[2023-03-18 00:21:56,069] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:21:56,069] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:21:56,070] [INFO] DQC Reference Directory: /var/lib/cwl/stg540f1e38-4af2-448a-ae31-b636a1fcaa74/dqc_reference
[2023-03-18 00:21:57,181] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:21:57,181] [INFO] Task started: Prodigal
[2023-03-18 00:21:57,181] [INFO] Running command: cat /var/lib/cwl/stg7564f0da-a19e-4796-84e3-ee24a270ba5e/OceanDNA-b37613.fa | prodigal -d OceanDNA-b37613/cds.fna -a OceanDNA-b37613/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:22:10,588] [INFO] Task succeeded: Prodigal
[2023-03-18 00:22:10,588] [INFO] Task started: HMMsearch
[2023-03-18 00:22:10,588] [INFO] Running command: hmmsearch --tblout OceanDNA-b37613/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg540f1e38-4af2-448a-ae31-b636a1fcaa74/dqc_reference/reference_markers.hmm OceanDNA-b37613/protein.faa > /dev/null
[2023-03-18 00:22:10,769] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:22:10,770] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7564f0da-a19e-4796-84e3-ee24a270ba5e/OceanDNA-b37613.fa]
[2023-03-18 00:22:10,791] [INFO] Query marker FASTA was written to OceanDNA-b37613/markers.fasta
[2023-03-18 00:22:10,792] [INFO] Task started: Blastn
[2023-03-18 00:22:10,792] [INFO] Running command: blastn -query OceanDNA-b37613/markers.fasta -db /var/lib/cwl/stg540f1e38-4af2-448a-ae31-b636a1fcaa74/dqc_reference/reference_markers.fasta -out OceanDNA-b37613/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:22:11,359] [INFO] Task succeeded: Blastn
[2023-03-18 00:22:11,360] [INFO] Selected 15 target genomes.
[2023-03-18 00:22:11,360] [INFO] Target genome list was writen to OceanDNA-b37613/target_genomes.txt
[2023-03-18 00:22:11,367] [INFO] Task started: fastANI
[2023-03-18 00:22:11,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg7564f0da-a19e-4796-84e3-ee24a270ba5e/OceanDNA-b37613.fa --refList OceanDNA-b37613/target_genomes.txt --output OceanDNA-b37613/fastani_result.tsv --threads 1
[2023-03-18 00:22:20,078] [INFO] Task succeeded: fastANI
[2023-03-18 00:22:20,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg540f1e38-4af2-448a-ae31-b636a1fcaa74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:22:20,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg540f1e38-4af2-448a-ae31-b636a1fcaa74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:22:20,085] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:22:20,085] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:22:20,085] [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
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	78.4857	275	676	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	77.9531	157	676	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	77.8771	250	676	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	77.7509	157	676	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	77.6439	168	676	95	below_threshold
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	77.6368	169	676	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	77.5934	170	676	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:22:20,085] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37613/tc_result.tsv
[2023-03-18 00:22:20,085] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:22:20,086] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:22:20,086] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg540f1e38-4af2-448a-ae31-b636a1fcaa74/dqc_reference/checkm_data
[2023-03-18 00:22:20,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:22:20,091] [INFO] Task started: CheckM
[2023-03-18 00:22:20,092] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37613/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37613/checkm_input OceanDNA-b37613/checkm_result
[2023-03-18 00:22:57,586] [INFO] Task succeeded: CheckM
[2023-03-18 00:22:57,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:22:57,589] [INFO] ===== Completeness check finished =====
[2023-03-18 00:22:57,589] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:22:57,589] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37613/markers.fasta)
[2023-03-18 00:22:57,590] [INFO] Task started: Blastn
[2023-03-18 00:22:57,590] [INFO] Running command: blastn -query OceanDNA-b37613/markers.fasta -db /var/lib/cwl/stg540f1e38-4af2-448a-ae31-b636a1fcaa74/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37613/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:22:58,391] [INFO] Task succeeded: Blastn
[2023-03-18 00:22:58,392] [INFO] Selected 14 target genomes.
[2023-03-18 00:22:58,392] [INFO] Target genome list was writen to OceanDNA-b37613/target_genomes_gtdb.txt
[2023-03-18 00:22:58,432] [INFO] Task started: fastANI
[2023-03-18 00:22:58,432] [INFO] Running command: fastANI --query /var/lib/cwl/stg7564f0da-a19e-4796-84e3-ee24a270ba5e/OceanDNA-b37613.fa --refList OceanDNA-b37613/target_genomes_gtdb.txt --output OceanDNA-b37613/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:23:08,677] [INFO] Task succeeded: fastANI
[2023-03-18 00:23:08,684] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:23:08,684] [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_003457605.1	s__Halioglobus sediminis	78.4857	275	676	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370495.1	s__Halioglobus sp008370495	78.0487	212	676	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	77.9615	156	676	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745945.1	s__Halioglobus sp004745945	77.9548	168	676	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937575.1	s__Halioglobus sp009937575	77.9447	211	676	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	77.9117	181	676	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	77.8771	250	676	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	77.7724	156	676	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001983995.1	s__Halioglobus japonicus	77.6439	168	676	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
GCF_009388985.1	s__Halioglobus maricola	77.259	164	676	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002414665.1	s__Haliea sp002414665	76.4418	91	676	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.89	99.89	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-18 00:23:08,684] [INFO] GTDB search result was written to OceanDNA-b37613/result_gtdb.tsv
[2023-03-18 00:23:08,684] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:23:08,685] [INFO] DFAST_QC result json was written to OceanDNA-b37613/dqc_result.json
[2023-03-18 00:23:08,685] [INFO] DFAST_QC completed!
[2023-03-18 00:23:08,685] [INFO] Total running time: 0h1m13s