[2023-03-14 14:00:44,853] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:00:44,853] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:00:44,853] [INFO] DQC Reference Directory: /var/lib/cwl/stgefc1081d-dad4-4c50-9325-0f775331655c/dqc_reference
[2023-03-14 14:00:45,971] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:00:45,972] [INFO] Task started: Prodigal
[2023-03-14 14:00:45,972] [INFO] Running command: cat /var/lib/cwl/stg8aeca9a8-1441-45ba-9e15-8d0c28cde897/OceanDNA-b40505.fa | prodigal -d OceanDNA-b40505/cds.fna -a OceanDNA-b40505/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:00:57,470] [INFO] Task succeeded: Prodigal
[2023-03-14 14:00:57,470] [INFO] Task started: HMMsearch
[2023-03-14 14:00:57,470] [INFO] Running command: hmmsearch --tblout OceanDNA-b40505/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefc1081d-dad4-4c50-9325-0f775331655c/dqc_reference/reference_markers.hmm OceanDNA-b40505/protein.faa > /dev/null
[2023-03-14 14:00:57,654] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:00:57,654] [INFO] Found 6/6 markers.
[2023-03-14 14:00:57,669] [INFO] Query marker FASTA was written to OceanDNA-b40505/markers.fasta
[2023-03-14 14:00:57,670] [INFO] Task started: Blastn
[2023-03-14 14:00:57,670] [INFO] Running command: blastn -query OceanDNA-b40505/markers.fasta -db /var/lib/cwl/stgefc1081d-dad4-4c50-9325-0f775331655c/dqc_reference/reference_markers.fasta -out OceanDNA-b40505/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:00:58,247] [INFO] Task succeeded: Blastn
[2023-03-14 14:00:58,248] [INFO] Selected 34 target genomes.
[2023-03-14 14:00:58,249] [INFO] Target genome list was writen to OceanDNA-b40505/target_genomes.txt
[2023-03-14 14:00:58,265] [INFO] Task started: fastANI
[2023-03-14 14:00:58,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg8aeca9a8-1441-45ba-9e15-8d0c28cde897/OceanDNA-b40505.fa --refList OceanDNA-b40505/target_genomes.txt --output OceanDNA-b40505/fastani_result.tsv --threads 1
[2023-03-14 14:01:19,502] [INFO] Task succeeded: fastANI
[2023-03-14 14:01:19,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefc1081d-dad4-4c50-9325-0f775331655c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:01:19,502] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefc1081d-dad4-4c50-9325-0f775331655c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:01:19,503] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:01:19,503] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 14:01:19,503] [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
--------------------------------------------------------------------------------
[2023-03-14 14:01:19,504] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40505/tc_result.tsv
[2023-03-14 14:01:19,504] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:01:19,504] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:01:19,504] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefc1081d-dad4-4c50-9325-0f775331655c/dqc_reference/checkm_data
[2023-03-14 14:01:19,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:01:19,631] [INFO] Task started: CheckM
[2023-03-14 14:01:19,631] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40505/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40505/checkm_input OceanDNA-b40505/checkm_result
[2023-03-14 14:01:59,665] [INFO] Task succeeded: CheckM
[2023-03-14 14:01:59,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.97%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:01:59,674] [INFO] ===== Completeness check finished =====
[2023-03-14 14:01:59,675] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:01:59,675] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40505/markers.fasta)
[2023-03-14 14:01:59,676] [INFO] Task started: Blastn
[2023-03-14 14:01:59,676] [INFO] Running command: blastn -query OceanDNA-b40505/markers.fasta -db /var/lib/cwl/stgefc1081d-dad4-4c50-9325-0f775331655c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40505/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:02:01,709] [INFO] Task succeeded: Blastn
[2023-03-14 14:02:01,711] [INFO] Selected 32 target genomes.
[2023-03-14 14:02:01,711] [INFO] Target genome list was writen to OceanDNA-b40505/target_genomes_gtdb.txt
[2023-03-14 14:02:01,735] [INFO] Task started: fastANI
[2023-03-14 14:02:01,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg8aeca9a8-1441-45ba-9e15-8d0c28cde897/OceanDNA-b40505.fa --refList OceanDNA-b40505/target_genomes_gtdb.txt --output OceanDNA-b40505/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:02:25,555] [INFO] Task succeeded: fastANI
[2023-03-14 14:02:25,558] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:02:25,558] [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_002746215.1	s__UBA5109 sp002746215	78.6826	358	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5109	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002414385.1	s__UBA5109 sp002414385	76.8004	68	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5109	95.0	99.32	99.09	0.94	0.90	5	-
--------------------------------------------------------------------------------
[2023-03-14 14:02:25,559] [INFO] GTDB search result was written to OceanDNA-b40505/result_gtdb.tsv
[2023-03-14 14:02:25,559] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:02:25,560] [INFO] DFAST_QC result json was written to OceanDNA-b40505/dqc_result.json
[2023-03-14 14:02:25,560] [INFO] DFAST_QC completed!
[2023-03-14 14:02:25,560] [INFO] Total running time: 0h1m41s