[2023-03-19 01:13:44,324] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:13:44,325] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:13:44,325] [INFO] DQC Reference Directory: /var/lib/cwl/stge03f1652-8164-4415-8143-b9abe1bd0b26/dqc_reference
[2023-03-19 01:13:45,532] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:13:45,532] [INFO] Task started: Prodigal
[2023-03-19 01:13:45,532] [INFO] Running command: cat /var/lib/cwl/stgcbde8db9-b606-40a7-bd27-dad846800ddc/OceanDNA-b46918.fa | prodigal -d OceanDNA-b46918/cds.fna -a OceanDNA-b46918/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:14:06,552] [INFO] Task succeeded: Prodigal
[2023-03-19 01:14:06,552] [INFO] Task started: HMMsearch
[2023-03-19 01:14:06,552] [INFO] Running command: hmmsearch --tblout OceanDNA-b46918/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge03f1652-8164-4415-8143-b9abe1bd0b26/dqc_reference/reference_markers.hmm OceanDNA-b46918/protein.faa > /dev/null
[2023-03-19 01:14:06,713] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:14:06,714] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgcbde8db9-b606-40a7-bd27-dad846800ddc/OceanDNA-b46918.fa]
[2023-03-19 01:14:06,738] [INFO] Query marker FASTA was written to OceanDNA-b46918/markers.fasta
[2023-03-19 01:14:06,739] [INFO] Task started: Blastn
[2023-03-19 01:14:06,739] [INFO] Running command: blastn -query OceanDNA-b46918/markers.fasta -db /var/lib/cwl/stge03f1652-8164-4415-8143-b9abe1bd0b26/dqc_reference/reference_markers.fasta -out OceanDNA-b46918/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:14:07,158] [INFO] Task succeeded: Blastn
[2023-03-19 01:14:07,159] [INFO] Selected 3 target genomes.
[2023-03-19 01:14:07,159] [INFO] Target genome list was writen to OceanDNA-b46918/target_genomes.txt
[2023-03-19 01:14:07,161] [INFO] Task started: fastANI
[2023-03-19 01:14:07,161] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbde8db9-b606-40a7-bd27-dad846800ddc/OceanDNA-b46918.fa --refList OceanDNA-b46918/target_genomes.txt --output OceanDNA-b46918/fastani_result.tsv --threads 1
[2023-03-19 01:14:09,978] [INFO] Task succeeded: fastANI
[2023-03-19 01:14:09,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge03f1652-8164-4415-8143-b9abe1bd0b26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:14:09,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge03f1652-8164-4415-8143-b9abe1bd0b26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:14:09,979] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:14:09,979] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:14:09,979] [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 01:14:10,077] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46918/tc_result.tsv
[2023-03-19 01:14:10,077] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:14:10,078] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:14:10,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge03f1652-8164-4415-8143-b9abe1bd0b26/dqc_reference/checkm_data
[2023-03-19 01:14:10,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:14:10,114] [INFO] Task started: CheckM
[2023-03-19 01:14:10,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46918/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46918/checkm_input OceanDNA-b46918/checkm_result
[2023-03-19 01:15:06,935] [INFO] Task succeeded: CheckM
[2023-03-19 01:15:06,935] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:15:06,938] [INFO] ===== Completeness check finished =====
[2023-03-19 01:15:06,938] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:15:06,938] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46918/markers.fasta)
[2023-03-19 01:15:06,939] [INFO] Task started: Blastn
[2023-03-19 01:15:06,939] [INFO] Running command: blastn -query OceanDNA-b46918/markers.fasta -db /var/lib/cwl/stge03f1652-8164-4415-8143-b9abe1bd0b26/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46918/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:15:07,301] [INFO] Task succeeded: Blastn
[2023-03-19 01:15:07,302] [INFO] Selected 5 target genomes.
[2023-03-19 01:15:07,302] [INFO] Target genome list was writen to OceanDNA-b46918/target_genomes_gtdb.txt
[2023-03-19 01:15:07,305] [INFO] Task started: fastANI
[2023-03-19 01:15:07,305] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbde8db9-b606-40a7-bd27-dad846800ddc/OceanDNA-b46918.fa --refList OceanDNA-b46918/target_genomes_gtdb.txt --output OceanDNA-b46918/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:15:12,537] [INFO] Task succeeded: fastANI
[2023-03-19 01:15:12,538] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:15:12,539] [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_009936795.1	s__JAACDM01 sp009936795	80.8509	338	545	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__JAACDM01	95.0	98.82	98.23	0.81	0.77	3	-
--------------------------------------------------------------------------------
[2023-03-19 01:15:12,539] [INFO] GTDB search result was written to OceanDNA-b46918/result_gtdb.tsv
[2023-03-19 01:15:12,539] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:15:12,539] [INFO] DFAST_QC result json was written to OceanDNA-b46918/dqc_result.json
[2023-03-19 01:15:12,539] [INFO] DFAST_QC completed!
[2023-03-19 01:15:12,539] [INFO] Total running time: 0h1m28s