[2023-03-16 03:23:49,881] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:23:49,881] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:23:49,881] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c8e8515-1109-4bac-af89-cd4ee3b79556/dqc_reference
[2023-03-16 03:23:51,081] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:23:51,081] [INFO] Task started: Prodigal
[2023-03-16 03:23:51,081] [INFO] Running command: cat /var/lib/cwl/stgb3e4b389-1769-46cd-9a23-1ce950e01a0c/OceanDNA-b42457.fa | prodigal -d OceanDNA-b42457/cds.fna -a OceanDNA-b42457/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:23:56,239] [INFO] Task succeeded: Prodigal
[2023-03-16 03:23:56,240] [INFO] Task started: HMMsearch
[2023-03-16 03:23:56,240] [INFO] Running command: hmmsearch --tblout OceanDNA-b42457/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c8e8515-1109-4bac-af89-cd4ee3b79556/dqc_reference/reference_markers.hmm OceanDNA-b42457/protein.faa > /dev/null
[2023-03-16 03:23:56,429] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:23:56,430] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb3e4b389-1769-46cd-9a23-1ce950e01a0c/OceanDNA-b42457.fa]
[2023-03-16 03:23:56,440] [INFO] Query marker FASTA was written to OceanDNA-b42457/markers.fasta
[2023-03-16 03:23:56,440] [INFO] Task started: Blastn
[2023-03-16 03:23:56,440] [INFO] Running command: blastn -query OceanDNA-b42457/markers.fasta -db /var/lib/cwl/stg7c8e8515-1109-4bac-af89-cd4ee3b79556/dqc_reference/reference_markers.fasta -out OceanDNA-b42457/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:23:56,938] [INFO] Task succeeded: Blastn
[2023-03-16 03:23:56,939] [INFO] Selected 15 target genomes.
[2023-03-16 03:23:56,939] [INFO] Target genome list was writen to OceanDNA-b42457/target_genomes.txt
[2023-03-16 03:23:56,949] [INFO] Task started: fastANI
[2023-03-16 03:23:56,949] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3e4b389-1769-46cd-9a23-1ce950e01a0c/OceanDNA-b42457.fa --refList OceanDNA-b42457/target_genomes.txt --output OceanDNA-b42457/fastani_result.tsv --threads 1
[2023-03-16 03:24:06,269] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:06,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c8e8515-1109-4bac-af89-cd4ee3b79556/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:24:06,270] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c8e8515-1109-4bac-af89-cd4ee3b79556/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:24:06,270] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:24:06,270] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 03:24:06,270] [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 03:24:06,270] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42457/tc_result.tsv
[2023-03-16 03:24:06,270] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:24:06,270] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:24:06,270] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c8e8515-1109-4bac-af89-cd4ee3b79556/dqc_reference/checkm_data
[2023-03-16 03:24:06,273] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:24:06,276] [INFO] Task started: CheckM
[2023-03-16 03:24:06,276] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42457/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42457/checkm_input OceanDNA-b42457/checkm_result
[2023-03-16 03:24:25,350] [INFO] Task succeeded: CheckM
[2023-03-16 03:24:25,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 03:24:25,352] [INFO] ===== Completeness check finished =====
[2023-03-16 03:24:25,352] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:24:25,352] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42457/markers.fasta)
[2023-03-16 03:24:25,353] [INFO] Task started: Blastn
[2023-03-16 03:24:25,353] [INFO] Running command: blastn -query OceanDNA-b42457/markers.fasta -db /var/lib/cwl/stg7c8e8515-1109-4bac-af89-cd4ee3b79556/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42457/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:26,059] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:26,060] [INFO] Selected 13 target genomes.
[2023-03-16 03:24:26,060] [INFO] Target genome list was writen to OceanDNA-b42457/target_genomes_gtdb.txt
[2023-03-16 03:24:26,410] [INFO] Task started: fastANI
[2023-03-16 03:24:26,410] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3e4b389-1769-46cd-9a23-1ce950e01a0c/OceanDNA-b42457.fa --refList OceanDNA-b42457/target_genomes_gtdb.txt --output OceanDNA-b42457/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:24:29,272] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:29,275] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 03:24:29,275] [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_015660645.1	s__CAJJAM01 sp015660645	96.614	284	327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__CAJJAM01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905182235.1	s__CAJJAM01 sp905182235	81.1161	178	327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__CAJJAM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:24:29,275] [INFO] GTDB search result was written to OceanDNA-b42457/result_gtdb.tsv
[2023-03-16 03:24:29,275] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:24:29,276] [INFO] DFAST_QC result json was written to OceanDNA-b42457/dqc_result.json
[2023-03-16 03:24:29,276] [INFO] DFAST_QC completed!
[2023-03-16 03:24:29,276] [INFO] Total running time: 0h0m39s