[2023-03-18 08:17:18,479] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:18,479] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:18,479] [INFO] DQC Reference Directory: /var/lib/cwl/stg4960387a-4dd0-48ec-b044-3b4728053443/dqc_reference
[2023-03-18 08:17:20,266] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:20,267] [INFO] Task started: Prodigal
[2023-03-18 08:17:20,267] [INFO] Running command: cat /var/lib/cwl/stgfcb0bc5e-7ac7-451e-bf19-5e1a852a0346/OceanDNA-b3414.fa | prodigal -d OceanDNA-b3414/cds.fna -a OceanDNA-b3414/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:26,094] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:26,094] [INFO] Task started: HMMsearch
[2023-03-18 08:17:26,094] [INFO] Running command: hmmsearch --tblout OceanDNA-b3414/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4960387a-4dd0-48ec-b044-3b4728053443/dqc_reference/reference_markers.hmm OceanDNA-b3414/protein.faa > /dev/null
[2023-03-18 08:17:26,231] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:26,231] [INFO] Found 6/6 markers.
[2023-03-18 08:17:26,243] [INFO] Query marker FASTA was written to OceanDNA-b3414/markers.fasta
[2023-03-18 08:17:26,243] [INFO] Task started: Blastn
[2023-03-18 08:17:26,243] [INFO] Running command: blastn -query OceanDNA-b3414/markers.fasta -db /var/lib/cwl/stg4960387a-4dd0-48ec-b044-3b4728053443/dqc_reference/reference_markers.fasta -out OceanDNA-b3414/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:26,867] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:26,868] [INFO] Selected 25 target genomes.
[2023-03-18 08:17:26,869] [INFO] Target genome list was writen to OceanDNA-b3414/target_genomes.txt
[2023-03-18 08:17:26,880] [INFO] Task started: fastANI
[2023-03-18 08:17:26,880] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcb0bc5e-7ac7-451e-bf19-5e1a852a0346/OceanDNA-b3414.fa --refList OceanDNA-b3414/target_genomes.txt --output OceanDNA-b3414/fastani_result.tsv --threads 1
[2023-03-18 08:17:46,135] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:46,135] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4960387a-4dd0-48ec-b044-3b4728053443/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:17:46,136] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4960387a-4dd0-48ec-b044-3b4728053443/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:17:46,139] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:17:46,140] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:17:46,140] [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	77.8688	97	236	95	below_threshold
Miltoncostaea oceani	strain=SCSIO 61214	GCA_018141545.1	2843216	2843216	type	True	77.6173	86	236	95	below_threshold
Kitasatospora viridis	strain=DSM 44826	GCA_007829815.1	281105	281105	type	True	75.3224	53	236	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:17:46,140] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3414/tc_result.tsv
[2023-03-18 08:17:46,140] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:17:46,140] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:17:46,140] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4960387a-4dd0-48ec-b044-3b4728053443/dqc_reference/checkm_data
[2023-03-18 08:17:46,141] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:17:46,143] [INFO] Task started: CheckM
[2023-03-18 08:17:46,143] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3414/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3414/checkm_input OceanDNA-b3414/checkm_result
[2023-03-18 08:18:06,022] [INFO] Task succeeded: CheckM
[2023-03-18 08:18:06,023] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.29%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:18:06,025] [INFO] ===== Completeness check finished =====
[2023-03-18 08:18:06,025] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:18:06,025] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3414/markers.fasta)
[2023-03-18 08:18:06,025] [INFO] Task started: Blastn
[2023-03-18 08:18:06,025] [INFO] Running command: blastn -query OceanDNA-b3414/markers.fasta -db /var/lib/cwl/stg4960387a-4dd0-48ec-b044-3b4728053443/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3414/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:18:07,075] [INFO] Task succeeded: Blastn
[2023-03-18 08:18:07,076] [INFO] Selected 8 target genomes.
[2023-03-18 08:18:07,076] [INFO] Target genome list was writen to OceanDNA-b3414/target_genomes_gtdb.txt
[2023-03-18 08:18:07,133] [INFO] Task started: fastANI
[2023-03-18 08:18:07,133] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcb0bc5e-7ac7-451e-bf19-5e1a852a0346/OceanDNA-b3414.fa --refList OceanDNA-b3414/target_genomes_gtdb.txt --output OceanDNA-b3414/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:18:09,319] [INFO] Task succeeded: fastANI
[2023-03-18 08:18:09,325] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:18:09,325] [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	83.3764	181	236	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	83.0936	180	236	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	82.7387	170	236	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	82.5478	185	236	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	82.1682	143	236	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	81.0876	136	236	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	80.0659	134	236	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	99.67	99.67	0.89	0.89	2	-
GCA_903866425.1	s__SYFI01 sp903866425	79.8273	124	236	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:18:09,325] [INFO] GTDB search result was written to OceanDNA-b3414/result_gtdb.tsv
[2023-03-18 08:18:09,325] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:18:09,326] [INFO] DFAST_QC result json was written to OceanDNA-b3414/dqc_result.json
[2023-03-18 08:18:09,326] [INFO] DFAST_QC completed!
[2023-03-18 08:18:09,326] [INFO] Total running time: 0h0m51s