[2023-03-16 09:16:56,163] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:16:56,163] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:16:56,163] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b52e18e-012c-48fe-a1af-569d3db12a1a/dqc_reference
[2023-03-16 09:16:58,672] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:16:58,673] [INFO] Task started: Prodigal
[2023-03-16 09:16:58,673] [INFO] Running command: cat /var/lib/cwl/stg87a7b448-11c5-432b-bdf5-82f73a69281e/OceanDNA-b35154.fa | prodigal -d OceanDNA-b35154/cds.fna -a OceanDNA-b35154/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:17:26,370] [INFO] Task succeeded: Prodigal
[2023-03-16 09:17:26,370] [INFO] Task started: HMMsearch
[2023-03-16 09:17:26,370] [INFO] Running command: hmmsearch --tblout OceanDNA-b35154/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b52e18e-012c-48fe-a1af-569d3db12a1a/dqc_reference/reference_markers.hmm OceanDNA-b35154/protein.faa > /dev/null
[2023-03-16 09:17:26,596] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:17:26,596] [INFO] Found 6/6 markers.
[2023-03-16 09:17:26,621] [INFO] Query marker FASTA was written to OceanDNA-b35154/markers.fasta
[2023-03-16 09:17:26,622] [INFO] Task started: Blastn
[2023-03-16 09:17:26,623] [INFO] Running command: blastn -query OceanDNA-b35154/markers.fasta -db /var/lib/cwl/stg2b52e18e-012c-48fe-a1af-569d3db12a1a/dqc_reference/reference_markers.fasta -out OceanDNA-b35154/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:17:27,410] [INFO] Task succeeded: Blastn
[2023-03-16 09:17:27,412] [INFO] Selected 18 target genomes.
[2023-03-16 09:17:27,412] [INFO] Target genome list was writen to OceanDNA-b35154/target_genomes.txt
[2023-03-16 09:17:27,422] [INFO] Task started: fastANI
[2023-03-16 09:17:27,422] [INFO] Running command: fastANI --query /var/lib/cwl/stg87a7b448-11c5-432b-bdf5-82f73a69281e/OceanDNA-b35154.fa --refList OceanDNA-b35154/target_genomes.txt --output OceanDNA-b35154/fastani_result.tsv --threads 1
[2023-03-16 09:17:44,962] [INFO] Task succeeded: fastANI
[2023-03-16 09:17:44,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b52e18e-012c-48fe-a1af-569d3db12a1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:17:44,962] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b52e18e-012c-48fe-a1af-569d3db12a1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:17:44,972] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2023-03-16 09:17:44,972] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 09:17:44,973] [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=DSM 30073	GCA_014155765.1	59814	59814	type	True	97.9803	1441	1528	95	conclusive
Pantoea dispersa	strain=CCUG 25232T	GCA_008692915.1	59814	59814	type	True	97.9644	1421	1528	95	conclusive
Pantoea wallisii	strain=LMG 26277	GCA_002095485.1	1076551	1076551	type	True	85.4063	1132	1528	95	below_threshold
Pantoea endophytica	strain=596	GCA_002858935.1	92488	92488	type	True	84.596	1177	1528	95	below_threshold
Pantoea rodasii	strain=DSM 26611	GCA_002811195.1	1076549	1076549	type	True	84.0753	1110	1528	95	below_threshold
Pantoea rodasii	strain=LMG 26273	GCA_002095465.1	1076549	1076549	type	True	84.0094	1122	1528	95	below_threshold
Pantoea cypripedii	strain=LMG 2657	GCA_002095535.1	55209	55209	type	True	83.3809	1071	1528	95	below_threshold
Pantoea eucrina	strain=LMG 5346	GCA_002095385.1	472693	472693	type	True	83.091	900	1528	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	81.7248	951	1528	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	80.2178	798	1528	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	80.1505	738	1528	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	79.1729	658	1528	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.1498	640	1528	95	below_threshold
Pseudomonas extremorientalis		GCA_900625005.1	169669	169669	type	True	75.775	87	1528	95	below_threshold
Alcanivorax indicus	strain=SW127	GCA_003259185.1	2202653	2202653	type	True	75.1848	50	1528	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:17:44,973] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35154/tc_result.tsv
[2023-03-16 09:17:44,973] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:17:44,973] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:17:44,973] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b52e18e-012c-48fe-a1af-569d3db12a1a/dqc_reference/checkm_data
[2023-03-16 09:17:44,974] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:17:44,980] [INFO] Task started: CheckM
[2023-03-16 09:17:44,980] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35154/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35154/checkm_input OceanDNA-b35154/checkm_result
[2023-03-16 09:18:52,424] [INFO] Task succeeded: CheckM
[2023-03-16 09:18:52,425] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.71%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:18:52,433] [INFO] ===== Completeness check finished =====
[2023-03-16 09:18:52,433] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:18:52,433] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35154/markers.fasta)
[2023-03-16 09:18:52,435] [INFO] Task started: Blastn
[2023-03-16 09:18:52,435] [INFO] Running command: blastn -query OceanDNA-b35154/markers.fasta -db /var/lib/cwl/stg2b52e18e-012c-48fe-a1af-569d3db12a1a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35154/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:18:53,838] [INFO] Task succeeded: Blastn
[2023-03-16 09:18:53,839] [INFO] Selected 17 target genomes.
[2023-03-16 09:18:53,839] [INFO] Target genome list was writen to OceanDNA-b35154/target_genomes_gtdb.txt
[2023-03-16 09:18:53,849] [INFO] Task started: fastANI
[2023-03-16 09:18:53,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg87a7b448-11c5-432b-bdf5-82f73a69281e/OceanDNA-b35154.fa --refList OceanDNA-b35154/target_genomes_gtdb.txt --output OceanDNA-b35154/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:19:11,990] [INFO] Task succeeded: fastANI
[2023-03-16 09:19:12,000] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 09:19:12,001] [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_014155765.1	s__Pantoea dispersa	97.9803	1441	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.93	96.36	0.92	0.86	38	conclusive
GCF_002095485.1	s__Pantoea wallisii	85.4181	1130	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007833795.1	s__Pantoea dispersa_B	85.29	1140	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002858935.1	s__Pantoea endophytica	84.6024	1176	1528	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	84.525	1152	1528	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	84.12	1149	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.42	98.35	0.91	0.90	3	-
GCF_016625195.1	s__Pantoea sp016625195	84.068	1122	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900068845.1	s__Pantoea ludwigii_A	83.95	1149	1528	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	83.9359	1034	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.95	97.99	0.91	0.89	3	-
GCF_002095535.1	s__Pantoea cypripedii	83.3673	1072	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.97	99.97	0.99	0.99	2	-
GCF_011395035.1	s__Pantoea cypripedii_A	83.252	1069	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000175935.2	s__Pantoea sp000175935	83.1089	1053	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002095385.1	s__Pantoea eucrina	83.091	900	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.84	96.54	0.93	0.90	17	-
GCF_001691555.1	s__Pantoea eucrina_A	82.8186	925	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.39	99.35	0.94	0.93	4	-
GCF_000973125.1	s__Xenorhabdus bovienii	76.7408	108	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	97.70	96.37	0.89	0.86	7	-
GCF_002632725.1	s__Xenorhabdus hominickii	76.7081	86	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.90	99.90	0.96	0.96	2	-
GCF_003259185.1	s__Alcanivorax_A indicus	75.1848	50	1528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:19:12,001] [INFO] GTDB search result was written to OceanDNA-b35154/result_gtdb.tsv
[2023-03-16 09:19:12,002] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:19:12,005] [INFO] DFAST_QC result json was written to OceanDNA-b35154/dqc_result.json
[2023-03-16 09:19:12,005] [INFO] DFAST_QC completed!
[2023-03-16 09:19:12,005] [INFO] Total running time: 0h2m16s