[2023-03-17 05:26:45,830] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:26:45,834] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:26:45,834] [INFO] DQC Reference Directory: /var/lib/cwl/stg5006a21d-df8e-41f5-abb6-64e4b6c7ff97/dqc_reference
[2023-03-17 05:26:46,934] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:26:46,934] [INFO] Task started: Prodigal
[2023-03-17 05:26:46,934] [INFO] Running command: cat /var/lib/cwl/stgc2aff378-adf8-439b-bc9f-79c700b5fc93/OceanDNA-b34793.fa | prodigal -d OceanDNA-b34793/cds.fna -a OceanDNA-b34793/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:27:10,011] [INFO] Task succeeded: Prodigal
[2023-03-17 05:27:10,011] [INFO] Task started: HMMsearch
[2023-03-17 05:27:10,011] [INFO] Running command: hmmsearch --tblout OceanDNA-b34793/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5006a21d-df8e-41f5-abb6-64e4b6c7ff97/dqc_reference/reference_markers.hmm OceanDNA-b34793/protein.faa > /dev/null
[2023-03-17 05:27:10,232] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:27:10,233] [INFO] Found 6/6 markers.
[2023-03-17 05:27:10,257] [INFO] Query marker FASTA was written to OceanDNA-b34793/markers.fasta
[2023-03-17 05:27:10,258] [INFO] Task started: Blastn
[2023-03-17 05:27:10,259] [INFO] Running command: blastn -query OceanDNA-b34793/markers.fasta -db /var/lib/cwl/stg5006a21d-df8e-41f5-abb6-64e4b6c7ff97/dqc_reference/reference_markers.fasta -out OceanDNA-b34793/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:27:10,904] [INFO] Task succeeded: Blastn
[2023-03-17 05:27:10,905] [INFO] Selected 20 target genomes.
[2023-03-17 05:27:10,905] [INFO] Target genome list was writen to OceanDNA-b34793/target_genomes.txt
[2023-03-17 05:27:10,915] [INFO] Task started: fastANI
[2023-03-17 05:27:10,915] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2aff378-adf8-439b-bc9f-79c700b5fc93/OceanDNA-b34793.fa --refList OceanDNA-b34793/target_genomes.txt --output OceanDNA-b34793/fastani_result.tsv --threads 1
[2023-03-17 05:27:24,783] [INFO] Task succeeded: fastANI
[2023-03-17 05:27:24,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5006a21d-df8e-41f5-abb6-64e4b6c7ff97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:27:24,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5006a21d-df8e-41f5-abb6-64e4b6c7ff97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:27:24,791] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 05:27:24,791] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 05:27:24,791] [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
Glaciecola nitratireducens	strain=FR1064	GCA_000226565.1	300231	300231	type	True	95.7201	1181	1372	95	conclusive
Paraglaciecola polaris	strain=LMG 21857	GCA_000315055.1	222814	222814	type	True	81.011	76	1372	95	below_threshold
Glaciecola pallidula	strain=DSM 14239	GCA_000428905.1	56807	56807	type	True	79.9082	606	1372	95	below_threshold
Glaciecola pallidula	strain=ACAM 615	GCA_000315035.1	56807	56807	type	True	79.8159	605	1372	95	below_threshold
Ningiella ruwaisensis	strain=B66	GCA_004798935.1	2364274	2364274	type	True	77.6547	75	1372	95	below_threshold
Glaciecola punicea	strain=ACAM 611	GCA_000252165.2	56804	56804	type	True	77.5501	80	1372	95	below_threshold
Alteromonas oceanisediminis	strain=SM 2104	GCA_018474025.1	2836180	2836180	type	True	77.5243	60	1372	95	below_threshold
Alteromonas facilis	strain=P0213	GCA_002807665.1	2048004	2048004	type	True	77.5089	65	1372	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	77.4498	70	1372	95	below_threshold
Paraglaciecola marina	strain=D3211	GCA_004360155.1	2500157	2500157	type	True	77.2801	64	1372	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:27:24,795] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34793/tc_result.tsv
[2023-03-17 05:27:24,795] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:27:24,795] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:27:24,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5006a21d-df8e-41f5-abb6-64e4b6c7ff97/dqc_reference/checkm_data
[2023-03-17 05:27:24,796] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:27:24,805] [INFO] Task started: CheckM
[2023-03-17 05:27:24,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34793/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34793/checkm_input OceanDNA-b34793/checkm_result
[2023-03-17 05:28:22,350] [INFO] Task succeeded: CheckM
[2023-03-17 05:28:22,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:28:22,408] [INFO] ===== Completeness check finished =====
[2023-03-17 05:28:22,409] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:28:22,409] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34793/markers.fasta)
[2023-03-17 05:28:22,410] [INFO] Task started: Blastn
[2023-03-17 05:28:22,410] [INFO] Running command: blastn -query OceanDNA-b34793/markers.fasta -db /var/lib/cwl/stg5006a21d-df8e-41f5-abb6-64e4b6c7ff97/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34793/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:28:23,488] [INFO] Task succeeded: Blastn
[2023-03-17 05:28:23,489] [INFO] Selected 13 target genomes.
[2023-03-17 05:28:23,489] [INFO] Target genome list was writen to OceanDNA-b34793/target_genomes_gtdb.txt
[2023-03-17 05:28:23,654] [INFO] Task started: fastANI
[2023-03-17 05:28:23,654] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2aff378-adf8-439b-bc9f-79c700b5fc93/OceanDNA-b34793.fa --refList OceanDNA-b34793/target_genomes_gtdb.txt --output OceanDNA-b34793/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:28:34,155] [INFO] Task succeeded: fastANI
[2023-03-17 05:28:34,162] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:28:34,162] [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_000226565.1	s__Glaciecola nitratireducens	95.7361	1180	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000315055.1	s__Paraglaciecola polaris	81.011	76	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428905.1	s__Glaciecola pallidula	79.9157	606	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002836745.1	s__Glaciecola sp002836745	79.6554	601	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479945.1	s__Glaciecola sp905479945	78.8044	337	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015595035.1	s__Glaciecola sp015595035	78.7393	209	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003203515.1	s__Glaciecola sp003203515	78.3365	116	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000753865.1	s__Alteromonas sp000753865	78.187	70	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009796745.1	s__Paraglaciecola sp009796745	77.9501	67	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018474025.1	s__Alteromonas_E sp018474025	77.5824	61	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000252165.1	s__Glaciecola punicea	77.5802	81	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	99.53	99.53	0.94	0.94	2	-
GCF_009796765.1	s__Paraglaciecola sp009796765	77.1801	83	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:28:34,164] [INFO] GTDB search result was written to OceanDNA-b34793/result_gtdb.tsv
[2023-03-17 05:28:34,166] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:28:34,169] [INFO] DFAST_QC result json was written to OceanDNA-b34793/dqc_result.json
[2023-03-17 05:28:34,169] [INFO] DFAST_QC completed!
[2023-03-17 05:28:34,169] [INFO] Total running time: 0h1m48s