[2023-03-16 08:58:01,915] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:58:01,915] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:58:01,915] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd0c9f3b-47e4-42f1-af22-017dad8125f9/dqc_reference
[2023-03-16 08:58:03,037] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:58:03,038] [INFO] Task started: Prodigal
[2023-03-16 08:58:03,038] [INFO] Running command: cat /var/lib/cwl/stg01e8c5ad-58e6-4ac8-90a9-b1c794407026/OceanDNA-b11573.fa | prodigal -d OceanDNA-b11573/cds.fna -a OceanDNA-b11573/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:58:11,684] [INFO] Task succeeded: Prodigal
[2023-03-16 08:58:11,685] [INFO] Task started: HMMsearch
[2023-03-16 08:58:11,685] [INFO] Running command: hmmsearch --tblout OceanDNA-b11573/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd0c9f3b-47e4-42f1-af22-017dad8125f9/dqc_reference/reference_markers.hmm OceanDNA-b11573/protein.faa > /dev/null
[2023-03-16 08:58:11,877] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:58:11,878] [INFO] Found 6/6 markers.
[2023-03-16 08:58:11,890] [INFO] Query marker FASTA was written to OceanDNA-b11573/markers.fasta
[2023-03-16 08:58:11,891] [INFO] Task started: Blastn
[2023-03-16 08:58:11,891] [INFO] Running command: blastn -query OceanDNA-b11573/markers.fasta -db /var/lib/cwl/stgfd0c9f3b-47e4-42f1-af22-017dad8125f9/dqc_reference/reference_markers.fasta -out OceanDNA-b11573/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:58:12,446] [INFO] Task succeeded: Blastn
[2023-03-16 08:58:12,448] [INFO] Selected 23 target genomes.
[2023-03-16 08:58:12,449] [INFO] Target genome list was writen to OceanDNA-b11573/target_genomes.txt
[2023-03-16 08:58:12,461] [INFO] Task started: fastANI
[2023-03-16 08:58:12,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg01e8c5ad-58e6-4ac8-90a9-b1c794407026/OceanDNA-b11573.fa --refList OceanDNA-b11573/target_genomes.txt --output OceanDNA-b11573/fastani_result.tsv --threads 1
[2023-03-16 08:58:23,950] [INFO] Task succeeded: fastANI
[2023-03-16 08:58:23,950] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd0c9f3b-47e4-42f1-af22-017dad8125f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:58:23,950] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd0c9f3b-47e4-42f1-af22-017dad8125f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:58:23,950] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:58:23,950] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:58:23,950] [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
--------------------------------------------------------------------------------
[2023-03-16 08:58:23,951] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11573/tc_result.tsv
[2023-03-16 08:58:23,951] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:58:23,951] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:58:23,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd0c9f3b-47e4-42f1-af22-017dad8125f9/dqc_reference/checkm_data
[2023-03-16 08:58:24,076] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:58:24,079] [INFO] Task started: CheckM
[2023-03-16 08:58:24,079] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11573/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11573/checkm_input OceanDNA-b11573/checkm_result
[2023-03-16 08:58:50,480] [INFO] Task succeeded: CheckM
[2023-03-16 08:58:50,481] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:58:50,483] [INFO] ===== Completeness check finished =====
[2023-03-16 08:58:50,483] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:58:50,483] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11573/markers.fasta)
[2023-03-16 08:58:50,484] [INFO] Task started: Blastn
[2023-03-16 08:58:50,484] [INFO] Running command: blastn -query OceanDNA-b11573/markers.fasta -db /var/lib/cwl/stgfd0c9f3b-47e4-42f1-af22-017dad8125f9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11573/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:58:51,413] [INFO] Task succeeded: Blastn
[2023-03-16 08:58:51,414] [INFO] Selected 13 target genomes.
[2023-03-16 08:58:51,414] [INFO] Target genome list was writen to OceanDNA-b11573/target_genomes_gtdb.txt
[2023-03-16 08:58:51,429] [INFO] Task started: fastANI
[2023-03-16 08:58:51,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg01e8c5ad-58e6-4ac8-90a9-b1c794407026/OceanDNA-b11573.fa --refList OceanDNA-b11573/target_genomes_gtdb.txt --output OceanDNA-b11573/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:58:54,727] [INFO] Task succeeded: fastANI
[2023-03-16 08:58:54,733] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 08:58:54,733] [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_002722215.1	s__SP256 sp002722215	97.2346	397	458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002713285.1	s__SP256 sp002713285	78.9911	267	458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714185.1	s__SP256 sp002714185	77.7887	216	458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707245.1	s__GCA-002707245 sp002707245	77.4402	121	458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-002707245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698365.1	s__GCA-002707245 sp002698365	77.3059	117	458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-002707245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701365.1	s__GCA-002701365 sp002701365	77.2647	165	458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-002701365	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171975.2	s__GCA-2696965 sp002171975	76.9547	130	458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2696965	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718895.1	s__GCA-2718895 sp002718895	76.3749	95	458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2718895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002863085.1	s__GCA-2863085 sp002863085	76.3035	51	458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2863085	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:58:54,733] [INFO] GTDB search result was written to OceanDNA-b11573/result_gtdb.tsv
[2023-03-16 08:58:54,733] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:58:54,734] [INFO] DFAST_QC result json was written to OceanDNA-b11573/dqc_result.json
[2023-03-16 08:58:54,734] [INFO] DFAST_QC completed!
[2023-03-16 08:58:54,734] [INFO] Total running time: 0h0m53s