[2023-03-17 09:24:44,922] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:24:44,940] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:24:44,940] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b71fe12-986a-4871-a0f4-d468f656aea5/dqc_reference
[2023-03-17 09:24:46,207] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:24:46,208] [INFO] Task started: Prodigal
[2023-03-17 09:24:46,208] [INFO] Running command: cat /var/lib/cwl/stgd31d5215-1c31-4c49-b7e4-2ae5a24ae495/OceanDNA-b41295.fa | prodigal -d OceanDNA-b41295/cds.fna -a OceanDNA-b41295/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:25:13,461] [INFO] Task succeeded: Prodigal
[2023-03-17 09:25:13,461] [INFO] Task started: HMMsearch
[2023-03-17 09:25:13,461] [INFO] Running command: hmmsearch --tblout OceanDNA-b41295/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b71fe12-986a-4871-a0f4-d468f656aea5/dqc_reference/reference_markers.hmm OceanDNA-b41295/protein.faa > /dev/null
[2023-03-17 09:25:13,723] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:25:13,724] [INFO] Found 6/6 markers.
[2023-03-17 09:25:13,853] [INFO] Query marker FASTA was written to OceanDNA-b41295/markers.fasta
[2023-03-17 09:25:13,854] [INFO] Task started: Blastn
[2023-03-17 09:25:13,854] [INFO] Running command: blastn -query OceanDNA-b41295/markers.fasta -db /var/lib/cwl/stg8b71fe12-986a-4871-a0f4-d468f656aea5/dqc_reference/reference_markers.fasta -out OceanDNA-b41295/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:25:15,078] [INFO] Task succeeded: Blastn
[2023-03-17 09:25:15,094] [INFO] Selected 15 target genomes.
[2023-03-17 09:25:15,095] [INFO] Target genome list was writen to OceanDNA-b41295/target_genomes.txt
[2023-03-17 09:25:15,437] [INFO] Task started: fastANI
[2023-03-17 09:25:15,437] [INFO] Running command: fastANI --query /var/lib/cwl/stgd31d5215-1c31-4c49-b7e4-2ae5a24ae495/OceanDNA-b41295.fa --refList OceanDNA-b41295/target_genomes.txt --output OceanDNA-b41295/fastani_result.tsv --threads 1
[2023-03-17 09:25:30,987] [INFO] Task succeeded: fastANI
[2023-03-17 09:25:30,988] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b71fe12-986a-4871-a0f4-d468f656aea5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:25:30,988] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b71fe12-986a-4871-a0f4-d468f656aea5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:25:31,200] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2023-03-17 09:25:31,200] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 09:25:31,200] [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_900099645.1	592361	592361	type	True	96.2255	1272	1435	95	conclusive
Pseudomonas peli	strain=DSM 17833	GCA_012986145.1	592361	592361	type	True	96.2109	1273	1435	95	conclusive
Pseudomonas guineae	strain=LMG 24016	GCA_900113745.1	425504	425504	type	True	84.3412	1033	1435	95	below_threshold
Pseudomonas cuatrocienegasensis	strain=CIP 109853	GCA_900110925.1	543360	543360	type	True	82.8092	890	1435	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	82.784	897	1435	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	82.6581	963	1435	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	82.5923	942	1435	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	82.1328	856	1435	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	81.8973	907	1435	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	81.7286	816	1435	95	below_threshold
Pseudomonas guryensis	strain=SR9	GCA_014164785.1	2759165	2759165	type	True	81.7285	858	1435	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	81.6823	946	1435	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	81.404	767	1435	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	81.1938	742	1435	95	below_threshold
Pseudomonas kuykendallii	strain=NRRL B-59562	GCA_900106975.1	1007099	1007099	type	True	80.3095	673	1435	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:25:31,200] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41295/tc_result.tsv
[2023-03-17 09:25:31,200] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:25:31,200] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:25:31,201] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b71fe12-986a-4871-a0f4-d468f656aea5/dqc_reference/checkm_data
[2023-03-17 09:25:31,201] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:25:31,210] [INFO] Task started: CheckM
[2023-03-17 09:25:31,210] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41295/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41295/checkm_input OceanDNA-b41295/checkm_result
[2023-03-17 09:26:43,930] [INFO] Task succeeded: CheckM
[2023-03-17 09:26:43,930] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.24%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 09:26:44,024] [INFO] ===== Completeness check finished =====
[2023-03-17 09:26:44,024] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:26:44,024] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41295/markers.fasta)
[2023-03-17 09:26:44,044] [INFO] Task started: Blastn
[2023-03-17 09:26:44,044] [INFO] Running command: blastn -query OceanDNA-b41295/markers.fasta -db /var/lib/cwl/stg8b71fe12-986a-4871-a0f4-d468f656aea5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41295/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:26:46,147] [INFO] Task succeeded: Blastn
[2023-03-17 09:26:46,172] [INFO] Selected 12 target genomes.
[2023-03-17 09:26:46,172] [INFO] Target genome list was writen to OceanDNA-b41295/target_genomes_gtdb.txt
[2023-03-17 09:26:46,796] [INFO] Task started: fastANI
[2023-03-17 09:26:46,796] [INFO] Running command: fastANI --query /var/lib/cwl/stgd31d5215-1c31-4c49-b7e4-2ae5a24ae495/OceanDNA-b41295.fa --refList OceanDNA-b41295/target_genomes_gtdb.txt --output OceanDNA-b41295/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:26:59,957] [INFO] Task succeeded: fastANI
[2023-03-17 09:26:59,965] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 09:26:59,965] [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_900099645.1	s__Pseudomonas_E peli	96.2255	1272	1435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.85	96.04	0.90	0.85	7	conclusive
GCA_002840155.1	s__Pseudomonas_E sp002840155	90.8668	1237	1435	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	89.9606	1162	1435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.12	96.12	0.88	0.88	2	-
GCA_018827205.1	s__Pseudomonas_E sp018827205	88.6387	1085	1435	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_003060885.1	s__Pseudomonas_E sp003060885	88.4936	1127	1435	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_018816095.1	s__Pseudomonas_E sp018816095	85.6964	937	1435	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_004920405.1	s__Pseudomonas_E leptonychotis	85.5235	1124	1435	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_001465025.1	s__Pseudomonas_E sp001465025	84.6378	952	1435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.96	95.96	0.61	0.61	2	-
GCA_002354655.1	s__Pseudomonas_E sp002354655	84.0855	1009	1435	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_009763245.1	s__Pseudomonas_E sp009763245	83.6422	932	1435	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	81.5519	797	1435	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_014851865.1	s__Pseudomonas_E sp014851865	80.9412	719	1435	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 09:26:59,993] [INFO] GTDB search result was written to OceanDNA-b41295/result_gtdb.tsv
[2023-03-17 09:27:00,041] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:27:00,066] [INFO] DFAST_QC result json was written to OceanDNA-b41295/dqc_result.json
[2023-03-17 09:27:00,066] [INFO] DFAST_QC completed!
[2023-03-17 09:27:00,066] [INFO] Total running time: 0h2m15s