[2023-03-15 16:25:57,001] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:25:57,006] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:25:57,006] [INFO] DQC Reference Directory: /var/lib/cwl/stgf883d316-f76d-41e5-bec8-0cc146fbee0f/dqc_reference
[2023-03-15 16:25:58,601] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:25:58,601] [INFO] Task started: Prodigal
[2023-03-15 16:25:58,602] [INFO] Running command: cat /var/lib/cwl/stg7518ea0d-5d5c-4540-b9f8-c4717849211b/OceanDNA-b33598.fa | prodigal -d OceanDNA-b33598/cds.fna -a OceanDNA-b33598/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:26:03,549] [INFO] Task succeeded: Prodigal
[2023-03-15 16:26:03,549] [INFO] Task started: HMMsearch
[2023-03-15 16:26:03,549] [INFO] Running command: hmmsearch --tblout OceanDNA-b33598/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf883d316-f76d-41e5-bec8-0cc146fbee0f/dqc_reference/reference_markers.hmm OceanDNA-b33598/protein.faa > /dev/null
[2023-03-15 16:26:03,720] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:26:03,720] [INFO] Found 6/6 markers.
[2023-03-15 16:26:03,790] [INFO] Query marker FASTA was written to OceanDNA-b33598/markers.fasta
[2023-03-15 16:26:03,790] [INFO] Task started: Blastn
[2023-03-15 16:26:03,790] [INFO] Running command: blastn -query OceanDNA-b33598/markers.fasta -db /var/lib/cwl/stgf883d316-f76d-41e5-bec8-0cc146fbee0f/dqc_reference/reference_markers.fasta -out OceanDNA-b33598/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:26:05,763] [INFO] Task succeeded: Blastn
[2023-03-15 16:26:05,779] [INFO] Selected 16 target genomes.
[2023-03-15 16:26:05,779] [INFO] Target genome list was writen to OceanDNA-b33598/target_genomes.txt
[2023-03-15 16:26:05,788] [INFO] Task started: fastANI
[2023-03-15 16:26:05,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg7518ea0d-5d5c-4540-b9f8-c4717849211b/OceanDNA-b33598.fa --refList OceanDNA-b33598/target_genomes.txt --output OceanDNA-b33598/fastani_result.tsv --threads 1
[2023-03-15 16:26:12,979] [INFO] Task succeeded: fastANI
[2023-03-15 16:26:12,980] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf883d316-f76d-41e5-bec8-0cc146fbee0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:26:12,980] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf883d316-f76d-41e5-bec8-0cc146fbee0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:26:12,980] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:26:12,980] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 16:26:12,980] [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 16:26:12,989] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33598/tc_result.tsv
[2023-03-15 16:26:13,001] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:26:13,001] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:26:13,001] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf883d316-f76d-41e5-bec8-0cc146fbee0f/dqc_reference/checkm_data
[2023-03-15 16:26:13,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:26:13,012] [INFO] Task started: CheckM
[2023-03-15 16:26:13,012] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33598/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33598/checkm_input OceanDNA-b33598/checkm_result
[2023-03-15 16:26:32,016] [INFO] Task succeeded: CheckM
[2023-03-15 16:26:32,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.04%
Contamintation: 4.69%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 16:26:32,135] [INFO] ===== Completeness check finished =====
[2023-03-15 16:26:32,135] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:26:32,135] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33598/markers.fasta)
[2023-03-15 16:26:32,136] [INFO] Task started: Blastn
[2023-03-15 16:26:32,136] [INFO] Running command: blastn -query OceanDNA-b33598/markers.fasta -db /var/lib/cwl/stgf883d316-f76d-41e5-bec8-0cc146fbee0f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33598/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:26:33,031] [INFO] Task succeeded: Blastn
[2023-03-15 16:26:33,046] [INFO] Selected 29 target genomes.
[2023-03-15 16:26:33,046] [INFO] Target genome list was writen to OceanDNA-b33598/target_genomes_gtdb.txt
[2023-03-15 16:26:33,094] [INFO] Task started: fastANI
[2023-03-15 16:26:33,094] [INFO] Running command: fastANI --query /var/lib/cwl/stg7518ea0d-5d5c-4540-b9f8-c4717849211b/OceanDNA-b33598.fa --refList OceanDNA-b33598/target_genomes_gtdb.txt --output OceanDNA-b33598/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:26:43,215] [INFO] Task succeeded: fastANI
[2023-03-15 16:26:43,217] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 16:26:43,218] [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_002170285.1	s__UBA7377 sp002170285	98.3867	233	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae_A;g__UBA7377	95.0	98.55	98.55	0.77	0.77	2	conclusive
GCA_002167365.1	s__UBA7377 sp002167365	80.0412	120	296	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae_A;g__UBA7377	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:26:43,220] [INFO] GTDB search result was written to OceanDNA-b33598/result_gtdb.tsv
[2023-03-15 16:26:43,223] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:26:43,229] [INFO] DFAST_QC result json was written to OceanDNA-b33598/dqc_result.json
[2023-03-15 16:26:43,229] [INFO] DFAST_QC completed!
[2023-03-15 16:26:43,229] [INFO] Total running time: 0h0m46s