[2023-03-15 09:25:29,088] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:25:29,089] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:25:29,089] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5091249-ef54-4fdc-b0cf-110fa5deb15f/dqc_reference
[2023-03-15 09:25:30,382] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:25:30,382] [INFO] Task started: Prodigal
[2023-03-15 09:25:30,382] [INFO] Running command: cat /var/lib/cwl/stg57e91a90-70b9-43b1-99c5-cf923c1d60c7/OceanDNA-b22823.fa | prodigal -d OceanDNA-b22823/cds.fna -a OceanDNA-b22823/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:26:01,545] [INFO] Task succeeded: Prodigal
[2023-03-15 09:26:01,546] [INFO] Task started: HMMsearch
[2023-03-15 09:26:01,546] [INFO] Running command: hmmsearch --tblout OceanDNA-b22823/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5091249-ef54-4fdc-b0cf-110fa5deb15f/dqc_reference/reference_markers.hmm OceanDNA-b22823/protein.faa > /dev/null
[2023-03-15 09:26:01,806] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:26:01,806] [INFO] Found 6/6 markers.
[2023-03-15 09:26:01,842] [INFO] Query marker FASTA was written to OceanDNA-b22823/markers.fasta
[2023-03-15 09:26:01,842] [INFO] Task started: Blastn
[2023-03-15 09:26:01,842] [INFO] Running command: blastn -query OceanDNA-b22823/markers.fasta -db /var/lib/cwl/stgf5091249-ef54-4fdc-b0cf-110fa5deb15f/dqc_reference/reference_markers.fasta -out OceanDNA-b22823/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:26:02,347] [INFO] Task succeeded: Blastn
[2023-03-15 09:26:02,348] [INFO] Selected 26 target genomes.
[2023-03-15 09:26:02,348] [INFO] Target genome list was writen to OceanDNA-b22823/target_genomes.txt
[2023-03-15 09:26:02,362] [INFO] Task started: fastANI
[2023-03-15 09:26:02,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg57e91a90-70b9-43b1-99c5-cf923c1d60c7/OceanDNA-b22823.fa --refList OceanDNA-b22823/target_genomes.txt --output OceanDNA-b22823/fastani_result.tsv --threads 1
[2023-03-15 09:26:26,896] [INFO] Task succeeded: fastANI
[2023-03-15 09:26:26,896] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5091249-ef54-4fdc-b0cf-110fa5deb15f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:26:26,896] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5091249-ef54-4fdc-b0cf-110fa5deb15f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:26:26,900] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:26:26,900] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 09:26:26,900] [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
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.5538	66	1589	95	below_threshold
Lignipirellula cremea	strain=Pla85_3_4	GCA_007751035.1	2528010	2528010	type	True	75.3955	54	1589	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 09:26:26,900] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22823/tc_result.tsv
[2023-03-15 09:26:26,900] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:26:26,900] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:26:26,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5091249-ef54-4fdc-b0cf-110fa5deb15f/dqc_reference/checkm_data
[2023-03-15 09:26:26,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:26:26,908] [INFO] Task started: CheckM
[2023-03-15 09:26:26,908] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22823/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22823/checkm_input OceanDNA-b22823/checkm_result
[2023-03-15 09:27:42,559] [INFO] Task succeeded: CheckM
[2023-03-15 09:27:42,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.70%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 09:27:42,563] [INFO] ===== Completeness check finished =====
[2023-03-15 09:27:42,563] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:27:42,564] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22823/markers.fasta)
[2023-03-15 09:27:42,565] [INFO] Task started: Blastn
[2023-03-15 09:27:42,565] [INFO] Running command: blastn -query OceanDNA-b22823/markers.fasta -db /var/lib/cwl/stgf5091249-ef54-4fdc-b0cf-110fa5deb15f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22823/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:27:43,282] [INFO] Task succeeded: Blastn
[2023-03-15 09:27:43,283] [INFO] Selected 28 target genomes.
[2023-03-15 09:27:43,283] [INFO] Target genome list was writen to OceanDNA-b22823/target_genomes_gtdb.txt
[2023-03-15 09:27:44,019] [INFO] Task started: fastANI
[2023-03-15 09:27:44,019] [INFO] Running command: fastANI --query /var/lib/cwl/stg57e91a90-70b9-43b1-99c5-cf923c1d60c7/OceanDNA-b22823.fa --refList OceanDNA-b22823/target_genomes_gtdb.txt --output OceanDNA-b22823/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:28:12,023] [INFO] Task succeeded: fastANI
[2023-03-15 09:28:12,027] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:28:12,027] [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_018699955.1	s__JABISG01 sp018699955	88.1105	1284	1589	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABISG01	95.0	99.95	99.95	0.96	0.96	3	-
GCF_007747795.1	s__Maioricimonas rarisocia	75.5661	65	1589	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795125.1	s__JAEUIG01 sp016795125	75.3917	72	1589	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JAEUIG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203845.1	s__JABMPE01 sp013203845	75.2922	71	1589	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200145.1	s__JACQFH01 sp016200145	75.2634	66	1589	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__JACQFH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 09:28:12,028] [INFO] GTDB search result was written to OceanDNA-b22823/result_gtdb.tsv
[2023-03-15 09:28:12,028] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:28:12,028] [INFO] DFAST_QC result json was written to OceanDNA-b22823/dqc_result.json
[2023-03-15 09:28:12,029] [INFO] DFAST_QC completed!
[2023-03-15 09:28:12,029] [INFO] Total running time: 0h2m43s