[2023-03-18 05:05:06,152] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:05:06,152] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:05:06,152] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2e7809e-89d8-40ab-859a-4ef88935298f/dqc_reference
[2023-03-18 05:05:07,312] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:05:07,312] [INFO] Task started: Prodigal
[2023-03-18 05:05:07,312] [INFO] Running command: cat /var/lib/cwl/stg6f6ab2f1-9c67-4d9d-804a-318234d48148/OceanDNA-b14029.fa | prodigal -d OceanDNA-b14029/cds.fna -a OceanDNA-b14029/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:05:12,929] [INFO] Task succeeded: Prodigal
[2023-03-18 05:05:12,930] [INFO] Task started: HMMsearch
[2023-03-18 05:05:12,930] [INFO] Running command: hmmsearch --tblout OceanDNA-b14029/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2e7809e-89d8-40ab-859a-4ef88935298f/dqc_reference/reference_markers.hmm OceanDNA-b14029/protein.faa > /dev/null
[2023-03-18 05:05:13,089] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:05:13,089] [INFO] Found 6/6 markers.
[2023-03-18 05:05:13,099] [INFO] Query marker FASTA was written to OceanDNA-b14029/markers.fasta
[2023-03-18 05:05:13,099] [INFO] Task started: Blastn
[2023-03-18 05:05:13,099] [INFO] Running command: blastn -query OceanDNA-b14029/markers.fasta -db /var/lib/cwl/stgb2e7809e-89d8-40ab-859a-4ef88935298f/dqc_reference/reference_markers.fasta -out OceanDNA-b14029/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:05:13,608] [INFO] Task succeeded: Blastn
[2023-03-18 05:05:13,608] [INFO] Selected 8 target genomes.
[2023-03-18 05:05:13,609] [INFO] Target genome list was writen to OceanDNA-b14029/target_genomes.txt
[2023-03-18 05:05:13,613] [INFO] Task started: fastANI
[2023-03-18 05:05:13,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f6ab2f1-9c67-4d9d-804a-318234d48148/OceanDNA-b14029.fa --refList OceanDNA-b14029/target_genomes.txt --output OceanDNA-b14029/fastani_result.tsv --threads 1
[2023-03-18 05:05:16,530] [INFO] Task succeeded: fastANI
[2023-03-18 05:05:16,531] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2e7809e-89d8-40ab-859a-4ef88935298f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:05:16,531] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2e7809e-89d8-40ab-859a-4ef88935298f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:05:16,531] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:05:16,531] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 05:05:16,531] [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
--------------------------------------------------------------------------------
[2023-03-18 05:05:16,532] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14029/tc_result.tsv
[2023-03-18 05:05:16,532] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:05:16,532] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:05:16,532] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2e7809e-89d8-40ab-859a-4ef88935298f/dqc_reference/checkm_data
[2023-03-18 05:05:16,535] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:05:16,601] [INFO] Task started: CheckM
[2023-03-18 05:05:16,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14029/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14029/checkm_input OceanDNA-b14029/checkm_result
[2023-03-18 05:05:36,812] [INFO] Task succeeded: CheckM
[2023-03-18 05:05:36,812] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 05:05:36,879] [INFO] ===== Completeness check finished =====
[2023-03-18 05:05:36,879] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:05:36,879] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14029/markers.fasta)
[2023-03-18 05:05:36,879] [INFO] Task started: Blastn
[2023-03-18 05:05:36,879] [INFO] Running command: blastn -query OceanDNA-b14029/markers.fasta -db /var/lib/cwl/stgb2e7809e-89d8-40ab-859a-4ef88935298f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14029/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:05:37,573] [INFO] Task succeeded: Blastn
[2023-03-18 05:05:37,574] [INFO] Selected 16 target genomes.
[2023-03-18 05:05:37,574] [INFO] Target genome list was writen to OceanDNA-b14029/target_genomes_gtdb.txt
[2023-03-18 05:05:37,775] [INFO] Task started: fastANI
[2023-03-18 05:05:37,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f6ab2f1-9c67-4d9d-804a-318234d48148/OceanDNA-b14029.fa --refList OceanDNA-b14029/target_genomes_gtdb.txt --output OceanDNA-b14029/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:05:42,689] [INFO] Task succeeded: fastANI
[2023-03-18 05:05:42,692] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 05:05:42,692] [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_003213095.1	s__AG-426-M11 sp003213095	96.354	285	362	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__AG-426-M11	95.0	97.10	96.18	0.80	0.72	9	conclusive
--------------------------------------------------------------------------------
[2023-03-18 05:05:42,694] [INFO] GTDB search result was written to OceanDNA-b14029/result_gtdb.tsv
[2023-03-18 05:05:42,696] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:05:42,697] [INFO] DFAST_QC result json was written to OceanDNA-b14029/dqc_result.json
[2023-03-18 05:05:42,698] [INFO] DFAST_QC completed!
[2023-03-18 05:05:42,698] [INFO] Total running time: 0h0m37s