[2023-03-17 03:03:53,464] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:03:53,464] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:03:53,464] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4656145-1093-4df2-af93-f84d33936008/dqc_reference
[2023-03-17 03:03:54,598] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:03:54,598] [INFO] Task started: Prodigal
[2023-03-17 03:03:54,598] [INFO] Running command: cat /var/lib/cwl/stg0555a888-06cd-46a7-937f-b27c33d1f625/OceanDNA-b45792.fa | prodigal -d OceanDNA-b45792/cds.fna -a OceanDNA-b45792/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:04:22,967] [INFO] Task succeeded: Prodigal
[2023-03-17 03:04:22,967] [INFO] Task started: HMMsearch
[2023-03-17 03:04:22,967] [INFO] Running command: hmmsearch --tblout OceanDNA-b45792/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4656145-1093-4df2-af93-f84d33936008/dqc_reference/reference_markers.hmm OceanDNA-b45792/protein.faa > /dev/null
[2023-03-17 03:04:23,177] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:04:23,178] [INFO] Found 6/6 markers.
[2023-03-17 03:04:23,201] [INFO] Query marker FASTA was written to OceanDNA-b45792/markers.fasta
[2023-03-17 03:04:23,202] [INFO] Task started: Blastn
[2023-03-17 03:04:23,202] [INFO] Running command: blastn -query OceanDNA-b45792/markers.fasta -db /var/lib/cwl/stgf4656145-1093-4df2-af93-f84d33936008/dqc_reference/reference_markers.fasta -out OceanDNA-b45792/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:04:23,769] [INFO] Task succeeded: Blastn
[2023-03-17 03:04:23,770] [INFO] Selected 16 target genomes.
[2023-03-17 03:04:23,770] [INFO] Target genome list was writen to OceanDNA-b45792/target_genomes.txt
[2023-03-17 03:04:23,808] [INFO] Task started: fastANI
[2023-03-17 03:04:23,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg0555a888-06cd-46a7-937f-b27c33d1f625/OceanDNA-b45792.fa --refList OceanDNA-b45792/target_genomes.txt --output OceanDNA-b45792/fastani_result.tsv --threads 1
[2023-03-17 03:04:34,820] [INFO] Task succeeded: fastANI
[2023-03-17 03:04:34,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4656145-1093-4df2-af93-f84d33936008/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:04:34,820] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4656145-1093-4df2-af93-f84d33936008/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:04:34,821] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:04:34,821] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 03:04:34,821] [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
--------------------------------------------------------------------------------
[2023-03-17 03:04:34,821] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45792/tc_result.tsv
[2023-03-17 03:04:34,821] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:04:34,821] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:04:34,821] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4656145-1093-4df2-af93-f84d33936008/dqc_reference/checkm_data
[2023-03-17 03:04:34,824] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:04:34,828] [INFO] Task started: CheckM
[2023-03-17 03:04:34,828] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45792/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45792/checkm_input OceanDNA-b45792/checkm_result
[2023-03-17 03:05:47,689] [INFO] Task succeeded: CheckM
[2023-03-17 03:05:47,689] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 03:05:47,692] [INFO] ===== Completeness check finished =====
[2023-03-17 03:05:47,692] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:05:47,692] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45792/markers.fasta)
[2023-03-17 03:05:47,693] [INFO] Task started: Blastn
[2023-03-17 03:05:47,693] [INFO] Running command: blastn -query OceanDNA-b45792/markers.fasta -db /var/lib/cwl/stgf4656145-1093-4df2-af93-f84d33936008/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45792/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:05:49,017] [INFO] Task succeeded: Blastn
[2023-03-17 03:05:49,018] [INFO] Selected 21 target genomes.
[2023-03-17 03:05:49,018] [INFO] Target genome list was writen to OceanDNA-b45792/target_genomes_gtdb.txt
[2023-03-17 03:05:49,116] [INFO] Task started: fastANI
[2023-03-17 03:05:49,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg0555a888-06cd-46a7-937f-b27c33d1f625/OceanDNA-b45792.fa --refList OceanDNA-b45792/target_genomes_gtdb.txt --output OceanDNA-b45792/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:05:59,349] [INFO] Task succeeded: fastANI
[2023-03-17 03:05:59,353] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 03:05:59,353] [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_002722545.1	s__MB11C04 sp002722545	99.6946	641	1026	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018645725.1	s__MB11C04 sp018645725	82.1215	661	1026	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002500665.1	s__MB11C04 sp002500665	78.371	239	1026	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	98.37	95.55	0.93	0.84	7	-
GCA_002167605.1	s__MB11C04 sp002167605	76.6346	51	1026	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	99.01	99.01	0.79	0.79	2	-
GCA_002692605.1	s__MB11C04 sp002692605	76.5355	63	1026	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	98.46	98.03	0.81	0.78	7	-
--------------------------------------------------------------------------------
[2023-03-17 03:05:59,353] [INFO] GTDB search result was written to OceanDNA-b45792/result_gtdb.tsv
[2023-03-17 03:05:59,354] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:05:59,354] [INFO] DFAST_QC result json was written to OceanDNA-b45792/dqc_result.json
[2023-03-17 03:05:59,355] [INFO] DFAST_QC completed!
[2023-03-17 03:05:59,355] [INFO] Total running time: 0h2m6s