[2023-03-15 16:03:34,277] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:03:34,277] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:03:34,277] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf352263-963c-4ec9-8450-220d57c5aa82/dqc_reference
[2023-03-15 16:03:35,745] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:03:35,745] [INFO] Task started: Prodigal
[2023-03-15 16:03:35,745] [INFO] Running command: cat /var/lib/cwl/stg8b0184e4-06cf-46f1-bb0e-d7c229063e64/OceanDNA-b20652.fa | prodigal -d OceanDNA-b20652/cds.fna -a OceanDNA-b20652/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:03:38,650] [INFO] Task succeeded: Prodigal
[2023-03-15 16:03:38,651] [INFO] Task started: HMMsearch
[2023-03-15 16:03:38,651] [INFO] Running command: hmmsearch --tblout OceanDNA-b20652/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf352263-963c-4ec9-8450-220d57c5aa82/dqc_reference/reference_markers.hmm OceanDNA-b20652/protein.faa > /dev/null
[2023-03-15 16:03:38,814] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:03:38,814] [INFO] Found 6/6 markers.
[2023-03-15 16:03:38,824] [INFO] Query marker FASTA was written to OceanDNA-b20652/markers.fasta
[2023-03-15 16:03:38,825] [INFO] Task started: Blastn
[2023-03-15 16:03:38,825] [INFO] Running command: blastn -query OceanDNA-b20652/markers.fasta -db /var/lib/cwl/stgdf352263-963c-4ec9-8450-220d57c5aa82/dqc_reference/reference_markers.fasta -out OceanDNA-b20652/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:03:40,939] [INFO] Task succeeded: Blastn
[2023-03-15 16:03:40,940] [INFO] Selected 18 target genomes.
[2023-03-15 16:03:40,940] [INFO] Target genome list was writen to OceanDNA-b20652/target_genomes.txt
[2023-03-15 16:03:40,952] [INFO] Task started: fastANI
[2023-03-15 16:03:40,952] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b0184e4-06cf-46f1-bb0e-d7c229063e64/OceanDNA-b20652.fa --refList OceanDNA-b20652/target_genomes.txt --output OceanDNA-b20652/fastani_result.tsv --threads 1
[2023-03-15 16:03:48,844] [INFO] Task succeeded: fastANI
[2023-03-15 16:03:48,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf352263-963c-4ec9-8450-220d57c5aa82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:03:48,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf352263-963c-4ec9-8450-220d57c5aa82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:03:48,845] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:03:48,845] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 16:03:48,845] [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 16:03:48,845] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20652/tc_result.tsv
[2023-03-15 16:03:48,846] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:03:48,846] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:03:48,846] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf352263-963c-4ec9-8450-220d57c5aa82/dqc_reference/checkm_data
[2023-03-15 16:03:48,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:03:48,881] [INFO] Task started: CheckM
[2023-03-15 16:03:48,881] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20652/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20652/checkm_input OceanDNA-b20652/checkm_result
[2023-03-15 16:04:02,677] [INFO] Task succeeded: CheckM
[2023-03-15 16:04:02,678] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.59%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:04:02,680] [INFO] ===== Completeness check finished =====
[2023-03-15 16:04:02,680] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:04:02,680] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20652/markers.fasta)
[2023-03-15 16:04:02,681] [INFO] Task started: Blastn
[2023-03-15 16:04:02,681] [INFO] Running command: blastn -query OceanDNA-b20652/markers.fasta -db /var/lib/cwl/stgdf352263-963c-4ec9-8450-220d57c5aa82/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20652/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:04:03,561] [INFO] Task succeeded: Blastn
[2023-03-15 16:04:03,562] [INFO] Selected 27 target genomes.
[2023-03-15 16:04:03,562] [INFO] Target genome list was writen to OceanDNA-b20652/target_genomes_gtdb.txt
[2023-03-15 16:04:03,590] [INFO] Task started: fastANI
[2023-03-15 16:04:03,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b0184e4-06cf-46f1-bb0e-d7c229063e64/OceanDNA-b20652.fa --refList OceanDNA-b20652/target_genomes_gtdb.txt --output OceanDNA-b20652/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:04:11,871] [INFO] Task succeeded: fastANI
[2023-03-15 16:04:11,874] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:04:11,874] [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_000405805.1	s__SCGC-AAA003-L08 sp000405805	78.4716	80	149	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__SCGC-AAA003-L08;g__SCGC-AAA003-L08	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701525.1	s__SCGC-AAA003-L08 sp002701525	77.6055	59	149	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__SCGC-AAA003-L08;g__SCGC-AAA003-L08	95.0	97.76	97.76	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2023-03-15 16:04:11,875] [INFO] GTDB search result was written to OceanDNA-b20652/result_gtdb.tsv
[2023-03-15 16:04:11,875] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:04:11,876] [INFO] DFAST_QC result json was written to OceanDNA-b20652/dqc_result.json
[2023-03-15 16:04:11,876] [INFO] DFAST_QC completed!
[2023-03-15 16:04:11,876] [INFO] Total running time: 0h0m38s