[2023-03-15 09:48:16,403] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:16,403] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:16,403] [INFO] DQC Reference Directory: /var/lib/cwl/stg1453e6a0-1be0-4880-8150-4e2e6aa3e67e/dqc_reference
[2023-03-15 09:48:18,052] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:18,054] [INFO] Task started: Prodigal
[2023-03-15 09:48:18,054] [INFO] Running command: cat /var/lib/cwl/stg20009762-e405-4941-bc21-b98cae412e4c/OceanDNA-b37615.fa | prodigal -d OceanDNA-b37615/cds.fna -a OceanDNA-b37615/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:31,254] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:31,255] [INFO] Task started: HMMsearch
[2023-03-15 09:48:31,255] [INFO] Running command: hmmsearch --tblout OceanDNA-b37615/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1453e6a0-1be0-4880-8150-4e2e6aa3e67e/dqc_reference/reference_markers.hmm OceanDNA-b37615/protein.faa > /dev/null
[2023-03-15 09:48:31,429] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:31,429] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg20009762-e405-4941-bc21-b98cae412e4c/OceanDNA-b37615.fa]
[2023-03-15 09:48:31,452] [INFO] Query marker FASTA was written to OceanDNA-b37615/markers.fasta
[2023-03-15 09:48:31,452] [INFO] Task started: Blastn
[2023-03-15 09:48:31,452] [INFO] Running command: blastn -query OceanDNA-b37615/markers.fasta -db /var/lib/cwl/stg1453e6a0-1be0-4880-8150-4e2e6aa3e67e/dqc_reference/reference_markers.fasta -out OceanDNA-b37615/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:31,986] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:31,987] [INFO] Selected 12 target genomes.
[2023-03-15 09:48:31,987] [INFO] Target genome list was writen to OceanDNA-b37615/target_genomes.txt
[2023-03-15 09:48:31,992] [INFO] Task started: fastANI
[2023-03-15 09:48:31,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg20009762-e405-4941-bc21-b98cae412e4c/OceanDNA-b37615.fa --refList OceanDNA-b37615/target_genomes.txt --output OceanDNA-b37615/fastani_result.tsv --threads 1
[2023-03-15 09:48:39,094] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:39,094] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1453e6a0-1be0-4880-8150-4e2e6aa3e67e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:48:39,095] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1453e6a0-1be0-4880-8150-4e2e6aa3e67e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:48:39,099] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:48:39,099] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 09:48:39,099] [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	79.0502	279	642	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	78.7555	291	642	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	77.7278	160	642	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	77.6739	161	642	95	below_threshold
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	77.6561	162	642	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 09:48:39,100] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37615/tc_result.tsv
[2023-03-15 09:48:39,100] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:48:39,100] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:48:39,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1453e6a0-1be0-4880-8150-4e2e6aa3e67e/dqc_reference/checkm_data
[2023-03-15 09:48:39,101] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:48:39,105] [INFO] Task started: CheckM
[2023-03-15 09:48:39,105] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37615/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37615/checkm_input OceanDNA-b37615/checkm_result
[2023-03-15 09:49:15,611] [INFO] Task succeeded: CheckM
[2023-03-15 09:49:15,611] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 30.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:49:15,614] [INFO] ===== Completeness check finished =====
[2023-03-15 09:49:15,614] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:49:15,614] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37615/markers.fasta)
[2023-03-15 09:49:15,614] [INFO] Task started: Blastn
[2023-03-15 09:49:15,614] [INFO] Running command: blastn -query OceanDNA-b37615/markers.fasta -db /var/lib/cwl/stg1453e6a0-1be0-4880-8150-4e2e6aa3e67e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37615/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:49:16,378] [INFO] Task succeeded: Blastn
[2023-03-15 09:49:16,379] [INFO] Selected 10 target genomes.
[2023-03-15 09:49:16,379] [INFO] Target genome list was writen to OceanDNA-b37615/target_genomes_gtdb.txt
[2023-03-15 09:49:16,534] [INFO] Task started: fastANI
[2023-03-15 09:49:16,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg20009762-e405-4941-bc21-b98cae412e4c/OceanDNA-b37615.fa --refList OceanDNA-b37615/target_genomes_gtdb.txt --output OceanDNA-b37615/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:49:23,742] [INFO] Task succeeded: fastANI
[2023-03-15 09:49:23,749] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:49:23,749] [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	79.0502	279	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004354085.1	s__Halioglobus sp004354085	78.7555	291	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001983995.1	s__Halioglobus japonicus	77.7477	159	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
GCA_009937575.1	s__Halioglobus sp009937575	77.3418	136	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009388985.1	s__Halioglobus maricola	77.2724	138	642	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	77.2688	130	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370495.1	s__Halioglobus sp008370495	77.1363	194	642	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	77.0876	117	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002866825.1	s__Halioglobus lutimaris	76.9418	141	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.98	98.98	0.91	0.91	2	-
GCF_003402235.1	s__Parahaliea mediterranea	76.8919	138	642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 09:49:23,749] [INFO] GTDB search result was written to OceanDNA-b37615/result_gtdb.tsv
[2023-03-15 09:49:23,750] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:49:23,751] [INFO] DFAST_QC result json was written to OceanDNA-b37615/dqc_result.json
[2023-03-15 09:49:23,751] [INFO] DFAST_QC completed!
[2023-03-15 09:49:23,751] [INFO] Total running time: 0h1m7s