[2023-03-17 14:51:39,401] [INFO] DFAST_QC pipeline started.
[2023-03-17 14:51:39,402] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 14:51:39,402] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d62b6d9-f4ea-40c4-8992-9d65b3a479da/dqc_reference
[2023-03-17 14:51:40,528] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 14:51:40,529] [INFO] Task started: Prodigal
[2023-03-17 14:51:40,529] [INFO] Running command: cat /var/lib/cwl/stg3143b387-53cf-4ffd-b64d-27c8ac7e76a4/OceanDNA-b37606.fa | prodigal -d OceanDNA-b37606/cds.fna -a OceanDNA-b37606/protein.faa -g 11 -q > /dev/null
[2023-03-17 14:51:54,362] [INFO] Task succeeded: Prodigal
[2023-03-17 14:51:54,362] [INFO] Task started: HMMsearch
[2023-03-17 14:51:54,362] [INFO] Running command: hmmsearch --tblout OceanDNA-b37606/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d62b6d9-f4ea-40c4-8992-9d65b3a479da/dqc_reference/reference_markers.hmm OceanDNA-b37606/protein.faa > /dev/null
[2023-03-17 14:51:54,763] [INFO] Task succeeded: HMMsearch
[2023-03-17 14:51:54,764] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3143b387-53cf-4ffd-b64d-27c8ac7e76a4/OceanDNA-b37606.fa]
[2023-03-17 14:51:54,793] [INFO] Query marker FASTA was written to OceanDNA-b37606/markers.fasta
[2023-03-17 14:51:54,793] [INFO] Task started: Blastn
[2023-03-17 14:51:54,793] [INFO] Running command: blastn -query OceanDNA-b37606/markers.fasta -db /var/lib/cwl/stg4d62b6d9-f4ea-40c4-8992-9d65b3a479da/dqc_reference/reference_markers.fasta -out OceanDNA-b37606/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 14:51:55,568] [INFO] Task succeeded: Blastn
[2023-03-17 14:51:55,569] [INFO] Selected 23 target genomes.
[2023-03-17 14:51:55,569] [INFO] Target genome list was writen to OceanDNA-b37606/target_genomes.txt
[2023-03-17 14:51:55,610] [INFO] Task started: fastANI
[2023-03-17 14:51:55,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg3143b387-53cf-4ffd-b64d-27c8ac7e76a4/OceanDNA-b37606.fa --refList OceanDNA-b37606/target_genomes.txt --output OceanDNA-b37606/fastani_result.tsv --threads 1
[2023-03-17 14:52:16,041] [INFO] Task succeeded: fastANI
[2023-03-17 14:52:16,042] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d62b6d9-f4ea-40c4-8992-9d65b3a479da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 14:52:16,042] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d62b6d9-f4ea-40c4-8992-9d65b3a479da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 14:52:16,046] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 14:52:16,046] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 14:52:16,047] [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 maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	76.9288	51	368	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	76.6994	52	368	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	76.641	56	368	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	76.5827	50	368	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 14:52:16,047] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37606/tc_result.tsv
[2023-03-17 14:52:16,047] [INFO] ===== Taxonomy check completed =====
[2023-03-17 14:52:16,047] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 14:52:16,047] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d62b6d9-f4ea-40c4-8992-9d65b3a479da/dqc_reference/checkm_data
[2023-03-17 14:52:16,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 14:52:16,053] [INFO] Task started: CheckM
[2023-03-17 14:52:16,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37606/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37606/checkm_input OceanDNA-b37606/checkm_result
[2023-03-17 14:52:58,387] [INFO] Task succeeded: CheckM
[2023-03-17 14:52:58,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 14:52:58,392] [INFO] ===== Completeness check finished =====
[2023-03-17 14:52:58,392] [INFO] ===== Start GTDB Search =====
[2023-03-17 14:52:58,393] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37606/markers.fasta)
[2023-03-17 14:52:58,394] [INFO] Task started: Blastn
[2023-03-17 14:52:58,394] [INFO] Running command: blastn -query OceanDNA-b37606/markers.fasta -db /var/lib/cwl/stg4d62b6d9-f4ea-40c4-8992-9d65b3a479da/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37606/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 14:52:58,910] [INFO] Task succeeded: Blastn
[2023-03-17 14:52:58,911] [INFO] Selected 19 target genomes.
[2023-03-17 14:52:58,911] [INFO] Target genome list was writen to OceanDNA-b37606/target_genomes_gtdb.txt
[2023-03-17 14:52:59,128] [INFO] Task started: fastANI
[2023-03-17 14:52:59,129] [INFO] Running command: fastANI --query /var/lib/cwl/stg3143b387-53cf-4ffd-b64d-27c8ac7e76a4/OceanDNA-b37606.fa --refList OceanDNA-b37606/target_genomes_gtdb.txt --output OceanDNA-b37606/fastani_result_gtdb.tsv --threads 1
[2023-03-17 14:53:12,067] [INFO] Task succeeded: fastANI
[2023-03-17 14:53:12,072] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 14:53:12,073] [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	77.3621	120	368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCF_008064665.1	s__Parahaliea maris	76.9288	51	368	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	76.8707	65	368	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	76.6994	52	368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745945.1	s__Halioglobus sp004745945	76.6242	61	368	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	76.5827	50	368	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	76.5757	60	368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 14:53:12,073] [INFO] GTDB search result was written to OceanDNA-b37606/result_gtdb.tsv
[2023-03-17 14:53:12,073] [INFO] ===== GTDB Search completed =====
[2023-03-17 14:53:12,074] [INFO] DFAST_QC result json was written to OceanDNA-b37606/dqc_result.json
[2023-03-17 14:53:12,074] [INFO] DFAST_QC completed!
[2023-03-17 14:53:12,074] [INFO] Total running time: 0h1m33s