[2023-03-18 10:37:58,275] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:37:58,275] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:37:58,275] [INFO] DQC Reference Directory: /var/lib/cwl/stgebcd1067-624f-4764-bae7-dd0772e31a85/dqc_reference
[2023-03-18 10:37:59,408] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:37:59,409] [INFO] Task started: Prodigal
[2023-03-18 10:37:59,409] [INFO] Running command: cat /var/lib/cwl/stg9d8ccbc1-b092-4b79-8897-fd080598196a/OceanDNA-b22166.fa | prodigal -d OceanDNA-b22166/cds.fna -a OceanDNA-b22166/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:38:06,383] [INFO] Task succeeded: Prodigal
[2023-03-18 10:38:06,383] [INFO] Task started: HMMsearch
[2023-03-18 10:38:06,383] [INFO] Running command: hmmsearch --tblout OceanDNA-b22166/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebcd1067-624f-4764-bae7-dd0772e31a85/dqc_reference/reference_markers.hmm OceanDNA-b22166/protein.faa > /dev/null
[2023-03-18 10:38:06,590] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:38:06,590] [INFO] Found 6/6 markers.
[2023-03-18 10:38:06,602] [INFO] Query marker FASTA was written to OceanDNA-b22166/markers.fasta
[2023-03-18 10:38:06,603] [INFO] Task started: Blastn
[2023-03-18 10:38:06,603] [INFO] Running command: blastn -query OceanDNA-b22166/markers.fasta -db /var/lib/cwl/stgebcd1067-624f-4764-bae7-dd0772e31a85/dqc_reference/reference_markers.fasta -out OceanDNA-b22166/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:38:07,186] [INFO] Task succeeded: Blastn
[2023-03-18 10:38:07,187] [INFO] Selected 16 target genomes.
[2023-03-18 10:38:07,187] [INFO] Target genome list was writen to OceanDNA-b22166/target_genomes.txt
[2023-03-18 10:38:07,206] [INFO] Task started: fastANI
[2023-03-18 10:38:07,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d8ccbc1-b092-4b79-8897-fd080598196a/OceanDNA-b22166.fa --refList OceanDNA-b22166/target_genomes.txt --output OceanDNA-b22166/fastani_result.tsv --threads 1
[2023-03-18 10:38:15,364] [INFO] Task succeeded: fastANI
[2023-03-18 10:38:15,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebcd1067-624f-4764-bae7-dd0772e31a85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:38:15,364] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebcd1067-624f-4764-bae7-dd0772e31a85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:38:15,364] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:38:15,364] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:38:15,364] [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
--------------------------------------------------------------------------------
[2023-03-18 10:38:15,365] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22166/tc_result.tsv
[2023-03-18 10:38:15,365] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:38:15,365] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:38:15,365] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebcd1067-624f-4764-bae7-dd0772e31a85/dqc_reference/checkm_data
[2023-03-18 10:38:15,416] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:38:15,419] [INFO] Task started: CheckM
[2023-03-18 10:38:15,419] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22166/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22166/checkm_input OceanDNA-b22166/checkm_result
[2023-03-18 10:38:41,703] [INFO] Task succeeded: CheckM
[2023-03-18 10:38:41,703] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:38:41,705] [INFO] ===== Completeness check finished =====
[2023-03-18 10:38:41,705] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:38:41,705] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22166/markers.fasta)
[2023-03-18 10:38:41,707] [INFO] Task started: Blastn
[2023-03-18 10:38:41,707] [INFO] Running command: blastn -query OceanDNA-b22166/markers.fasta -db /var/lib/cwl/stgebcd1067-624f-4764-bae7-dd0772e31a85/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22166/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:38:42,755] [INFO] Task succeeded: Blastn
[2023-03-18 10:38:42,756] [INFO] Selected 19 target genomes.
[2023-03-18 10:38:42,756] [INFO] Target genome list was writen to OceanDNA-b22166/target_genomes_gtdb.txt
[2023-03-18 10:38:42,775] [INFO] Task started: fastANI
[2023-03-18 10:38:42,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d8ccbc1-b092-4b79-8897-fd080598196a/OceanDNA-b22166.fa --refList OceanDNA-b22166/target_genomes_gtdb.txt --output OceanDNA-b22166/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:38:49,794] [INFO] Task succeeded: fastANI
[2023-03-18 10:38:49,797] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:38:49,797] [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_014238125.1	s__GCA-002718515 sp014238125	78.8577	160	352	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018656645.1	s__GCA-002718515 sp018656645	78.5469	150	352	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381305.1	s__GCA-002718515 sp014381305	78.1852	137	352	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:38:49,797] [INFO] GTDB search result was written to OceanDNA-b22166/result_gtdb.tsv
[2023-03-18 10:38:49,797] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:38:49,798] [INFO] DFAST_QC result json was written to OceanDNA-b22166/dqc_result.json
[2023-03-18 10:38:49,798] [INFO] DFAST_QC completed!
[2023-03-18 10:38:49,798] [INFO] Total running time: 0h0m52s