[2023-03-17 16:38:19,329] [INFO] DFAST_QC pipeline started.
[2023-03-17 16:38:19,329] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 16:38:19,329] [INFO] DQC Reference Directory: /var/lib/cwl/stg23aeca2f-196d-4858-a449-031624c1696b/dqc_reference
[2023-03-17 16:38:21,308] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 16:38:21,308] [INFO] Task started: Prodigal
[2023-03-17 16:38:21,308] [INFO] Running command: cat /var/lib/cwl/stg3e92b904-0f38-4d5b-a407-d1a726147d4d/OceanDNA-b35159.fa | prodigal -d OceanDNA-b35159/cds.fna -a OceanDNA-b35159/protein.faa -g 11 -q > /dev/null
[2023-03-17 16:38:58,461] [INFO] Task succeeded: Prodigal
[2023-03-17 16:38:58,461] [INFO] Task started: HMMsearch
[2023-03-17 16:38:58,461] [INFO] Running command: hmmsearch --tblout OceanDNA-b35159/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23aeca2f-196d-4858-a449-031624c1696b/dqc_reference/reference_markers.hmm OceanDNA-b35159/protein.faa > /dev/null
[2023-03-17 16:38:58,705] [INFO] Task succeeded: HMMsearch
[2023-03-17 16:38:58,705] [INFO] Found 6/6 markers.
[2023-03-17 16:38:58,746] [INFO] Query marker FASTA was written to OceanDNA-b35159/markers.fasta
[2023-03-17 16:38:58,746] [INFO] Task started: Blastn
[2023-03-17 16:38:58,746] [INFO] Running command: blastn -query OceanDNA-b35159/markers.fasta -db /var/lib/cwl/stg23aeca2f-196d-4858-a449-031624c1696b/dqc_reference/reference_markers.fasta -out OceanDNA-b35159/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 16:38:59,529] [INFO] Task succeeded: Blastn
[2023-03-17 16:38:59,529] [INFO] Selected 14 target genomes.
[2023-03-17 16:38:59,530] [INFO] Target genome list was writen to OceanDNA-b35159/target_genomes.txt
[2023-03-17 16:38:59,577] [INFO] Task started: fastANI
[2023-03-17 16:38:59,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e92b904-0f38-4d5b-a407-d1a726147d4d/OceanDNA-b35159.fa --refList OceanDNA-b35159/target_genomes.txt --output OceanDNA-b35159/fastani_result.tsv --threads 1
[2023-03-17 16:39:19,028] [INFO] Task succeeded: fastANI
[2023-03-17 16:39:19,029] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23aeca2f-196d-4858-a449-031624c1696b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 16:39:19,029] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23aeca2f-196d-4858-a449-031624c1696b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 16:39:19,038] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 16:39:19,038] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 16:39:19,038] [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	86.4435	1214	1428	95	below_threshold
Pantoea rodasii	strain=DSM 26611	GCA_002811195.1	1076549	1076549	type	True	86.4315	1236	1428	95	below_threshold
Pantoea rwandensis	strain=LMG 26275	GCA_002095475.1	1076550	1076550	type	True	86.3835	1204	1428	95	below_threshold
Pantoea endophytica	strain=596	GCA_002858935.1	92488	92488	type	True	84.5128	1124	1428	95	below_threshold
Pantoea dispersa	strain=CCUG 25232T	GCA_008692915.1	59814	59814	type	True	83.9273	1016	1428	95	below_threshold
Pantoea dispersa	strain=DSM 30073	GCA_014155765.1	59814	59814	type	True	83.9031	1022	1428	95	below_threshold
Pantoea wallisii	strain=LMG 26277	GCA_002095485.1	1076551	1076551	type	True	83.3672	966	1428	95	below_threshold
Pantoea cypripedii	strain=LMG 2657	GCA_002095535.1	55209	55209	type	True	82.822	1047	1428	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	80.4345	764	1428	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	79.6521	646	1428	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	79.2862	601	1428	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	78.5538	496	1428	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	78.3854	420	1428	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	78.2569	448	1428	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 16:39:19,038] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35159/tc_result.tsv
[2023-03-17 16:39:19,038] [INFO] ===== Taxonomy check completed =====
[2023-03-17 16:39:19,038] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 16:39:19,038] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23aeca2f-196d-4858-a449-031624c1696b/dqc_reference/checkm_data
[2023-03-17 16:39:19,039] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 16:39:19,054] [INFO] Task started: CheckM
[2023-03-17 16:39:19,054] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35159/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35159/checkm_input OceanDNA-b35159/checkm_result
[2023-03-17 16:40:28,890] [INFO] Task succeeded: CheckM
[2023-03-17 16:40:28,891] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 16:40:28,894] [INFO] ===== Completeness check finished =====
[2023-03-17 16:40:28,894] [INFO] ===== Start GTDB Search =====
[2023-03-17 16:40:28,894] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35159/markers.fasta)
[2023-03-17 16:40:28,894] [INFO] Task started: Blastn
[2023-03-17 16:40:28,894] [INFO] Running command: blastn -query OceanDNA-b35159/markers.fasta -db /var/lib/cwl/stg23aeca2f-196d-4858-a449-031624c1696b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35159/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 16:40:29,941] [INFO] Task succeeded: Blastn
[2023-03-17 16:40:29,942] [INFO] Selected 12 target genomes.
[2023-03-17 16:40:29,942] [INFO] Target genome list was writen to OceanDNA-b35159/target_genomes_gtdb.txt
[2023-03-17 16:40:30,040] [INFO] Task started: fastANI
[2023-03-17 16:40:30,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e92b904-0f38-4d5b-a407-d1a726147d4d/OceanDNA-b35159.fa --refList OceanDNA-b35159/target_genomes_gtdb.txt --output OceanDNA-b35159/fastani_result_gtdb.tsv --threads 1
[2023-03-17 16:40:45,161] [INFO] Task succeeded: fastANI
[2023-03-17 16:40:45,168] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 16:40:45,169] [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_001506165.1	s__Pantoea vagans_C	98.8123	1244	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.95	97.99	0.91	0.89	3	conclusive
GCF_000759475.1	s__Pantoea rwandensis_B	86.9007	1122	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.54	98.22	0.92	0.90	5	-
GCF_016625195.1	s__Pantoea sp016625195	86.7331	1237	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000773965.1	s__Pantoea cancerogena_A	86.7104	1238	1428	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	86.4632	1212	1428	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	86.457	1229	1428	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	86.3735	1205	1428	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	84.5559	1158	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.17	96.60	0.91	0.89	10	-
GCF_001187905.1	s__Pantoea sp001187905	84.3162	1124	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.42	98.35	0.91	0.90	3	-
GCF_018141005.1	s__Erwinia sp001422605	79.0339	563	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.39	98.36	0.92	0.92	3	-
GCA_019132875.1	s__Erwinia sp019132875	78.5476	498	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002858675.1	s__Chimaeribacter californicus	78.0758	423	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chimaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 16:40:45,169] [INFO] GTDB search result was written to OceanDNA-b35159/result_gtdb.tsv
[2023-03-17 16:40:45,169] [INFO] ===== GTDB Search completed =====
[2023-03-17 16:40:45,170] [INFO] DFAST_QC result json was written to OceanDNA-b35159/dqc_result.json
[2023-03-17 16:40:45,171] [INFO] DFAST_QC completed!
[2023-03-17 16:40:45,171] [INFO] Total running time: 0h2m26s