[2023-03-15 07:03:38,808] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:03:38,808] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:03:38,808] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7c98135-3e91-4a09-bdc7-03a8091f8253/dqc_reference
[2023-03-15 07:03:39,908] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:03:39,908] [INFO] Task started: Prodigal
[2023-03-15 07:03:39,908] [INFO] Running command: cat /var/lib/cwl/stgb664d43e-e71e-46b8-b977-58599678380b/OceanDNA-a3202.fa | prodigal -d OceanDNA-a3202/cds.fna -a OceanDNA-a3202/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:03:49,095] [INFO] Task succeeded: Prodigal
[2023-03-15 07:03:49,095] [INFO] Task started: HMMsearch
[2023-03-15 07:03:49,095] [INFO] Running command: hmmsearch --tblout OceanDNA-a3202/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7c98135-3e91-4a09-bdc7-03a8091f8253/dqc_reference/reference_markers.hmm OceanDNA-a3202/protein.faa > /dev/null
[2023-03-15 07:03:49,283] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:03:49,283] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb664d43e-e71e-46b8-b977-58599678380b/OceanDNA-a3202.fa]
[2023-03-15 07:03:49,308] [INFO] Query marker FASTA was written to OceanDNA-a3202/markers.fasta
[2023-03-15 07:03:49,308] [INFO] Task started: Blastn
[2023-03-15 07:03:49,308] [INFO] Running command: blastn -query OceanDNA-a3202/markers.fasta -db /var/lib/cwl/stgd7c98135-3e91-4a09-bdc7-03a8091f8253/dqc_reference/reference_markers.fasta -out OceanDNA-a3202/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:03:49,737] [INFO] Task succeeded: Blastn
[2023-03-15 07:03:49,745] [INFO] Selected 7 target genomes.
[2023-03-15 07:03:49,746] [INFO] Target genome list was writen to OceanDNA-a3202/target_genomes.txt
[2023-03-15 07:03:49,749] [INFO] Task started: fastANI
[2023-03-15 07:03:49,750] [INFO] Running command: fastANI --query /var/lib/cwl/stgb664d43e-e71e-46b8-b977-58599678380b/OceanDNA-a3202.fa --refList OceanDNA-a3202/target_genomes.txt --output OceanDNA-a3202/fastani_result.tsv --threads 1
[2023-03-15 07:03:53,253] [INFO] Task succeeded: fastANI
[2023-03-15 07:03:53,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7c98135-3e91-4a09-bdc7-03a8091f8253/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:03:53,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7c98135-3e91-4a09-bdc7-03a8091f8253/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:03:53,254] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:03:53,254] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:03:53,254] [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 07:03:53,257] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3202/tc_result.tsv
[2023-03-15 07:03:53,260] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:03:53,260] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:03:53,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7c98135-3e91-4a09-bdc7-03a8091f8253/dqc_reference/checkm_data
[2023-03-15 07:03:53,264] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:03:53,274] [INFO] Task started: CheckM
[2023-03-15 07:03:53,274] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3202/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3202/checkm_input OceanDNA-a3202/checkm_result
[2023-03-15 07:04:21,746] [INFO] Task succeeded: CheckM
[2023-03-15 07:04:21,747] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.90%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 07:04:21,750] [INFO] ===== Completeness check finished =====
[2023-03-15 07:04:21,750] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:04:21,750] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3202/markers.fasta)
[2023-03-15 07:04:21,751] [INFO] Task started: Blastn
[2023-03-15 07:04:21,751] [INFO] Running command: blastn -query OceanDNA-a3202/markers.fasta -db /var/lib/cwl/stgd7c98135-3e91-4a09-bdc7-03a8091f8253/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3202/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:04:22,203] [INFO] Task succeeded: Blastn
[2023-03-15 07:04:22,209] [INFO] Selected 7 target genomes.
[2023-03-15 07:04:22,209] [INFO] Target genome list was writen to OceanDNA-a3202/target_genomes_gtdb.txt
[2023-03-15 07:04:22,245] [INFO] Task started: fastANI
[2023-03-15 07:04:22,245] [INFO] Running command: fastANI --query /var/lib/cwl/stgb664d43e-e71e-46b8-b977-58599678380b/OceanDNA-a3202.fa --refList OceanDNA-a3202/target_genomes_gtdb.txt --output OceanDNA-a3202/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:04:24,797] [INFO] Task succeeded: fastANI
[2023-03-15 07:04:24,800] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:04:24,801] [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_014384685.1	s__MGIIb-Q1 sp014384685	93.6411	272	521	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845345.1	s__MGIIb-Q1 sp016845345	89.399	451	521	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959435.1	s__MGIIb-Q1 sp012959435	86.7781	440	521	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012964335.1	s__MGIIb-Q1 sp012964335	85.3987	449	521	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	99.77	99.71	0.95	0.94	8	-
GCA_018650285.1	s__MGIIb-Q1 sp018650285	79.1511	234	521	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:04:24,801] [INFO] GTDB search result was written to OceanDNA-a3202/result_gtdb.tsv
[2023-03-15 07:04:24,801] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:04:24,802] [INFO] DFAST_QC result json was written to OceanDNA-a3202/dqc_result.json
[2023-03-15 07:04:24,802] [INFO] DFAST_QC completed!
[2023-03-15 07:04:24,802] [INFO] Total running time: 0h0m46s