[2023-03-15 05:00:03,409] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:00:03,410] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:00:03,410] [INFO] DQC Reference Directory: /var/lib/cwl/stg46adc41e-174b-4445-a042-3127807f5d81/dqc_reference
[2023-03-15 05:00:04,485] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:00:04,485] [INFO] Task started: Prodigal
[2023-03-15 05:00:04,485] [INFO] Running command: cat /var/lib/cwl/stg9a001135-3bdc-421b-93e1-78f8404fdcb3/OceanDNA-b32857.fa | prodigal -d OceanDNA-b32857/cds.fna -a OceanDNA-b32857/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:00:15,572] [INFO] Task succeeded: Prodigal
[2023-03-15 05:00:15,572] [INFO] Task started: HMMsearch
[2023-03-15 05:00:15,572] [INFO] Running command: hmmsearch --tblout OceanDNA-b32857/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46adc41e-174b-4445-a042-3127807f5d81/dqc_reference/reference_markers.hmm OceanDNA-b32857/protein.faa > /dev/null
[2023-03-15 05:00:15,756] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:00:15,756] [INFO] Found 6/6 markers.
[2023-03-15 05:00:15,790] [INFO] Query marker FASTA was written to OceanDNA-b32857/markers.fasta
[2023-03-15 05:00:15,791] [INFO] Task started: Blastn
[2023-03-15 05:00:15,791] [INFO] Running command: blastn -query OceanDNA-b32857/markers.fasta -db /var/lib/cwl/stg46adc41e-174b-4445-a042-3127807f5d81/dqc_reference/reference_markers.fasta -out OceanDNA-b32857/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:00:16,308] [INFO] Task succeeded: Blastn
[2023-03-15 05:00:16,318] [INFO] Selected 28 target genomes.
[2023-03-15 05:00:16,318] [INFO] Target genome list was writen to OceanDNA-b32857/target_genomes.txt
[2023-03-15 05:00:16,333] [INFO] Task started: fastANI
[2023-03-15 05:00:16,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a001135-3bdc-421b-93e1-78f8404fdcb3/OceanDNA-b32857.fa --refList OceanDNA-b32857/target_genomes.txt --output OceanDNA-b32857/fastani_result.tsv --threads 1
[2023-03-15 05:00:37,303] [INFO] Task succeeded: fastANI
[2023-03-15 05:00:37,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46adc41e-174b-4445-a042-3127807f5d81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:00:37,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46adc41e-174b-4445-a042-3127807f5d81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:00:37,304] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:00:37,304] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 05:00:37,304] [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 05:00:37,306] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32857/tc_result.tsv
[2023-03-15 05:00:37,311] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:00:37,311] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:00:37,311] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46adc41e-174b-4445-a042-3127807f5d81/dqc_reference/checkm_data
[2023-03-15 05:00:37,313] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:00:37,341] [INFO] Task started: CheckM
[2023-03-15 05:00:37,341] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32857/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32857/checkm_input OceanDNA-b32857/checkm_result
[2023-03-15 05:01:10,052] [INFO] Task succeeded: CheckM
[2023-03-15 05:01:10,052] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.13%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:01:10,061] [INFO] ===== Completeness check finished =====
[2023-03-15 05:01:10,061] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:01:10,062] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32857/markers.fasta)
[2023-03-15 05:01:10,063] [INFO] Task started: Blastn
[2023-03-15 05:01:10,063] [INFO] Running command: blastn -query OceanDNA-b32857/markers.fasta -db /var/lib/cwl/stg46adc41e-174b-4445-a042-3127807f5d81/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32857/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:01:10,794] [INFO] Task succeeded: Blastn
[2023-03-15 05:01:10,795] [INFO] Selected 27 target genomes.
[2023-03-15 05:01:10,795] [INFO] Target genome list was writen to OceanDNA-b32857/target_genomes_gtdb.txt
[2023-03-15 05:01:10,856] [INFO] Task started: fastANI
[2023-03-15 05:01:10,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a001135-3bdc-421b-93e1-78f8404fdcb3/OceanDNA-b32857.fa --refList OceanDNA-b32857/target_genomes_gtdb.txt --output OceanDNA-b32857/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:01:26,183] [INFO] Task succeeded: fastANI
[2023-03-15 05:01:26,186] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:01:26,186] [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_905480445.1	s__CAJQQZ01 sp905480445	98.6324	438	526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__CAJQQZ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905480575.1	s__CAJQQZ01 sp905480575	81.1261	186	526	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__CAJQQZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:01:26,189] [INFO] GTDB search result was written to OceanDNA-b32857/result_gtdb.tsv
[2023-03-15 05:01:26,192] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:01:26,195] [INFO] DFAST_QC result json was written to OceanDNA-b32857/dqc_result.json
[2023-03-15 05:01:26,195] [INFO] DFAST_QC completed!
[2023-03-15 05:01:26,195] [INFO] Total running time: 0h1m23s