[2023-03-15 13:20:51,623] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:20:51,623] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:20:51,624] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbafa341-5fe9-4176-997d-a312ca7524cd/dqc_reference
[2023-03-15 13:20:52,709] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:20:52,709] [INFO] Task started: Prodigal
[2023-03-15 13:20:52,710] [INFO] Running command: cat /var/lib/cwl/stgd499f007-92e3-4da6-aa4e-25f835c0ffde/OceanDNA-a3396.fa | prodigal -d OceanDNA-a3396/cds.fna -a OceanDNA-a3396/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:21:00,909] [INFO] Task succeeded: Prodigal
[2023-03-15 13:21:00,909] [INFO] Task started: HMMsearch
[2023-03-15 13:21:00,909] [INFO] Running command: hmmsearch --tblout OceanDNA-a3396/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbafa341-5fe9-4176-997d-a312ca7524cd/dqc_reference/reference_markers.hmm OceanDNA-a3396/protein.faa > /dev/null
[2023-03-15 13:21:01,186] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:21:01,187] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd499f007-92e3-4da6-aa4e-25f835c0ffde/OceanDNA-a3396.fa]
[2023-03-15 13:21:01,203] [INFO] Query marker FASTA was written to OceanDNA-a3396/markers.fasta
[2023-03-15 13:21:01,211] [INFO] Task started: Blastn
[2023-03-15 13:21:01,211] [INFO] Running command: blastn -query OceanDNA-a3396/markers.fasta -db /var/lib/cwl/stgdbafa341-5fe9-4176-997d-a312ca7524cd/dqc_reference/reference_markers.fasta -out OceanDNA-a3396/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:01,695] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:01,696] [INFO] Selected 1 target genomes.
[2023-03-15 13:21:01,696] [INFO] Target genome list was writen to OceanDNA-a3396/target_genomes.txt
[2023-03-15 13:21:01,697] [INFO] Task started: fastANI
[2023-03-15 13:21:01,697] [INFO] Running command: fastANI --query /var/lib/cwl/stgd499f007-92e3-4da6-aa4e-25f835c0ffde/OceanDNA-a3396.fa --refList OceanDNA-a3396/target_genomes.txt --output OceanDNA-a3396/fastani_result.tsv --threads 1
[2023-03-15 13:21:02,167] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:02,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbafa341-5fe9-4176-997d-a312ca7524cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:21:02,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbafa341-5fe9-4176-997d-a312ca7524cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:21:02,168] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:21:02,168] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:21:02,168] [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
--------------------------------------------------------------------------------
[2023-03-15 13:21:02,169] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3396/tc_result.tsv
[2023-03-15 13:21:02,169] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:21:02,169] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:21:02,169] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbafa341-5fe9-4176-997d-a312ca7524cd/dqc_reference/checkm_data
[2023-03-15 13:21:02,229] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:21:02,233] [INFO] Task started: CheckM
[2023-03-15 13:21:02,233] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3396/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3396/checkm_input OceanDNA-a3396/checkm_result
[2023-03-15 13:21:28,766] [INFO] Task succeeded: CheckM
[2023-03-15 13:21:28,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:21:28,771] [INFO] ===== Completeness check finished =====
[2023-03-15 13:21:28,771] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:21:28,772] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3396/markers.fasta)
[2023-03-15 13:21:28,773] [INFO] Task started: Blastn
[2023-03-15 13:21:28,774] [INFO] Running command: blastn -query OceanDNA-a3396/markers.fasta -db /var/lib/cwl/stgdbafa341-5fe9-4176-997d-a312ca7524cd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3396/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:29,294] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:29,296] [INFO] Selected 8 target genomes.
[2023-03-15 13:21:29,296] [INFO] Target genome list was writen to OceanDNA-a3396/target_genomes_gtdb.txt
[2023-03-15 13:21:29,316] [INFO] Task started: fastANI
[2023-03-15 13:21:29,316] [INFO] Running command: fastANI --query /var/lib/cwl/stgd499f007-92e3-4da6-aa4e-25f835c0ffde/OceanDNA-a3396.fa --refList OceanDNA-a3396/target_genomes_gtdb.txt --output OceanDNA-a3396/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:21:31,932] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:31,940] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:21:31,941] [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_002708015.1	s__MGIIb-N2 sp002708015	98.6825	398	475	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002502625.1	s__MGIIb-N2 sp002502625	90.6766	419	475	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	99.71	99.70	0.87	0.83	3	-
GCA_002702985.1	s__MGIIb-N2 sp002702985	90.5494	351	475	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002697105.1	s__MGIIb-N2 sp002697105	88.8165	331	475	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	96.01	96.01	0.68	0.68	2	-
GCA_002503665.1	s__MGIIb-N2 sp002503665	78.6816	133	475	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:21:31,942] [INFO] GTDB search result was written to OceanDNA-a3396/result_gtdb.tsv
[2023-03-15 13:21:31,942] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:21:31,945] [INFO] DFAST_QC result json was written to OceanDNA-a3396/dqc_result.json
[2023-03-15 13:21:31,945] [INFO] DFAST_QC completed!
[2023-03-15 13:21:31,945] [INFO] Total running time: 0h0m40s