[2023-03-15 11:24:11,509] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:24:11,510] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:24:11,510] [INFO] DQC Reference Directory: /var/lib/cwl/stg402e1a04-ceb0-4d37-a416-d521de95bbbf/dqc_reference
[2023-03-15 11:24:12,587] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:24:12,587] [INFO] Task started: Prodigal
[2023-03-15 11:24:12,587] [INFO] Running command: cat /var/lib/cwl/stg3e2d8157-1f41-455c-a69c-09ed6fdf958d/OceanDNA-b41265.fa | prodigal -d OceanDNA-b41265/cds.fna -a OceanDNA-b41265/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:24:19,513] [INFO] Task succeeded: Prodigal
[2023-03-15 11:24:19,513] [INFO] Task started: HMMsearch
[2023-03-15 11:24:19,513] [INFO] Running command: hmmsearch --tblout OceanDNA-b41265/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg402e1a04-ceb0-4d37-a416-d521de95bbbf/dqc_reference/reference_markers.hmm OceanDNA-b41265/protein.faa > /dev/null
[2023-03-15 11:24:19,643] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:24:19,643] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3e2d8157-1f41-455c-a69c-09ed6fdf958d/OceanDNA-b41265.fa]
[2023-03-15 11:24:19,657] [INFO] Query marker FASTA was written to OceanDNA-b41265/markers.fasta
[2023-03-15 11:24:19,657] [INFO] Task started: Blastn
[2023-03-15 11:24:19,657] [INFO] Running command: blastn -query OceanDNA-b41265/markers.fasta -db /var/lib/cwl/stg402e1a04-ceb0-4d37-a416-d521de95bbbf/dqc_reference/reference_markers.fasta -out OceanDNA-b41265/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:24:20,214] [INFO] Task succeeded: Blastn
[2023-03-15 11:24:20,215] [INFO] Selected 10 target genomes.
[2023-03-15 11:24:20,215] [INFO] Target genome list was writen to OceanDNA-b41265/target_genomes.txt
[2023-03-15 11:24:20,221] [INFO] Task started: fastANI
[2023-03-15 11:24:20,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e2d8157-1f41-455c-a69c-09ed6fdf958d/OceanDNA-b41265.fa --refList OceanDNA-b41265/target_genomes.txt --output OceanDNA-b41265/fastani_result.tsv --threads 1
[2023-03-15 11:24:29,004] [INFO] Task succeeded: fastANI
[2023-03-15 11:24:29,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg402e1a04-ceb0-4d37-a416-d521de95bbbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:24:29,005] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg402e1a04-ceb0-4d37-a416-d521de95bbbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:24:29,012] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2023-03-15 11:24:29,012] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 11:24:29,012] [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
Pseudomonas extremaustralis	strain=DSM 17835	GCA_900102035.1	359110	359110	type	True	98.6617	251	254	95	conclusive
Pseudomonas extremaustralis	strain=DSM 17835	GCA_007858235.1	359110	359110	type	True	98.6098	249	254	95	conclusive
Pseudomonas extremaustralis	strain=14-3 substr. 14-3b	GCA_000242115.2	359110	359110	type	True	98.5658	251	254	95	conclusive
Pseudomonas extremaustralis		GCA_900625045.1	359110	359110	type	True	98.5656	250	254	95	conclusive
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	89.8815	247	254	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	89.2421	244	254	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	89.0281	246	254	95	below_threshold
Pseudomonas paralactis	strain=DSM 29164	GCA_001439735.1	1615673	1615673	type	True	88.0392	235	254	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	86.7036	234	254	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	85.5652	230	254	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:24:29,012] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41265/tc_result.tsv
[2023-03-15 11:24:29,012] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:24:29,012] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:24:29,012] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg402e1a04-ceb0-4d37-a416-d521de95bbbf/dqc_reference/checkm_data
[2023-03-15 11:24:29,013] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:24:29,078] [INFO] Task started: CheckM
[2023-03-15 11:24:29,078] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41265/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41265/checkm_input OceanDNA-b41265/checkm_result
[2023-03-15 11:24:51,748] [INFO] Task succeeded: CheckM
[2023-03-15 11:24:51,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:24:51,751] [INFO] ===== Completeness check finished =====
[2023-03-15 11:24:51,751] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:24:51,751] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41265/markers.fasta)
[2023-03-15 11:24:51,751] [INFO] Task started: Blastn
[2023-03-15 11:24:51,751] [INFO] Running command: blastn -query OceanDNA-b41265/markers.fasta -db /var/lib/cwl/stg402e1a04-ceb0-4d37-a416-d521de95bbbf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41265/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:24:52,619] [INFO] Task succeeded: Blastn
[2023-03-15 11:24:52,620] [INFO] Selected 14 target genomes.
[2023-03-15 11:24:52,620] [INFO] Target genome list was writen to OceanDNA-b41265/target_genomes_gtdb.txt
[2023-03-15 11:24:52,631] [INFO] Task started: fastANI
[2023-03-15 11:24:52,631] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e2d8157-1f41-455c-a69c-09ed6fdf958d/OceanDNA-b41265.fa --refList OceanDNA-b41265/target_genomes_gtdb.txt --output OceanDNA-b41265/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:25:06,136] [INFO] Task succeeded: fastANI
[2023-03-15 11:25:06,145] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:25:06,145] [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_900102035.1	s__Pseudomonas_E extremaustralis	98.6617	251	254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.74	98.99	0.98	0.92	5	conclusive
GCF_001439695.1	s__Pseudomonas_E veronii	90.4241	246	254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.79	98.13	0.89	0.82	43	-
GCF_900105325.1	s__Pseudomonas_E marginalis	89.9522	249	254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.53	96.47	0.90	0.85	19	-
GCF_002843605.1	s__Pseudomonas_E sp002843605	89.8049	246	254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.70	97.45	0.92	0.91	7	-
GCF_000612585.1	s__Pseudomonas_E sp000612585	89.5169	243	254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001708445.1	s__Pseudomonas_E fluorescens_AN	89.4071	244	254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.17	98.56	0.90	0.82	34	-
GCF_002563895.1	s__Pseudomonas_E lurida	89.0281	246	254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.19	99.03	0.94	0.91	25	-
GCF_019139815.1	s__Pseudomonas_E sp900005815	88.9272	240	254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.55	99.31	0.95	0.92	7	-
GCF_900215245.1	s__Pseudomonas_E fluorescens	88.6106	241	254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.25	0.98	0.92	14	-
GCF_001983175.1	s__Pseudomonas_E cedrina	88.4673	246	254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.10	97.30	0.97	0.92	4	-
GCF_001439735.1	s__Pseudomonas_E paralactis	88.0392	235	254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.61	98.52	0.94	0.92	4	-
GCF_000263715.2	s__Pseudomonas_E synxantha_A	87.9363	240	254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.66	97.33	0.90	0.88	8	-
GCA_016937595.1	s__Pseudomonas_E fulgida	87.3295	213	254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626995.1	s__Pseudomonas_E fluorescens_BA	87.065	234	254	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.95	98.57	0.93	0.88	19	-
--------------------------------------------------------------------------------
[2023-03-15 11:25:06,146] [INFO] GTDB search result was written to OceanDNA-b41265/result_gtdb.tsv
[2023-03-15 11:25:06,146] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:25:06,148] [INFO] DFAST_QC result json was written to OceanDNA-b41265/dqc_result.json
[2023-03-15 11:25:06,148] [INFO] DFAST_QC completed!
[2023-03-15 11:25:06,148] [INFO] Total running time: 0h0m55s