[2023-03-17 08:11:32,977] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:11:32,977] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:11:32,977] [INFO] DQC Reference Directory: /var/lib/cwl/stgf58a370e-ca01-4018-ab2a-65eed40283ba/dqc_reference
[2023-03-17 08:11:34,671] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:11:34,671] [INFO] Task started: Prodigal
[2023-03-17 08:11:34,671] [INFO] Running command: cat /var/lib/cwl/stgda211342-a60e-41c9-86e2-63aacade9f20/OceanDNA-b41268.fa | prodigal -d OceanDNA-b41268/cds.fna -a OceanDNA-b41268/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:11:56,632] [INFO] Task succeeded: Prodigal
[2023-03-17 08:11:56,632] [INFO] Task started: HMMsearch
[2023-03-17 08:11:56,632] [INFO] Running command: hmmsearch --tblout OceanDNA-b41268/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf58a370e-ca01-4018-ab2a-65eed40283ba/dqc_reference/reference_markers.hmm OceanDNA-b41268/protein.faa > /dev/null
[2023-03-17 08:11:56,846] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:11:56,846] [INFO] Found 6/6 markers.
[2023-03-17 08:11:56,870] [INFO] Query marker FASTA was written to OceanDNA-b41268/markers.fasta
[2023-03-17 08:11:56,871] [INFO] Task started: Blastn
[2023-03-17 08:11:56,871] [INFO] Running command: blastn -query OceanDNA-b41268/markers.fasta -db /var/lib/cwl/stgf58a370e-ca01-4018-ab2a-65eed40283ba/dqc_reference/reference_markers.fasta -out OceanDNA-b41268/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:11:57,664] [INFO] Task succeeded: Blastn
[2023-03-17 08:11:57,665] [INFO] Selected 12 target genomes.
[2023-03-17 08:11:57,665] [INFO] Target genome list was writen to OceanDNA-b41268/target_genomes.txt
[2023-03-17 08:11:57,672] [INFO] Task started: fastANI
[2023-03-17 08:11:57,673] [INFO] Running command: fastANI --query /var/lib/cwl/stgda211342-a60e-41c9-86e2-63aacade9f20/OceanDNA-b41268.fa --refList OceanDNA-b41268/target_genomes.txt --output OceanDNA-b41268/fastani_result.tsv --threads 1
[2023-03-17 08:12:08,749] [INFO] Task succeeded: fastANI
[2023-03-17 08:12:08,749] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf58a370e-ca01-4018-ab2a-65eed40283ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:12:08,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf58a370e-ca01-4018-ab2a-65eed40283ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:12:08,758] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 08:12:08,758] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 08:12:08,758] [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 guineae	strain=LMG 24016	GCA_900113745.1	425504	425504	type	True	98.8604	1059	1169	95	conclusive
Pseudomonas peli	strain=DSM 17833	GCA_900099645.1	592361	592361	type	True	84.2995	885	1169	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_012986145.1	592361	592361	type	True	84.2521	888	1169	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	81.2327	713	1169	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	81.1827	729	1169	95	below_threshold
Pseudomonas cuatrocienegasensis	strain=CIP 109853	GCA_900110925.1	543360	543360	type	True	80.8469	663	1169	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	80.6549	664	1169	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	80.3222	612	1169	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	80.1856	664	1169	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	80.1559	598	1169	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	79.6957	561	1169	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	79.3851	536	1169	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 08:12:08,758] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41268/tc_result.tsv
[2023-03-17 08:12:08,758] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:12:08,758] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:12:08,759] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf58a370e-ca01-4018-ab2a-65eed40283ba/dqc_reference/checkm_data
[2023-03-17 08:12:08,759] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:12:08,765] [INFO] Task started: CheckM
[2023-03-17 08:12:08,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41268/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41268/checkm_input OceanDNA-b41268/checkm_result
[2023-03-17 08:13:03,592] [INFO] Task succeeded: CheckM
[2023-03-17 08:13:03,592] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.40%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:13:03,595] [INFO] ===== Completeness check finished =====
[2023-03-17 08:13:03,595] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:13:03,595] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41268/markers.fasta)
[2023-03-17 08:13:03,596] [INFO] Task started: Blastn
[2023-03-17 08:13:03,596] [INFO] Running command: blastn -query OceanDNA-b41268/markers.fasta -db /var/lib/cwl/stgf58a370e-ca01-4018-ab2a-65eed40283ba/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41268/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:13:05,086] [INFO] Task succeeded: Blastn
[2023-03-17 08:13:05,086] [INFO] Selected 10 target genomes.
[2023-03-17 08:13:05,087] [INFO] Target genome list was writen to OceanDNA-b41268/target_genomes_gtdb.txt
[2023-03-17 08:13:05,163] [INFO] Task started: fastANI
[2023-03-17 08:13:05,164] [INFO] Running command: fastANI --query /var/lib/cwl/stgda211342-a60e-41c9-86e2-63aacade9f20/OceanDNA-b41268.fa --refList OceanDNA-b41268/target_genomes_gtdb.txt --output OceanDNA-b41268/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:13:14,517] [INFO] Task succeeded: fastANI
[2023-03-17 08:13:14,524] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 08:13:14,524] [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_900113745.1	s__Pseudomonas_E guineae	98.8604	1059	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018816095.1	s__Pseudomonas_E sp018816095	87.5988	852	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.20	96.15	0.83	0.82	4	-
GCA_002840155.1	s__Pseudomonas_E sp002840155	85.0126	909	1169	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_004920405.1	s__Pseudomonas_E leptonychotis	84.8575	898	1169	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_018827205.1	s__Pseudomonas_E sp018827205	84.3716	831	1169	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_900105355.1	s__Pseudomonas_E anguilliseptica	84.3271	877	1169	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	84.291	886	1169	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_017886405.1	s__Pseudomonas_E sp017886405	83.6061	615	1169	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	81.9848	759	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.84	99.84	0.95	0.95	2	-
GCF_002025205.1	s__Pseudomonas_E sp002025205	81.0184	734	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 08:13:14,524] [INFO] GTDB search result was written to OceanDNA-b41268/result_gtdb.tsv
[2023-03-17 08:13:14,525] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:13:14,526] [INFO] DFAST_QC result json was written to OceanDNA-b41268/dqc_result.json
[2023-03-17 08:13:14,526] [INFO] DFAST_QC completed!
[2023-03-17 08:13:14,526] [INFO] Total running time: 0h1m42s