[2023-03-19 00:15:41,732] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:15:41,732] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:15:41,732] [INFO] DQC Reference Directory: /var/lib/cwl/stg53f91ea8-3a58-4648-b118-d470c216a325/dqc_reference
[2023-03-19 00:15:43,441] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:15:43,441] [INFO] Task started: Prodigal
[2023-03-19 00:15:43,441] [INFO] Running command: cat /var/lib/cwl/stgcd1aa49b-e005-44e1-bbd4-a6a9613365bd/OceanDNA-b45676.fa | prodigal -d OceanDNA-b45676/cds.fna -a OceanDNA-b45676/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:16:04,955] [INFO] Task succeeded: Prodigal
[2023-03-19 00:16:04,955] [INFO] Task started: HMMsearch
[2023-03-19 00:16:04,956] [INFO] Running command: hmmsearch --tblout OceanDNA-b45676/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53f91ea8-3a58-4648-b118-d470c216a325/dqc_reference/reference_markers.hmm OceanDNA-b45676/protein.faa > /dev/null
[2023-03-19 00:16:05,177] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:16:05,177] [INFO] Found 6/6 markers.
[2023-03-19 00:16:05,198] [INFO] Query marker FASTA was written to OceanDNA-b45676/markers.fasta
[2023-03-19 00:16:05,198] [INFO] Task started: Blastn
[2023-03-19 00:16:05,198] [INFO] Running command: blastn -query OceanDNA-b45676/markers.fasta -db /var/lib/cwl/stg53f91ea8-3a58-4648-b118-d470c216a325/dqc_reference/reference_markers.fasta -out OceanDNA-b45676/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:16:05,698] [INFO] Task succeeded: Blastn
[2023-03-19 00:16:05,699] [INFO] Selected 10 target genomes.
[2023-03-19 00:16:05,699] [INFO] Target genome list was writen to OceanDNA-b45676/target_genomes.txt
[2023-03-19 00:16:05,707] [INFO] Task started: fastANI
[2023-03-19 00:16:05,707] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd1aa49b-e005-44e1-bbd4-a6a9613365bd/OceanDNA-b45676.fa --refList OceanDNA-b45676/target_genomes.txt --output OceanDNA-b45676/fastani_result.tsv --threads 1
[2023-03-19 00:16:10,894] [INFO] Task succeeded: fastANI
[2023-03-19 00:16:10,895] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53f91ea8-3a58-4648-b118-d470c216a325/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:16:10,895] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53f91ea8-3a58-4648-b118-d470c216a325/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:16:10,895] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:16:10,895] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:16:10,895] [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
--------------------------------------------------------------------------------
[2023-03-19 00:16:10,895] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45676/tc_result.tsv
[2023-03-19 00:16:10,895] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:16:10,896] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:16:10,896] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53f91ea8-3a58-4648-b118-d470c216a325/dqc_reference/checkm_data
[2023-03-19 00:16:10,899] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:16:10,903] [INFO] Task started: CheckM
[2023-03-19 00:16:10,903] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45676/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45676/checkm_input OceanDNA-b45676/checkm_result
[2023-03-19 00:17:07,885] [INFO] Task succeeded: CheckM
[2023-03-19 00:17:07,886] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 2.29%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 00:17:07,889] [INFO] ===== Completeness check finished =====
[2023-03-19 00:17:07,889] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:17:07,889] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45676/markers.fasta)
[2023-03-19 00:17:07,889] [INFO] Task started: Blastn
[2023-03-19 00:17:07,889] [INFO] Running command: blastn -query OceanDNA-b45676/markers.fasta -db /var/lib/cwl/stg53f91ea8-3a58-4648-b118-d470c216a325/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45676/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:17:08,560] [INFO] Task succeeded: Blastn
[2023-03-19 00:17:08,562] [INFO] Selected 18 target genomes.
[2023-03-19 00:17:08,562] [INFO] Target genome list was writen to OceanDNA-b45676/target_genomes_gtdb.txt
[2023-03-19 00:17:08,579] [INFO] Task started: fastANI
[2023-03-19 00:17:08,579] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd1aa49b-e005-44e1-bbd4-a6a9613365bd/OceanDNA-b45676.fa --refList OceanDNA-b45676/target_genomes_gtdb.txt --output OceanDNA-b45676/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:17:16,484] [INFO] Task succeeded: fastANI
[2023-03-19 00:17:16,488] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:17:16,488] [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_002167605.1	s__MB11C04 sp002167605	98.9112	577	748	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	99.01	99.01	0.79	0.79	2	conclusive
GCA_002692605.1	s__MB11C04 sp002692605	80.5632	407	748	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	98.46	98.03	0.81	0.78	7	-
GCA_902618175.1	s__MB11C04 sp902618175	80.0926	50	748	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902612125.1	s__MB11C04 sp902612125	78.3272	57	748	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:17:16,488] [INFO] GTDB search result was written to OceanDNA-b45676/result_gtdb.tsv
[2023-03-19 00:17:16,488] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:17:16,489] [INFO] DFAST_QC result json was written to OceanDNA-b45676/dqc_result.json
[2023-03-19 00:17:16,489] [INFO] DFAST_QC completed!
[2023-03-19 00:17:16,489] [INFO] Total running time: 0h1m35s