[2023-03-14 11:14:12,763] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:14:12,765] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:14:12,765] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdee4f65-3a66-410c-9ffc-7927e6b68609/dqc_reference
[2023-03-14 11:14:14,202] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:14,202] [INFO] Task started: Prodigal
[2023-03-14 11:14:14,202] [INFO] Running command: cat /var/lib/cwl/stg0c57a8b2-80d0-43ad-bf53-4b68aa3e41f4/OceanDNA-b1711.fa | prodigal -d OceanDNA-b1711/cds.fna -a OceanDNA-b1711/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:36,457] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:36,458] [INFO] Task started: HMMsearch
[2023-03-14 11:14:36,458] [INFO] Running command: hmmsearch --tblout OceanDNA-b1711/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdee4f65-3a66-410c-9ffc-7927e6b68609/dqc_reference/reference_markers.hmm OceanDNA-b1711/protein.faa > /dev/null
[2023-03-14 11:14:36,708] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:36,709] [INFO] Found 6/6 markers.
[2023-03-14 11:14:36,731] [INFO] Query marker FASTA was written to OceanDNA-b1711/markers.fasta
[2023-03-14 11:14:36,731] [INFO] Task started: Blastn
[2023-03-14 11:14:36,732] [INFO] Running command: blastn -query OceanDNA-b1711/markers.fasta -db /var/lib/cwl/stgbdee4f65-3a66-410c-9ffc-7927e6b68609/dqc_reference/reference_markers.fasta -out OceanDNA-b1711/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:37,314] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:37,315] [INFO] Selected 34 target genomes.
[2023-03-14 11:14:37,315] [INFO] Target genome list was writen to OceanDNA-b1711/target_genomes.txt
[2023-03-14 11:14:37,342] [INFO] Task started: fastANI
[2023-03-14 11:14:37,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c57a8b2-80d0-43ad-bf53-4b68aa3e41f4/OceanDNA-b1711.fa --refList OceanDNA-b1711/target_genomes.txt --output OceanDNA-b1711/fastani_result.tsv --threads 1
[2023-03-14 11:14:57,953] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:57,953] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdee4f65-3a66-410c-9ffc-7927e6b68609/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:57,954] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdee4f65-3a66-410c-9ffc-7927e6b68609/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:57,954] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:57,954] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:14:57,954] [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 11:14:57,954] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1711/tc_result.tsv
[2023-03-14 11:14:57,954] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:57,954] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:57,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdee4f65-3a66-410c-9ffc-7927e6b68609/dqc_reference/checkm_data
[2023-03-14 11:14:57,958] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:58,095] [INFO] Task started: CheckM
[2023-03-14 11:14:58,096] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1711/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1711/checkm_input OceanDNA-b1711/checkm_result
[2023-03-14 11:15:53,662] [INFO] Task succeeded: CheckM
[2023-03-14 11:15:53,663] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:15:53,665] [INFO] ===== Completeness check finished =====
[2023-03-14 11:15:53,665] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:15:53,666] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1711/markers.fasta)
[2023-03-14 11:15:53,667] [INFO] Task started: Blastn
[2023-03-14 11:15:53,667] [INFO] Running command: blastn -query OceanDNA-b1711/markers.fasta -db /var/lib/cwl/stgbdee4f65-3a66-410c-9ffc-7927e6b68609/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1711/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:15:54,442] [INFO] Task succeeded: Blastn
[2023-03-14 11:15:54,443] [INFO] Selected 32 target genomes.
[2023-03-14 11:15:54,443] [INFO] Target genome list was writen to OceanDNA-b1711/target_genomes_gtdb.txt
[2023-03-14 11:15:54,483] [INFO] Task started: fastANI
[2023-03-14 11:15:54,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c57a8b2-80d0-43ad-bf53-4b68aa3e41f4/OceanDNA-b1711.fa --refList OceanDNA-b1711/target_genomes_gtdb.txt --output OceanDNA-b1711/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:16:08,668] [INFO] Task succeeded: fastANI
[2023-03-14 11:16:08,671] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:16:08,671] [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_905182135.1	s__UBA10347 sp905182135	99.8824	742	1157	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA10347;g__UBA10347	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003485885.1	s__UBA10347 sp003485885	78.3683	292	1157	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA10347;g__UBA10347	95.0	98.91	98.91	0.90	0.90	2	-
GCA_016845585.1	s__UBA11606 sp016845585	75.3789	51	1157	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:16:08,671] [INFO] GTDB search result was written to OceanDNA-b1711/result_gtdb.tsv
[2023-03-14 11:16:08,672] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:16:08,672] [INFO] DFAST_QC result json was written to OceanDNA-b1711/dqc_result.json
[2023-03-14 11:16:08,672] [INFO] DFAST_QC completed!
[2023-03-14 11:16:08,672] [INFO] Total running time: 0h1m56s