[2023-03-17 07:44:36,993] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:44:36,993] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:44:36,993] [INFO] DQC Reference Directory: /var/lib/cwl/stga8d8f67e-05b0-4c7a-9e3b-10485419e334/dqc_reference
[2023-03-17 07:44:38,847] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:44:38,848] [INFO] Task started: Prodigal
[2023-03-17 07:44:38,848] [INFO] Running command: cat /var/lib/cwl/stgdeb13bfe-f22b-402f-a4d0-ee19a696e34a/OceanDNA-b37529.fa | prodigal -d OceanDNA-b37529/cds.fna -a OceanDNA-b37529/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:44:54,428] [INFO] Task succeeded: Prodigal
[2023-03-17 07:44:54,429] [INFO] Task started: HMMsearch
[2023-03-17 07:44:54,429] [INFO] Running command: hmmsearch --tblout OceanDNA-b37529/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8d8f67e-05b0-4c7a-9e3b-10485419e334/dqc_reference/reference_markers.hmm OceanDNA-b37529/protein.faa > /dev/null
[2023-03-17 07:44:54,608] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:44:54,608] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgdeb13bfe-f22b-402f-a4d0-ee19a696e34a/OceanDNA-b37529.fa]
[2023-03-17 07:44:54,629] [INFO] Query marker FASTA was written to OceanDNA-b37529/markers.fasta
[2023-03-17 07:44:54,630] [INFO] Task started: Blastn
[2023-03-17 07:44:54,630] [INFO] Running command: blastn -query OceanDNA-b37529/markers.fasta -db /var/lib/cwl/stga8d8f67e-05b0-4c7a-9e3b-10485419e334/dqc_reference/reference_markers.fasta -out OceanDNA-b37529/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:44:55,266] [INFO] Task succeeded: Blastn
[2023-03-17 07:44:55,267] [INFO] Selected 15 target genomes.
[2023-03-17 07:44:55,267] [INFO] Target genome list was writen to OceanDNA-b37529/target_genomes.txt
[2023-03-17 07:44:55,276] [INFO] Task started: fastANI
[2023-03-17 07:44:55,276] [INFO] Running command: fastANI --query /var/lib/cwl/stgdeb13bfe-f22b-402f-a4d0-ee19a696e34a/OceanDNA-b37529.fa --refList OceanDNA-b37529/target_genomes.txt --output OceanDNA-b37529/fastani_result.tsv --threads 1
[2023-03-17 07:45:04,975] [INFO] Task succeeded: fastANI
[2023-03-17 07:45:04,976] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8d8f67e-05b0-4c7a-9e3b-10485419e334/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:45:04,976] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8d8f67e-05b0-4c7a-9e3b-10485419e334/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:45:04,983] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:45:04,983] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:45:04,984] [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	78.1681	284	819	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	77.909	282	819	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	77.6661	239	819	95	below_threshold
Sediminihaliea albiluteola	strain=F7430	GCA_014077625.1	2758564	2758564	type	True	77.6108	164	819	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	77.074	130	819	95	below_threshold
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	76.8603	129	819	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	76.8472	152	819	95	below_threshold
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	76.805	139	819	95	below_threshold
Kineobactrum sediminis	strain=F02	GCA_002868715.1	1905677	1905677	type	True	76.714	99	819	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	76.6245	122	819	95	below_threshold
Halioglobus pacificus	strain=KCTC 23430	GCA_014652275.1	930806	930806	type	True	76.3212	80	819	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:45:04,984] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37529/tc_result.tsv
[2023-03-17 07:45:04,984] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:45:04,984] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:45:04,984] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8d8f67e-05b0-4c7a-9e3b-10485419e334/dqc_reference/checkm_data
[2023-03-17 07:45:04,985] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:45:04,989] [INFO] Task started: CheckM
[2023-03-17 07:45:04,989] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37529/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37529/checkm_input OceanDNA-b37529/checkm_result
[2023-03-17 07:45:46,403] [INFO] Task succeeded: CheckM
[2023-03-17 07:45:46,404] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:45:46,406] [INFO] ===== Completeness check finished =====
[2023-03-17 07:45:46,407] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:45:46,407] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37529/markers.fasta)
[2023-03-17 07:45:46,407] [INFO] Task started: Blastn
[2023-03-17 07:45:46,407] [INFO] Running command: blastn -query OceanDNA-b37529/markers.fasta -db /var/lib/cwl/stga8d8f67e-05b0-4c7a-9e3b-10485419e334/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37529/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:45:47,424] [INFO] Task succeeded: Blastn
[2023-03-17 07:45:47,425] [INFO] Selected 11 target genomes.
[2023-03-17 07:45:47,425] [INFO] Target genome list was writen to OceanDNA-b37529/target_genomes_gtdb.txt
[2023-03-17 07:45:47,434] [INFO] Task started: fastANI
[2023-03-17 07:45:47,434] [INFO] Running command: fastANI --query /var/lib/cwl/stgdeb13bfe-f22b-402f-a4d0-ee19a696e34a/OceanDNA-b37529.fa --refList OceanDNA-b37529/target_genomes_gtdb.txt --output OceanDNA-b37529/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:45:54,928] [INFO] Task succeeded: fastANI
[2023-03-17 07:45:54,935] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:45:54,936] [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_003402235.1	s__Parahaliea mediterranea	78.1427	286	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	78.0023	326	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064635.1	s__Parahaliea aestuarii	77.909	282	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064665.1	s__Parahaliea maris	77.6661	239	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077625.1	s__Parahaliea sp014077625	77.6108	164	819	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	77.2467	117	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010669285.1	s__Kineobactrum salinum	77.074	130	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003457605.1	s__Halioglobus sediminis	76.8472	152	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423125.1	s__Haliea salexigens	76.8433	130	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	96.91	96.59	0.87	0.83	15	-
GCA_004354085.1	s__Halioglobus sp004354085	76.6084	123	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002416125.1	s__Haliea sp002416125	76.4649	125	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.96	99.96	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-17 07:45:54,936] [INFO] GTDB search result was written to OceanDNA-b37529/result_gtdb.tsv
[2023-03-17 07:45:54,936] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:45:54,937] [INFO] DFAST_QC result json was written to OceanDNA-b37529/dqc_result.json
[2023-03-17 07:45:54,937] [INFO] DFAST_QC completed!
[2023-03-17 07:45:54,938] [INFO] Total running time: 0h1m18s