[2023-03-16 05:50:18,331] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:50:18,331] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:50:18,331] [INFO] DQC Reference Directory: /var/lib/cwl/stg78cf3799-8441-4e6d-9a5e-45e0e2751580/dqc_reference
[2023-03-16 05:50:20,128] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:50:20,129] [INFO] Task started: Prodigal
[2023-03-16 05:50:20,129] [INFO] Running command: cat /var/lib/cwl/stg7824b619-dc97-4603-b908-c7c391f9e036/OceanDNA-b32638.fa | prodigal -d OceanDNA-b32638/cds.fna -a OceanDNA-b32638/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:50:27,106] [INFO] Task succeeded: Prodigal
[2023-03-16 05:50:27,107] [INFO] Task started: HMMsearch
[2023-03-16 05:50:27,107] [INFO] Running command: hmmsearch --tblout OceanDNA-b32638/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78cf3799-8441-4e6d-9a5e-45e0e2751580/dqc_reference/reference_markers.hmm OceanDNA-b32638/protein.faa > /dev/null
[2023-03-16 05:50:27,347] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:50:27,348] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7824b619-dc97-4603-b908-c7c391f9e036/OceanDNA-b32638.fa]
[2023-03-16 05:50:27,358] [INFO] Query marker FASTA was written to OceanDNA-b32638/markers.fasta
[2023-03-16 05:50:27,359] [INFO] Task started: Blastn
[2023-03-16 05:50:27,359] [INFO] Running command: blastn -query OceanDNA-b32638/markers.fasta -db /var/lib/cwl/stg78cf3799-8441-4e6d-9a5e-45e0e2751580/dqc_reference/reference_markers.fasta -out OceanDNA-b32638/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:50:30,094] [INFO] Task succeeded: Blastn
[2023-03-16 05:50:30,094] [INFO] Selected 20 target genomes.
[2023-03-16 05:50:30,095] [INFO] Target genome list was writen to OceanDNA-b32638/target_genomes.txt
[2023-03-16 05:50:30,112] [INFO] Task started: fastANI
[2023-03-16 05:50:30,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg7824b619-dc97-4603-b908-c7c391f9e036/OceanDNA-b32638.fa --refList OceanDNA-b32638/target_genomes.txt --output OceanDNA-b32638/fastani_result.tsv --threads 1
[2023-03-16 05:50:41,696] [INFO] Task succeeded: fastANI
[2023-03-16 05:50:41,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78cf3799-8441-4e6d-9a5e-45e0e2751580/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:50:41,696] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78cf3799-8441-4e6d-9a5e-45e0e2751580/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:50:41,697] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:50:41,697] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 05:50:41,697] [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
--------------------------------------------------------------------------------
[2023-03-16 05:50:41,697] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32638/tc_result.tsv
[2023-03-16 05:50:41,697] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:50:41,697] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:50:41,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78cf3799-8441-4e6d-9a5e-45e0e2751580/dqc_reference/checkm_data
[2023-03-16 05:50:41,700] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:50:41,931] [INFO] Task started: CheckM
[2023-03-16 05:50:41,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32638/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32638/checkm_input OceanDNA-b32638/checkm_result
[2023-03-16 05:51:04,567] [INFO] Task succeeded: CheckM
[2023-03-16 05:51:04,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:51:04,569] [INFO] ===== Completeness check finished =====
[2023-03-16 05:51:04,569] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:51:04,569] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32638/markers.fasta)
[2023-03-16 05:51:04,571] [INFO] Task started: Blastn
[2023-03-16 05:51:04,571] [INFO] Running command: blastn -query OceanDNA-b32638/markers.fasta -db /var/lib/cwl/stg78cf3799-8441-4e6d-9a5e-45e0e2751580/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32638/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:51:05,241] [INFO] Task succeeded: Blastn
[2023-03-16 05:51:05,242] [INFO] Selected 16 target genomes.
[2023-03-16 05:51:05,242] [INFO] Target genome list was writen to OceanDNA-b32638/target_genomes_gtdb.txt
[2023-03-16 05:51:05,253] [INFO] Task started: fastANI
[2023-03-16 05:51:05,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg7824b619-dc97-4603-b908-c7c391f9e036/OceanDNA-b32638.fa --refList OceanDNA-b32638/target_genomes_gtdb.txt --output OceanDNA-b32638/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:51:11,045] [INFO] Task succeeded: fastANI
[2023-03-16 05:51:11,047] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 05:51:11,048] [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_002689455.1	s__UBA2136 sp002689455	99.9823	373	415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA1280;f__UBA2136;g__UBA2136	95.0	99.82	99.82	0.87	0.87	2	conclusive
GCA_002328405.1	s__UBA2136 sp002328405	78.5325	157	415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA1280;f__UBA2136;g__UBA2136	95.0	99.98	99.96	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2023-03-16 05:51:11,048] [INFO] GTDB search result was written to OceanDNA-b32638/result_gtdb.tsv
[2023-03-16 05:51:11,048] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:51:11,048] [INFO] DFAST_QC result json was written to OceanDNA-b32638/dqc_result.json
[2023-03-16 05:51:11,049] [INFO] DFAST_QC completed!
[2023-03-16 05:51:11,049] [INFO] Total running time: 0h0m53s