[2023-03-15 14:21:30,623] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:21:30,631] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:21:30,631] [INFO] DQC Reference Directory: /var/lib/cwl/stgea82c249-aed8-4e7f-b9e8-180726e4536f/dqc_reference
[2023-03-15 14:21:31,736] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:21:31,736] [INFO] Task started: Prodigal
[2023-03-15 14:21:31,736] [INFO] Running command: cat /var/lib/cwl/stg1e079260-d1db-480f-a1ff-5e0a8b639ea3/OceanDNA-b2959.fa | prodigal -d OceanDNA-b2959/cds.fna -a OceanDNA-b2959/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:21:35,613] [INFO] Task succeeded: Prodigal
[2023-03-15 14:21:35,614] [INFO] Task started: HMMsearch
[2023-03-15 14:21:35,614] [INFO] Running command: hmmsearch --tblout OceanDNA-b2959/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea82c249-aed8-4e7f-b9e8-180726e4536f/dqc_reference/reference_markers.hmm OceanDNA-b2959/protein.faa > /dev/null
[2023-03-15 14:21:35,788] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:21:35,789] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1e079260-d1db-480f-a1ff-5e0a8b639ea3/OceanDNA-b2959.fa]
[2023-03-15 14:21:35,887] [INFO] Query marker FASTA was written to OceanDNA-b2959/markers.fasta
[2023-03-15 14:21:35,889] [INFO] Task started: Blastn
[2023-03-15 14:21:35,889] [INFO] Running command: blastn -query OceanDNA-b2959/markers.fasta -db /var/lib/cwl/stgea82c249-aed8-4e7f-b9e8-180726e4536f/dqc_reference/reference_markers.fasta -out OceanDNA-b2959/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:21:36,603] [INFO] Task succeeded: Blastn
[2023-03-15 14:21:36,638] [INFO] Selected 26 target genomes.
[2023-03-15 14:21:36,638] [INFO] Target genome list was writen to OceanDNA-b2959/target_genomes.txt
[2023-03-15 14:21:36,652] [INFO] Task started: fastANI
[2023-03-15 14:21:36,652] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e079260-d1db-480f-a1ff-5e0a8b639ea3/OceanDNA-b2959.fa --refList OceanDNA-b2959/target_genomes.txt --output OceanDNA-b2959/fastani_result.tsv --threads 1
[2023-03-15 14:21:49,180] [INFO] Task succeeded: fastANI
[2023-03-15 14:21:49,181] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea82c249-aed8-4e7f-b9e8-180726e4536f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:21:49,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea82c249-aed8-4e7f-b9e8-180726e4536f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:21:49,181] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:21:49,181] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 14:21:49,181] [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 14:21:49,194] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2959/tc_result.tsv
[2023-03-15 14:21:49,215] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:21:49,215] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:21:49,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea82c249-aed8-4e7f-b9e8-180726e4536f/dqc_reference/checkm_data
[2023-03-15 14:21:49,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:21:49,265] [INFO] Task started: CheckM
[2023-03-15 14:21:49,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2959/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2959/checkm_input OceanDNA-b2959/checkm_result
[2023-03-15 14:22:09,565] [INFO] Task succeeded: CheckM
[2023-03-15 14:22:09,565] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:22:09,652] [INFO] ===== Completeness check finished =====
[2023-03-15 14:22:09,652] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:22:09,652] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2959/markers.fasta)
[2023-03-15 14:22:09,653] [INFO] Task started: Blastn
[2023-03-15 14:22:09,653] [INFO] Running command: blastn -query OceanDNA-b2959/markers.fasta -db /var/lib/cwl/stgea82c249-aed8-4e7f-b9e8-180726e4536f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2959/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:22:10,711] [INFO] Task succeeded: Blastn
[2023-03-15 14:22:10,744] [INFO] Selected 22 target genomes.
[2023-03-15 14:22:10,745] [INFO] Target genome list was writen to OceanDNA-b2959/target_genomes_gtdb.txt
[2023-03-15 14:22:10,758] [INFO] Task started: fastANI
[2023-03-15 14:22:10,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e079260-d1db-480f-a1ff-5e0a8b639ea3/OceanDNA-b2959.fa --refList OceanDNA-b2959/target_genomes_gtdb.txt --output OceanDNA-b2959/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:22:15,142] [INFO] Task succeeded: fastANI
[2023-03-15 14:22:15,148] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:22:15,148] [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_903939005.1	s__Planktophila sp903939005	90.9088	125	204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903922325.1	s__Planktophila sp903922325	86.7355	148	204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009924725.1	s__Planktophila sp009924725	85.7261	130	204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002287925.1	s__Planktophila lacus	78.4691	59	204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	95.55	95.24	0.96	0.95	3	-
GCA_000378885.1	s__Planktophila sp000378885	77.9146	57	204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	96.66	96.52	0.78	0.69	3	-
GCF_002288365.1	s__Planktophila limnetica	77.8105	50	204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	97.17	97.12	0.96	0.96	5	-
GCA_002284875.1	s__Planktophila sp002284875	77.714	51	204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	100.00	100.00	1.00	1.00	2	-
GCA_009698815.1	s__Planktophila sp009698815	76.8751	62	204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.97	99.90	0.95	0.89	10	-
--------------------------------------------------------------------------------
[2023-03-15 14:22:15,162] [INFO] GTDB search result was written to OceanDNA-b2959/result_gtdb.tsv
[2023-03-15 14:22:15,181] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:22:15,193] [INFO] DFAST_QC result json was written to OceanDNA-b2959/dqc_result.json
[2023-03-15 14:22:15,193] [INFO] DFAST_QC completed!
[2023-03-15 14:22:15,193] [INFO] Total running time: 0h0m45s