO] Target genome list was writen to OceanDNA-b35158/target_genomes_gtdb.txt
[2023-03-18 00:23:14,236] [INFO] Task started: fastANI
[2023-03-18 00:23:14,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg2861907d-9430-4ff1-a2a5-2657740106b0/OceanDNA-b35158.fa --refList OceanDNA-b35158/target_genomes_gtdb.txt --output OceanDNA-b35158/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:23:30,350] [INFO] Task succeeded: fastANI
[2023-03-18 00:23:30,360] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:23:30,360] [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_000295955.2	s__Pantoea sp000295955	97.2169	886	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	96.16	96.16	0.90	0.90	2	conclusive
GCF_014155765.1	s__Pantoea dispersa	80.5838	509	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.93	96.36	0.92	0.86	38	-
GCF_011752625.1	s__Pantoea sp011752625	80.3873	492	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759475.1	s__Pantoea rwandensis_B	80.3588	515	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.54	98.22	0.92	0.90	5	-
GCF_001506165.1	s__Pantoea vagans_C	80.3356	509	962	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	80.318	517	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.84	95.24	0.93	0.88	7	-
GCF_000773965.1	s__Pantoea cancerogena_A	80.3158	510	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	96.89	96.70	0.91	0.89	9	-
GCF_002095465.1	s__Pantoea rodasii	80.2947	525	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.97	99.97	1.00	1.00	2	-
GCF_011395035.1	s__Pantoea cypripedii_A	80.222	518	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900068835.1	s__Pantoea ludwigii_B	80.1038	537	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.17	96.60	0.91	0.89	10	-
GCF_002095315.1	s__Pantoea conspicua	79.9982	472	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002434205.1	s__Pantoea sp002434205	79.9683	508	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002095305.1	s__Pantoea brenneri	79.9133	480	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.27	99.10	0.90	0.85	24	-
GCF_004792415.1	s__Pantoea vagans	79.7353	490	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.00	95.86	0.91	0.88	14	-
GCF_018842675.1	s__Pantoea sp018842675	79.5226	445	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013753875.1	s__Pantoea persica	79.198	336	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001267535.1	s__Erwinia iniecta	79.0615	400	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.95	99.95	0.99	0.99	2	-
GCF_017875465.1	s__Erwinia toletana	78.925	427	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.93	99.93	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-03-18 00:23:30,361] [INFO] GTDB search result was written to OceanDNA-b35158/result_gtdb.tsv
[2023-03-18 00:23:30,361] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:23:30,363] [INFO] DFAST_QC result json was written to OceanDNA-b35158/dqc_result.json
[2023-03-18 00:23:30,363] [INFO] DFAST_QC completed!
[2023-03-18 00:23:30,363] [INFO] Total running time: 0h1m36s