[2023-03-17 02:57:51,816] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:57:51,816] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:57:51,816] [INFO] DQC Reference Directory: /var/lib/cwl/stg30ac7fca-46b9-48e4-b2ab-e46799d99add/dqc_reference
[2023-03-17 02:57:53,077] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:57:53,077] [INFO] Task started: Prodigal
[2023-03-17 02:57:53,078] [INFO] Running command: cat /var/lib/cwl/stg2e4679cd-0876-450e-b903-d100f96e08a3/OceanDNA-b40457.fa | prodigal -d OceanDNA-b40457/cds.fna -a OceanDNA-b40457/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:58:15,020] [INFO] Task succeeded: Prodigal
[2023-03-17 02:58:15,020] [INFO] Task started: HMMsearch
[2023-03-17 02:58:15,020] [INFO] Running command: hmmsearch --tblout OceanDNA-b40457/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30ac7fca-46b9-48e4-b2ab-e46799d99add/dqc_reference/reference_markers.hmm OceanDNA-b40457/protein.faa > /dev/null
[2023-03-17 02:58:15,229] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:58:15,230] [INFO] Found 6/6 markers.
[2023-03-17 02:58:15,278] [INFO] Query marker FASTA was written to OceanDNA-b40457/markers.fasta
[2023-03-17 02:58:15,279] [INFO] Task started: Blastn
[2023-03-17 02:58:15,279] [INFO] Running command: blastn -query OceanDNA-b40457/markers.fasta -db /var/lib/cwl/stg30ac7fca-46b9-48e4-b2ab-e46799d99add/dqc_reference/reference_markers.fasta -out OceanDNA-b40457/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:58:15,963] [INFO] Task succeeded: Blastn
[2023-03-17 02:58:15,969] [INFO] Selected 25 target genomes.
[2023-03-17 02:58:15,970] [INFO] Target genome list was writen to OceanDNA-b40457/target_genomes.txt
[2023-03-17 02:58:15,982] [INFO] Task started: fastANI
[2023-03-17 02:58:15,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e4679cd-0876-450e-b903-d100f96e08a3/OceanDNA-b40457.fa --refList OceanDNA-b40457/target_genomes.txt --output OceanDNA-b40457/fastani_result.tsv --threads 1
[2023-03-17 02:58:31,988] [INFO] Task succeeded: fastANI
[2023-03-17 02:58:31,988] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30ac7fca-46b9-48e4-b2ab-e46799d99add/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:58:31,989] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30ac7fca-46b9-48e4-b2ab-e46799d99add/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:58:31,994] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:58:31,994] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 02:58:31,994] [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
Pseudohongiella spirulinae	strain=KCTC 32221	GCA_001444425.1	1249552	1249552	type	True	78.2709	304	1174	95	below_threshold
Pseudohongiella acticola	strain=KCTC 42131	GCA_001758195.1	1524254	1524254	type	True	78.2102	256	1174	95	below_threshold
Pseudohongiella nitratireducens	strain=CGMCC 1.15425	GCA_014642795.1	1768907	1768907	type	True	78.1845	176	1174	95	below_threshold
Pseudohongiella nitratireducens	strain=SCS-49	GCA_001642735.1	1768907	1768907	type	True	78.1489	178	1174	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	75.5467	51	1174	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	75.4081	50	1174	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:58:32,003] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40457/tc_result.tsv
[2023-03-17 02:58:32,011] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:58:32,011] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:58:32,011] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30ac7fca-46b9-48e4-b2ab-e46799d99add/dqc_reference/checkm_data
[2023-03-17 02:58:32,012] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:58:32,017] [INFO] Task started: CheckM
[2023-03-17 02:58:32,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40457/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40457/checkm_input OceanDNA-b40457/checkm_result
[2023-03-17 02:59:27,910] [INFO] Task succeeded: CheckM
[2023-03-17 02:59:27,910] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:59:27,920] [INFO] ===== Completeness check finished =====
[2023-03-17 02:59:27,920] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:59:27,921] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40457/markers.fasta)
[2023-03-17 02:59:27,922] [INFO] Task started: Blastn
[2023-03-17 02:59:27,922] [INFO] Running command: blastn -query OceanDNA-b40457/markers.fasta -db /var/lib/cwl/stg30ac7fca-46b9-48e4-b2ab-e46799d99add/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40457/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:59:29,075] [INFO] Task succeeded: Blastn
[2023-03-17 02:59:29,076] [INFO] Selected 13 target genomes.
[2023-03-17 02:59:29,076] [INFO] Target genome list was writen to OceanDNA-b40457/target_genomes_gtdb.txt
[2023-03-17 02:59:29,200] [INFO] Task started: fastANI
[2023-03-17 02:59:29,201] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e4679cd-0876-450e-b903-d100f96e08a3/OceanDNA-b40457.fa --refList OceanDNA-b40457/target_genomes_gtdb.txt --output OceanDNA-b40457/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:59:37,060] [INFO] Task succeeded: fastANI
[2023-03-17 02:59:37,066] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:59:37,066] [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_002354805.1	s__Pseudohongiella sp002354805	99.9967	1152	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.49	99.10	0.99	0.98	3	conclusive
GCA_002706685.1	s__Pseudohongiella sp002706685	94.2431	1050	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.93	99.90	0.98	0.96	5	-
GCA_011050365.1	s__Pseudohongiella sp011050365	78.472	272	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001444425.1	s__Pseudohongiella spirulinae	78.2779	304	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001758195.1	s__Pseudohongiella acticola	78.2245	255	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711845.1	s__Pseudohongiella sp002711845	77.3237	304	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.97	99.97	0.98	0.98	2	-
GCA_001802565.1	s__UBA5078 sp001802565	76.9167	79	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:59:37,066] [INFO] GTDB search result was written to OceanDNA-b40457/result_gtdb.tsv
[2023-03-17 02:59:37,066] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:59:37,067] [INFO] DFAST_QC result json was written to OceanDNA-b40457/dqc_result.json
[2023-03-17 02:59:37,067] [INFO] DFAST_QC completed!
[2023-03-17 02:59:37,067] [INFO] Total running time: 0h1m45s