[2023-03-15 07:58:33,368] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:58:33,371] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:58:33,371] [INFO] DQC Reference Directory: /var/lib/cwl/stg5809713e-ad5b-4a35-9f9e-ddb87d98f32c/dqc_reference
[2023-03-15 07:58:35,137] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:58:35,137] [INFO] Task started: Prodigal
[2023-03-15 07:58:35,137] [INFO] Running command: cat /var/lib/cwl/stg2db59e62-716b-431c-82ac-8dd1a8fbab7c/OceanDNA-b15098.fa | prodigal -d OceanDNA-b15098/cds.fna -a OceanDNA-b15098/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:58:43,643] [INFO] Task succeeded: Prodigal
[2023-03-15 07:58:43,643] [INFO] Task started: HMMsearch
[2023-03-15 07:58:43,644] [INFO] Running command: hmmsearch --tblout OceanDNA-b15098/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5809713e-ad5b-4a35-9f9e-ddb87d98f32c/dqc_reference/reference_markers.hmm OceanDNA-b15098/protein.faa > /dev/null
[2023-03-15 07:58:43,786] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:58:43,786] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2db59e62-716b-431c-82ac-8dd1a8fbab7c/OceanDNA-b15098.fa]
[2023-03-15 07:58:43,821] [INFO] Query marker FASTA was written to OceanDNA-b15098/markers.fasta
[2023-03-15 07:58:43,822] [INFO] Task started: Blastn
[2023-03-15 07:58:43,822] [INFO] Running command: blastn -query OceanDNA-b15098/markers.fasta -db /var/lib/cwl/stg5809713e-ad5b-4a35-9f9e-ddb87d98f32c/dqc_reference/reference_markers.fasta -out OceanDNA-b15098/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:58:44,320] [INFO] Task succeeded: Blastn
[2023-03-15 07:58:44,324] [INFO] Selected 15 target genomes.
[2023-03-15 07:58:44,324] [INFO] Target genome list was writen to OceanDNA-b15098/target_genomes.txt
[2023-03-15 07:58:44,332] [INFO] Task started: fastANI
[2023-03-15 07:58:44,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg2db59e62-716b-431c-82ac-8dd1a8fbab7c/OceanDNA-b15098.fa --refList OceanDNA-b15098/target_genomes.txt --output OceanDNA-b15098/fastani_result.tsv --threads 1
[2023-03-15 07:58:53,124] [INFO] Task succeeded: fastANI
[2023-03-15 07:58:53,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5809713e-ad5b-4a35-9f9e-ddb87d98f32c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:58:53,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5809713e-ad5b-4a35-9f9e-ddb87d98f32c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:58:53,124] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:58:53,125] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:58:53,125] [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 07:58:53,127] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15098/tc_result.tsv
[2023-03-15 07:58:53,130] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:58:53,130] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:58:53,130] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5809713e-ad5b-4a35-9f9e-ddb87d98f32c/dqc_reference/checkm_data
[2023-03-15 07:58:53,133] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:58:53,139] [INFO] Task started: CheckM
[2023-03-15 07:58:53,139] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15098/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15098/checkm_input OceanDNA-b15098/checkm_result
[2023-03-15 07:59:19,842] [INFO] Task succeeded: CheckM
[2023-03-15 07:59:19,842] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.98%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 07:59:20,057] [INFO] ===== Completeness check finished =====
[2023-03-15 07:59:20,057] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:59:20,057] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15098/markers.fasta)
[2023-03-15 07:59:20,058] [INFO] Task started: Blastn
[2023-03-15 07:59:20,058] [INFO] Running command: blastn -query OceanDNA-b15098/markers.fasta -db /var/lib/cwl/stg5809713e-ad5b-4a35-9f9e-ddb87d98f32c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15098/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:59:20,728] [INFO] Task succeeded: Blastn
[2023-03-15 07:59:20,735] [INFO] Selected 14 target genomes.
[2023-03-15 07:59:20,735] [INFO] Target genome list was writen to OceanDNA-b15098/target_genomes_gtdb.txt
[2023-03-15 07:59:20,750] [INFO] Task started: fastANI
[2023-03-15 07:59:20,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg2db59e62-716b-431c-82ac-8dd1a8fbab7c/OceanDNA-b15098.fa --refList OceanDNA-b15098/target_genomes_gtdb.txt --output OceanDNA-b15098/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:59:26,837] [INFO] Task succeeded: fastANI
[2023-03-15 07:59:26,840] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:59:26,840] [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_002730555.1	s__GCA-2730555 sp002730555	78.7173	243	464	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__GCA-2730555	95.0	99.68	99.68	0.93	0.93	2	-
GCA_018650185.1	s__GCA-2730555 sp018650185	77.936	222	464	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__GCA-2730555	95.0	99.67	99.66	0.92	0.91	4	-
GCA_014239685.1	s__GCA-2730555 sp014239685	77.6886	139	464	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1151;g__GCA-2730555	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:59:26,847] [INFO] GTDB search result was written to OceanDNA-b15098/result_gtdb.tsv
[2023-03-15 07:59:26,859] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:59:26,870] [INFO] DFAST_QC result json was written to OceanDNA-b15098/dqc_result.json
[2023-03-15 07:59:26,870] [INFO] DFAST_QC completed!
[2023-03-15 07:59:26,870] [INFO] Total running time: 0h0m54s