[2023-03-15 03:56:21,753] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:56:21,753] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:56:21,753] [INFO] DQC Reference Directory: /var/lib/cwl/stgef954a5c-f0da-4b1d-bb1d-4881bc978d11/dqc_reference
[2023-03-15 03:56:23,415] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:56:23,415] [INFO] Task started: Prodigal
[2023-03-15 03:56:23,415] [INFO] Running command: cat /var/lib/cwl/stgc0206de9-2144-4eb5-b989-2cd49c61dd6f/OceanDNA-b3412.fa | prodigal -d OceanDNA-b3412/cds.fna -a OceanDNA-b3412/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:56:28,404] [INFO] Task succeeded: Prodigal
[2023-03-15 03:56:28,405] [INFO] Task started: HMMsearch
[2023-03-15 03:56:28,405] [INFO] Running command: hmmsearch --tblout OceanDNA-b3412/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef954a5c-f0da-4b1d-bb1d-4881bc978d11/dqc_reference/reference_markers.hmm OceanDNA-b3412/protein.faa > /dev/null
[2023-03-15 03:56:28,617] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:56:28,618] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc0206de9-2144-4eb5-b989-2cd49c61dd6f/OceanDNA-b3412.fa]
[2023-03-15 03:56:28,629] [INFO] Query marker FASTA was written to OceanDNA-b3412/markers.fasta
[2023-03-15 03:56:28,629] [INFO] Task started: Blastn
[2023-03-15 03:56:28,629] [INFO] Running command: blastn -query OceanDNA-b3412/markers.fasta -db /var/lib/cwl/stgef954a5c-f0da-4b1d-bb1d-4881bc978d11/dqc_reference/reference_markers.fasta -out OceanDNA-b3412/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:56:29,131] [INFO] Task succeeded: Blastn
[2023-03-15 03:56:29,132] [INFO] Selected 19 target genomes.
[2023-03-15 03:56:29,132] [INFO] Target genome list was writen to OceanDNA-b3412/target_genomes.txt
[2023-03-15 03:56:29,149] [INFO] Task started: fastANI
[2023-03-15 03:56:29,149] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0206de9-2144-4eb5-b989-2cd49c61dd6f/OceanDNA-b3412.fa --refList OceanDNA-b3412/target_genomes.txt --output OceanDNA-b3412/fastani_result.tsv --threads 1
[2023-03-15 03:56:44,422] [INFO] Task succeeded: fastANI
[2023-03-15 03:56:44,423] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef954a5c-f0da-4b1d-bb1d-4881bc978d11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:56:44,423] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef954a5c-f0da-4b1d-bb1d-4881bc978d11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:56:44,426] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:56:44,426] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:56:44,427] [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
Miltoncostaea marina	strain=SCSIO 60955	GCA_018141525.1	2843215	2843215	type	True	78.0717	91	180	95	below_threshold
Miltoncostaea oceani	strain=SCSIO 61214	GCA_018141545.1	2843216	2843216	type	True	77.8909	75	180	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:56:44,427] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3412/tc_result.tsv
[2023-03-15 03:56:44,427] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:56:44,427] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:56:44,427] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef954a5c-f0da-4b1d-bb1d-4881bc978d11/dqc_reference/checkm_data
[2023-03-15 03:56:44,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:56:44,431] [INFO] Task started: CheckM
[2023-03-15 03:56:44,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3412/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3412/checkm_input OceanDNA-b3412/checkm_result
[2023-03-15 03:57:02,899] [INFO] Task succeeded: CheckM
[2023-03-15 03:57:02,899] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.96%
Contamintation: 4.69%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 03:57:02,901] [INFO] ===== Completeness check finished =====
[2023-03-15 03:57:02,901] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:57:02,901] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3412/markers.fasta)
[2023-03-15 03:57:02,902] [INFO] Task started: Blastn
[2023-03-15 03:57:02,902] [INFO] Running command: blastn -query OceanDNA-b3412/markers.fasta -db /var/lib/cwl/stgef954a5c-f0da-4b1d-bb1d-4881bc978d11/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3412/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:57:03,490] [INFO] Task succeeded: Blastn
[2023-03-15 03:57:03,491] [INFO] Selected 7 target genomes.
[2023-03-15 03:57:03,491] [INFO] Target genome list was writen to OceanDNA-b3412/target_genomes_gtdb.txt
[2023-03-15 03:57:03,500] [INFO] Task started: fastANI
[2023-03-15 03:57:03,500] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0206de9-2144-4eb5-b989-2cd49c61dd6f/OceanDNA-b3412.fa --refList OceanDNA-b3412/target_genomes_gtdb.txt --output OceanDNA-b3412/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:57:05,424] [INFO] Task succeeded: fastANI
[2023-03-15 03:57:05,429] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:57:05,429] [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_016780995.1	s__SYFI01 sp016780995	84.5695	147	180	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853415.1	s__SYFI01 sp017853415	83.9173	155	180	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870155.1	s__SYFI01 sp016870155	83.4122	157	180	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969105.1	s__SYFI01 sp018969105	83.3672	149	180	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928615.1	s__SYFI01 sp903928615	83.0916	119	180	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005788075.1	s__SYFI01 sp005788075	81.9679	121	180	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005792725.1	s__SYFI01 sp005792725	80.2411	117	180	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	99.67	99.67	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-15 03:57:05,429] [INFO] GTDB search result was written to OceanDNA-b3412/result_gtdb.tsv
[2023-03-15 03:57:05,429] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:57:05,430] [INFO] DFAST_QC result json was written to OceanDNA-b3412/dqc_result.json
[2023-03-15 03:57:05,430] [INFO] DFAST_QC completed!
[2023-03-15 03:57:05,430] [INFO] Total running time: 0h0m44s