[2023-03-15 12:33:51,640] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:33:51,640] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:33:51,641] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e909c24-282b-406d-903f-7ff729db2ec3/dqc_reference
[2023-03-15 12:33:52,804] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:33:52,804] [INFO] Task started: Prodigal
[2023-03-15 12:33:52,805] [INFO] Running command: cat /var/lib/cwl/stgaace02cb-9d0a-4db9-8438-aeab96506cab/OceanDNA-b26781.fa | prodigal -d OceanDNA-b26781/cds.fna -a OceanDNA-b26781/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:33:59,518] [INFO] Task succeeded: Prodigal
[2023-03-15 12:33:59,518] [INFO] Task started: HMMsearch
[2023-03-15 12:33:59,518] [INFO] Running command: hmmsearch --tblout OceanDNA-b26781/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e909c24-282b-406d-903f-7ff729db2ec3/dqc_reference/reference_markers.hmm OceanDNA-b26781/protein.faa > /dev/null
[2023-03-15 12:33:59,651] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:33:59,651] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgaace02cb-9d0a-4db9-8438-aeab96506cab/OceanDNA-b26781.fa]
[2023-03-15 12:33:59,667] [INFO] Query marker FASTA was written to OceanDNA-b26781/markers.fasta
[2023-03-15 12:33:59,667] [INFO] Task started: Blastn
[2023-03-15 12:33:59,667] [INFO] Running command: blastn -query OceanDNA-b26781/markers.fasta -db /var/lib/cwl/stg7e909c24-282b-406d-903f-7ff729db2ec3/dqc_reference/reference_markers.fasta -out OceanDNA-b26781/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:34:00,144] [INFO] Task succeeded: Blastn
[2023-03-15 12:34:00,145] [INFO] Selected 10 target genomes.
[2023-03-15 12:34:00,146] [INFO] Target genome list was writen to OceanDNA-b26781/target_genomes.txt
[2023-03-15 12:34:00,153] [INFO] Task started: fastANI
[2023-03-15 12:34:00,153] [INFO] Running command: fastANI --query /var/lib/cwl/stgaace02cb-9d0a-4db9-8438-aeab96506cab/OceanDNA-b26781.fa --refList OceanDNA-b26781/target_genomes.txt --output OceanDNA-b26781/fastani_result.tsv --threads 1
[2023-03-15 12:34:08,022] [INFO] Task succeeded: fastANI
[2023-03-15 12:34:08,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e909c24-282b-406d-903f-7ff729db2ec3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:34:08,023] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e909c24-282b-406d-903f-7ff729db2ec3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:34:08,027] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:34:08,027] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 12:34:08,027] [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
Methylobacterium currus	strain=PR1016A	GCA_003058325.1	2051553	2051553	type	True	75.8872	52	249	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	75.8092	50	249	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	75.6821	52	249	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:34:08,028] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26781/tc_result.tsv
[2023-03-15 12:34:08,028] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:34:08,028] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:34:08,028] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e909c24-282b-406d-903f-7ff729db2ec3/dqc_reference/checkm_data
[2023-03-15 12:34:08,029] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:34:08,033] [INFO] Task started: CheckM
[2023-03-15 12:34:08,033] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26781/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26781/checkm_input OceanDNA-b26781/checkm_result
[2023-03-15 12:34:29,540] [INFO] Task succeeded: CheckM
[2023-03-15 12:34:29,540] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:34:29,543] [INFO] ===== Completeness check finished =====
[2023-03-15 12:34:29,543] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:34:29,543] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26781/markers.fasta)
[2023-03-15 12:34:29,544] [INFO] Task started: Blastn
[2023-03-15 12:34:29,544] [INFO] Running command: blastn -query OceanDNA-b26781/markers.fasta -db /var/lib/cwl/stg7e909c24-282b-406d-903f-7ff729db2ec3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26781/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:34:30,168] [INFO] Task succeeded: Blastn
[2023-03-15 12:34:30,169] [INFO] Selected 10 target genomes.
[2023-03-15 12:34:30,169] [INFO] Target genome list was writen to OceanDNA-b26781/target_genomes_gtdb.txt
[2023-03-15 12:34:30,222] [INFO] Task started: fastANI
[2023-03-15 12:34:30,222] [INFO] Running command: fastANI --query /var/lib/cwl/stgaace02cb-9d0a-4db9-8438-aeab96506cab/OceanDNA-b26781.fa --refList OceanDNA-b26781/target_genomes_gtdb.txt --output OceanDNA-b26781/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:34:37,592] [INFO] Task succeeded: fastANI
[2023-03-15 12:34:37,595] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:34:37,595] [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
GCF_003058325.1	s__Methylobacterium currus	75.9151	51	249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:34:37,597] [INFO] GTDB search result was written to OceanDNA-b26781/result_gtdb.tsv
[2023-03-15 12:34:37,603] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:34:37,607] [INFO] DFAST_QC result json was written to OceanDNA-b26781/dqc_result.json
[2023-03-15 12:34:37,607] [INFO] DFAST_QC completed!
[2023-03-15 12:34:37,607] [INFO] Total running time: 0h0m46s