[2023-03-18 20:59:43,931] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:59:43,931] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:59:43,931] [INFO] DQC Reference Directory: /var/lib/cwl/stg7fcf0bd5-8ea0-4df6-ac09-ca26f0bc70d7/dqc_reference
[2023-03-18 20:59:45,685] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:59:45,685] [INFO] Task started: Prodigal
[2023-03-18 20:59:45,686] [INFO] Running command: cat /var/lib/cwl/stg25c462a5-4521-4b9e-9175-9cdae509b46c/OceanDNA-b23039.fa | prodigal -d OceanDNA-b23039/cds.fna -a OceanDNA-b23039/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:59:57,244] [INFO] Task succeeded: Prodigal
[2023-03-18 20:59:57,245] [INFO] Task started: HMMsearch
[2023-03-18 20:59:57,245] [INFO] Running command: hmmsearch --tblout OceanDNA-b23039/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7fcf0bd5-8ea0-4df6-ac09-ca26f0bc70d7/dqc_reference/reference_markers.hmm OceanDNA-b23039/protein.faa > /dev/null
[2023-03-18 20:59:57,391] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:59:57,391] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg25c462a5-4521-4b9e-9175-9cdae509b46c/OceanDNA-b23039.fa]
[2023-03-18 20:59:57,405] [INFO] Query marker FASTA was written to OceanDNA-b23039/markers.fasta
[2023-03-18 20:59:57,406] [INFO] Task started: Blastn
[2023-03-18 20:59:57,406] [INFO] Running command: blastn -query OceanDNA-b23039/markers.fasta -db /var/lib/cwl/stg7fcf0bd5-8ea0-4df6-ac09-ca26f0bc70d7/dqc_reference/reference_markers.fasta -out OceanDNA-b23039/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:59:57,847] [INFO] Task succeeded: Blastn
[2023-03-18 20:59:57,848] [INFO] Selected 12 target genomes.
[2023-03-18 20:59:57,848] [INFO] Target genome list was writen to OceanDNA-b23039/target_genomes.txt
[2023-03-18 20:59:57,856] [INFO] Task started: fastANI
[2023-03-18 20:59:57,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg25c462a5-4521-4b9e-9175-9cdae509b46c/OceanDNA-b23039.fa --refList OceanDNA-b23039/target_genomes.txt --output OceanDNA-b23039/fastani_result.tsv --threads 1
[2023-03-18 21:00:04,700] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:04,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7fcf0bd5-8ea0-4df6-ac09-ca26f0bc70d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:00:04,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7fcf0bd5-8ea0-4df6-ac09-ca26f0bc70d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:00:04,701] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:00:04,701] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:00:04,701] [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 21:00:04,701] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23039/tc_result.tsv
[2023-03-18 21:00:04,701] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:00:04,701] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:00:04,701] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7fcf0bd5-8ea0-4df6-ac09-ca26f0bc70d7/dqc_reference/checkm_data
[2023-03-18 21:00:04,704] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:00:04,707] [INFO] Task started: CheckM
[2023-03-18 21:00:04,708] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23039/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23039/checkm_input OceanDNA-b23039/checkm_result
[2023-03-18 21:00:38,331] [INFO] Task succeeded: CheckM
[2023-03-18 21:00:38,331] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.36%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:00:38,340] [INFO] ===== Completeness check finished =====
[2023-03-18 21:00:38,341] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:00:38,341] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23039/markers.fasta)
[2023-03-18 21:00:38,342] [INFO] Task started: Blastn
[2023-03-18 21:00:38,342] [INFO] Running command: blastn -query OceanDNA-b23039/markers.fasta -db /var/lib/cwl/stg7fcf0bd5-8ea0-4df6-ac09-ca26f0bc70d7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23039/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:00:38,799] [INFO] Task succeeded: Blastn
[2023-03-18 21:00:38,803] [INFO] Selected 13 target genomes.
[2023-03-18 21:00:38,803] [INFO] Target genome list was writen to OceanDNA-b23039/target_genomes_gtdb.txt
[2023-03-18 21:00:38,842] [INFO] Task started: fastANI
[2023-03-18 21:00:38,842] [INFO] Running command: fastANI --query /var/lib/cwl/stg25c462a5-4521-4b9e-9175-9cdae509b46c/OceanDNA-b23039.fa --refList OceanDNA-b23039/target_genomes_gtdb.txt --output OceanDNA-b23039/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:00:46,973] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:46,976] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:00:46,976] [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_012959525.1	s__GCA-2720975 sp012959525	83.8021	221	238	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2720975	95.0	99.90	99.90	0.93	0.93	2	-
GCA_002720975.1	s__GCA-2720975 sp002720975	83.0644	185	238	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2720975	95.0	96.24	96.24	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2023-03-18 21:00:46,979] [INFO] GTDB search result was written to OceanDNA-b23039/result_gtdb.tsv
[2023-03-18 21:00:46,982] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:00:46,985] [INFO] DFAST_QC result json was written to OceanDNA-b23039/dqc_result.json
[2023-03-18 21:00:46,985] [INFO] DFAST_QC completed!
[2023-03-18 21:00:46,986] [INFO] Total running time: 0h1m3s