[2023-03-19 03:36:54,131] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:36:54,132] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:36:54,132] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fc808d4-f5e5-41fa-a719-9b7572de22ec/dqc_reference
[2023-03-19 03:36:55,287] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:36:55,288] [INFO] Task started: Prodigal
[2023-03-19 03:36:55,288] [INFO] Running command: cat /var/lib/cwl/stg7cc2cf0f-a76c-4078-aff9-ac6d77b1b64c/OceanDNA-b37662.fa | prodigal -d OceanDNA-b37662/cds.fna -a OceanDNA-b37662/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:37:21,488] [INFO] Task succeeded: Prodigal
[2023-03-19 03:37:21,489] [INFO] Task started: HMMsearch
[2023-03-19 03:37:21,489] [INFO] Running command: hmmsearch --tblout OceanDNA-b37662/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fc808d4-f5e5-41fa-a719-9b7572de22ec/dqc_reference/reference_markers.hmm OceanDNA-b37662/protein.faa > /dev/null
[2023-03-19 03:37:21,695] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:37:21,696] [INFO] Found 6/6 markers.
[2023-03-19 03:37:21,720] [INFO] Query marker FASTA was written to OceanDNA-b37662/markers.fasta
[2023-03-19 03:37:21,721] [INFO] Task started: Blastn
[2023-03-19 03:37:21,722] [INFO] Running command: blastn -query OceanDNA-b37662/markers.fasta -db /var/lib/cwl/stg9fc808d4-f5e5-41fa-a719-9b7572de22ec/dqc_reference/reference_markers.fasta -out OceanDNA-b37662/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:37:22,646] [INFO] Task succeeded: Blastn
[2023-03-19 03:37:22,647] [INFO] Selected 17 target genomes.
[2023-03-19 03:37:22,647] [INFO] Target genome list was writen to OceanDNA-b37662/target_genomes.txt
[2023-03-19 03:37:22,659] [INFO] Task started: fastANI
[2023-03-19 03:37:22,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cc2cf0f-a76c-4078-aff9-ac6d77b1b64c/OceanDNA-b37662.fa --refList OceanDNA-b37662/target_genomes.txt --output OceanDNA-b37662/fastani_result.tsv --threads 1
[2023-03-19 03:37:35,216] [INFO] Task succeeded: fastANI
[2023-03-19 03:37:35,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fc808d4-f5e5-41fa-a719-9b7572de22ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:37:35,216] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fc808d4-f5e5-41fa-a719-9b7572de22ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:37:35,227] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:37:35,227] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 03:37:35,227] [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
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	78.7449	462	1407	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	78.6553	445	1407	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	78.5579	433	1407	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	78.3136	401	1407	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	77.9616	308	1407	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	77.7048	345	1407	95	below_threshold
Pseudohaliea rubra	strain=DSM 19751	GCA_000764025.1	475795	475795	type	True	77.4263	263	1407	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	77.2114	257	1407	95	below_threshold
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	77.1517	269	1407	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	77.0687	246	1407	95	below_threshold
Chromatocurvus halotolerans	strain=DSM 23344	GCA_004340525.1	1132028	1132028	type	True	76.9461	205	1407	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.5255	174	1407	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	76.3066	93	1407	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	76.2992	93	1407	95	below_threshold
Pseudomonas tolaasii		GCA_900625075.1	29442	29442	type	True	75.7651	118	1407	95	below_threshold
Pseudomonas tolaasii	strain=CCUG 23369	GCA_008801395.1	29442	29442	type	True	75.7538	117	1407	95	below_threshold
Pseudomonas tolaasii	strain=NCPPB 2192	GCA_002813445.1	29442	29442	type	True	75.7306	117	1407	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:37:35,227] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37662/tc_result.tsv
[2023-03-19 03:37:35,227] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:37:35,227] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:37:35,228] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fc808d4-f5e5-41fa-a719-9b7572de22ec/dqc_reference/checkm_data
[2023-03-19 03:37:35,228] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:37:35,234] [INFO] Task started: CheckM
[2023-03-19 03:37:35,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37662/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37662/checkm_input OceanDNA-b37662/checkm_result
[2023-03-19 03:38:38,392] [INFO] Task succeeded: CheckM
[2023-03-19 03:38:38,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:38:38,395] [INFO] ===== Completeness check finished =====
[2023-03-19 03:38:38,395] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:38:38,396] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37662/markers.fasta)
[2023-03-19 03:38:38,397] [INFO] Task started: Blastn
[2023-03-19 03:38:38,397] [INFO] Running command: blastn -query OceanDNA-b37662/markers.fasta -db /var/lib/cwl/stg9fc808d4-f5e5-41fa-a719-9b7572de22ec/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37662/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:38:40,505] [INFO] Task succeeded: Blastn
[2023-03-19 03:38:40,506] [INFO] Selected 12 target genomes.
[2023-03-19 03:38:40,506] [INFO] Target genome list was writen to OceanDNA-b37662/target_genomes_gtdb.txt
[2023-03-19 03:38:40,517] [INFO] Task started: fastANI
[2023-03-19 03:38:40,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cc2cf0f-a76c-4078-aff9-ac6d77b1b64c/OceanDNA-b37662.fa --refList OceanDNA-b37662/target_genomes_gtdb.txt --output OceanDNA-b37662/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:38:50,910] [INFO] Task succeeded: fastANI
[2023-03-19 03:38:50,918] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:38:50,918] [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_002699145.1	s__Halioglobus sp002699145	99.9633	1393	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	conclusive
GCF_004745945.1	s__Halioglobus sp004745945	79.5861	498	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	79.2434	499	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	78.763	459	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003457605.1	s__Halioglobus sediminis	78.6553	445	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064635.1	s__Parahaliea aestuarii	78.5575	433	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937575.1	s__Halioglobus sp009937575	78.5505	401	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064665.1	s__Parahaliea maris	78.3136	401	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004354085.1	s__Halioglobus sp004354085	77.7141	344	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009799925.1	s__Pseudomonas_E sp009799925	76.8755	226	1407	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_000761545.1	s__Pseudomonas_E sp000761545	76.3771	219	1407	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_002813445.1	s__Pseudomonas_E tolaasii	75.742	118	1407	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.61	99.17	0.97	0.93	14	-
--------------------------------------------------------------------------------
[2023-03-19 03:38:50,918] [INFO] GTDB search result was written to OceanDNA-b37662/result_gtdb.tsv
[2023-03-19 03:38:50,918] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:38:50,920] [INFO] DFAST_QC result json was written to OceanDNA-b37662/dqc_result.json
[2023-03-19 03:38:50,920] [INFO] DFAST_QC completed!
[2023-03-19 03:38:50,920] [INFO] Total running time: 0h1m57s