[2023-03-19 05:19:33,810] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:19:33,810] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:19:33,810] [INFO] DQC Reference Directory: /var/lib/cwl/stg365145fd-1a90-4a9a-8682-29b460e3e1e4/dqc_reference
[2023-03-19 05:19:35,412] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:19:35,413] [INFO] Task started: Prodigal
[2023-03-19 05:19:35,413] [INFO] Running command: cat /var/lib/cwl/stgb5b67da0-f93a-4c9e-a922-1eea20840233/OceanDNA-b41227.fa | prodigal -d OceanDNA-b41227/cds.fna -a OceanDNA-b41227/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:19:45,743] [INFO] Task succeeded: Prodigal
[2023-03-19 05:19:45,743] [INFO] Task started: HMMsearch
[2023-03-19 05:19:45,743] [INFO] Running command: hmmsearch --tblout OceanDNA-b41227/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg365145fd-1a90-4a9a-8682-29b460e3e1e4/dqc_reference/reference_markers.hmm OceanDNA-b41227/protein.faa > /dev/null
[2023-03-19 05:19:45,941] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:19:45,942] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb5b67da0-f93a-4c9e-a922-1eea20840233/OceanDNA-b41227.fa]
[2023-03-19 05:19:45,957] [INFO] Query marker FASTA was written to OceanDNA-b41227/markers.fasta
[2023-03-19 05:19:45,957] [INFO] Task started: Blastn
[2023-03-19 05:19:45,957] [INFO] Running command: blastn -query OceanDNA-b41227/markers.fasta -db /var/lib/cwl/stg365145fd-1a90-4a9a-8682-29b460e3e1e4/dqc_reference/reference_markers.fasta -out OceanDNA-b41227/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:19:46,822] [INFO] Task succeeded: Blastn
[2023-03-19 05:19:46,823] [INFO] Selected 11 target genomes.
[2023-03-19 05:19:46,823] [INFO] Target genome list was writen to OceanDNA-b41227/target_genomes.txt
[2023-03-19 05:19:46,829] [INFO] Task started: fastANI
[2023-03-19 05:19:46,830] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5b67da0-f93a-4c9e-a922-1eea20840233/OceanDNA-b41227.fa --refList OceanDNA-b41227/target_genomes.txt --output OceanDNA-b41227/fastani_result.tsv --threads 1
[2023-03-19 05:19:56,294] [INFO] Task succeeded: fastANI
[2023-03-19 05:19:56,294] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg365145fd-1a90-4a9a-8682-29b460e3e1e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:19:56,294] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg365145fd-1a90-4a9a-8682-29b460e3e1e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:19:56,302] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:19:56,302] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 05:19:56,302] [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 peli	strain=DSM 17833	GCA_012986145.1	592361	592361	type	True	86.3291	468	542	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_900099645.1	592361	592361	type	True	86.3198	468	542	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	85.6628	451	542	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	85.5349	480	542	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	85.2461	477	542	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	84.7921	450	542	95	below_threshold
Pseudomonas cuatrocienegasensis	strain=CIP 109853	GCA_900110925.1	543360	543360	type	True	83.9246	440	542	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	83.7909	449	542	95	below_threshold
Pseudomonas guineae	strain=LMG 24016	GCA_900113745.1	425504	425504	type	True	83.7399	439	542	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	82.5737	399	542	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	82.4989	389	542	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 05:19:56,302] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41227/tc_result.tsv
[2023-03-19 05:19:56,303] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:19:56,303] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:19:56,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg365145fd-1a90-4a9a-8682-29b460e3e1e4/dqc_reference/checkm_data
[2023-03-19 05:19:56,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:19:56,307] [INFO] Task started: CheckM
[2023-03-19 05:19:56,307] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41227/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41227/checkm_input OceanDNA-b41227/checkm_result
[2023-03-19 05:20:26,275] [INFO] Task succeeded: CheckM
[2023-03-19 05:20:26,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.35%
Contamintation: 4.92%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-19 05:20:26,278] [INFO] ===== Completeness check finished =====
[2023-03-19 05:20:26,278] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:20:26,278] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41227/markers.fasta)
[2023-03-19 05:20:26,278] [INFO] Task started: Blastn
[2023-03-19 05:20:26,278] [INFO] Running command: blastn -query OceanDNA-b41227/markers.fasta -db /var/lib/cwl/stg365145fd-1a90-4a9a-8682-29b460e3e1e4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41227/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:20:27,781] [INFO] Task succeeded: Blastn
[2023-03-19 05:20:27,782] [INFO] Selected 17 target genomes.
[2023-03-19 05:20:27,782] [INFO] Target genome list was writen to OceanDNA-b41227/target_genomes_gtdb.txt
[2023-03-19 05:20:27,856] [INFO] Task started: fastANI
[2023-03-19 05:20:27,857] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5b67da0-f93a-4c9e-a922-1eea20840233/OceanDNA-b41227.fa --refList OceanDNA-b41227/target_genomes_gtdb.txt --output OceanDNA-b41227/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:20:42,176] [INFO] Task succeeded: fastANI
[2023-03-19 05:20:42,186] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 05:20:42,186] [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
GCA_002840155.1	s__Pseudomonas_E sp002840155	87.5527	473	542	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_900105355.1	s__Pseudomonas_E anguilliseptica	86.6347	463	542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.12	96.12	0.88	0.88	2	-
GCF_900099645.1	s__Pseudomonas_E peli	86.3198	468	542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.85	96.04	0.90	0.85	7	-
GCA_018827205.1	s__Pseudomonas_E sp018827205	85.8907	431	542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.54	99.51	0.89	0.88	4	-
GCF_009763245.1	s__Pseudomonas_E sp009763245	85.761	450	542	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_900115555.1	s__Pseudomonas_E borbori	85.6628	451	542	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_013184545.1	s__Pseudomonas_E sp013184545	85.5242	481	542	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_003060885.1	s__Pseudomonas_E sp003060885	85.3975	447	542	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_900100495.1	s__Pseudomonas_E benzenivorans	85.2461	477	542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354655.1	s__Pseudomonas_E sp002354655	85.1562	456	542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.84	99.84	0.95	0.95	2	-
GCA_018816095.1	s__Pseudomonas_E sp018816095	84.6756	407	542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.20	96.15	0.83	0.82	4	-
GCF_002025205.1	s__Pseudomonas_E sp002025205	84.4236	459	542	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_900110925.1	s__Pseudomonas_E cuatrocienegasensis	83.9275	439	542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009799925.1	s__Pseudomonas_E sp009799925	83.6782	438	542	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_014164785.1	s__Pseudomonas_E sp014164785	83.1193	405	542	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_014174475.1	s__Pseudomonas_E sp014174475	82.9168	424	542	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_014851905.1	s__Pseudomonas_E sp014851905	82.6492	407	542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 05:20:42,186] [INFO] GTDB search result was written to OceanDNA-b41227/result_gtdb.tsv
[2023-03-19 05:20:42,187] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:20:42,188] [INFO] DFAST_QC result json was written to OceanDNA-b41227/dqc_result.json
[2023-03-19 05:20:42,188] [INFO] DFAST_QC completed!
[2023-03-19 05:20:42,188] [INFO] Total running time: 0h1m8s