[2023-03-14 12:03:55,349] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:03:55,352] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:03:55,352] [INFO] DQC Reference Directory: /var/lib/cwl/stg09b8621e-36ed-442c-a8b7-973779a2b014/dqc_reference
[2023-03-14 12:03:56,865] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:03:56,865] [INFO] Task started: Prodigal
[2023-03-14 12:03:56,865] [INFO] Running command: cat /var/lib/cwl/stg33e0cf9d-fbe9-479a-b65f-c04a04aeb2cd/OceanDNA-b3416.fa | prodigal -d OceanDNA-b3416/cds.fna -a OceanDNA-b3416/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:04:03,492] [INFO] Task succeeded: Prodigal
[2023-03-14 12:04:03,492] [INFO] Task started: HMMsearch
[2023-03-14 12:04:03,492] [INFO] Running command: hmmsearch --tblout OceanDNA-b3416/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09b8621e-36ed-442c-a8b7-973779a2b014/dqc_reference/reference_markers.hmm OceanDNA-b3416/protein.faa > /dev/null
[2023-03-14 12:04:03,633] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:04:03,633] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg33e0cf9d-fbe9-479a-b65f-c04a04aeb2cd/OceanDNA-b3416.fa]
[2023-03-14 12:04:03,654] [INFO] Query marker FASTA was written to OceanDNA-b3416/markers.fasta
[2023-03-14 12:04:03,656] [INFO] Task started: Blastn
[2023-03-14 12:04:03,656] [INFO] Running command: blastn -query OceanDNA-b3416/markers.fasta -db /var/lib/cwl/stg09b8621e-36ed-442c-a8b7-973779a2b014/dqc_reference/reference_markers.fasta -out OceanDNA-b3416/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:04:04,196] [INFO] Task succeeded: Blastn
[2023-03-14 12:04:04,199] [INFO] Selected 13 target genomes.
[2023-03-14 12:04:04,199] [INFO] Target genome list was writen to OceanDNA-b3416/target_genomes.txt
[2023-03-14 12:04:04,207] [INFO] Task started: fastANI
[2023-03-14 12:04:04,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg33e0cf9d-fbe9-479a-b65f-c04a04aeb2cd/OceanDNA-b3416.fa --refList OceanDNA-b3416/target_genomes.txt --output OceanDNA-b3416/fastani_result.tsv --threads 1
[2023-03-14 12:04:13,380] [INFO] Task succeeded: fastANI
[2023-03-14 12:04:13,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09b8621e-36ed-442c-a8b7-973779a2b014/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:04:13,381] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09b8621e-36ed-442c-a8b7-973779a2b014/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:04:13,385] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:04:13,385] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:04:13,385] [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 oceani	strain=SCSIO 61214	GCA_018141545.1	2843216	2843216	type	True	77.2625	61	293	95	below_threshold
Miltoncostaea marina	strain=SCSIO 60955	GCA_018141525.1	2843215	2843215	type	True	77.2006	68	293	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:04:13,387] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3416/tc_result.tsv
[2023-03-14 12:04:13,389] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:04:13,389] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:04:13,389] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09b8621e-36ed-442c-a8b7-973779a2b014/dqc_reference/checkm_data
[2023-03-14 12:04:13,390] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:04:13,435] [INFO] Task started: CheckM
[2023-03-14 12:04:13,435] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3416/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3416/checkm_input OceanDNA-b3416/checkm_result
[2023-03-14 12:04:35,492] [INFO] Task succeeded: CheckM
[2023-03-14 12:04:35,492] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.74%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 12:04:35,496] [INFO] ===== Completeness check finished =====
[2023-03-14 12:04:35,497] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:04:35,497] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3416/markers.fasta)
[2023-03-14 12:04:35,498] [INFO] Task started: Blastn
[2023-03-14 12:04:35,498] [INFO] Running command: blastn -query OceanDNA-b3416/markers.fasta -db /var/lib/cwl/stg09b8621e-36ed-442c-a8b7-973779a2b014/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3416/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:04:36,278] [INFO] Task succeeded: Blastn
[2023-03-14 12:04:36,281] [INFO] Selected 10 target genomes.
[2023-03-14 12:04:36,281] [INFO] Target genome list was writen to OceanDNA-b3416/target_genomes_gtdb.txt
[2023-03-14 12:04:36,310] [INFO] Task started: fastANI
[2023-03-14 12:04:36,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg33e0cf9d-fbe9-479a-b65f-c04a04aeb2cd/OceanDNA-b3416.fa --refList OceanDNA-b3416/target_genomes_gtdb.txt --output OceanDNA-b3416/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:04:39,690] [INFO] Task succeeded: fastANI
[2023-03-14 12:04:39,696] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:04:39,697] [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_903943955.1	s__SYFI01 sp903943955	94.6857	278	293	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	99.59	99.47	0.92	0.89	6	-
GCA_005800465.1	s__SYFI01 sp005800465	93.7537	220	293	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903866425.1	s__SYFI01 sp903866425	81.2617	184	293	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	80.1849	158	293	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780995.1	s__SYFI01 sp016780995	79.9716	161	293	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	79.8516	174	293	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	79.3098	175	293	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	79.1354	125	293	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	78.4844	121	293	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:04:39,698] [INFO] GTDB search result was written to OceanDNA-b3416/result_gtdb.tsv
[2023-03-14 12:04:39,698] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:04:39,701] [INFO] DFAST_QC result json was written to OceanDNA-b3416/dqc_result.json
[2023-03-14 12:04:39,701] [INFO] DFAST_QC completed!
[2023-03-14 12:04:39,701] [INFO] Total running time: 0h0m44s