[2023-03-15 23:07:02,632] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:07:02,632] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:07:02,632] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1e10e92-443b-4938-8ca2-36c2160ca160/dqc_reference
[2023-03-15 23:07:03,966] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:07:03,966] [INFO] Task started: Prodigal
[2023-03-15 23:07:03,966] [INFO] Running command: cat /var/lib/cwl/stgb1b09936-6de5-4433-b39b-189632e2be3b/OceanDNA-b42458.fa | prodigal -d OceanDNA-b42458/cds.fna -a OceanDNA-b42458/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:07:06,861] [INFO] Task succeeded: Prodigal
[2023-03-15 23:07:06,861] [INFO] Task started: HMMsearch
[2023-03-15 23:07:06,861] [INFO] Running command: hmmsearch --tblout OceanDNA-b42458/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1e10e92-443b-4938-8ca2-36c2160ca160/dqc_reference/reference_markers.hmm OceanDNA-b42458/protein.faa > /dev/null
[2023-03-15 23:07:07,031] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:07:07,032] [INFO] Found 6/6 markers.
[2023-03-15 23:07:07,038] [INFO] Query marker FASTA was written to OceanDNA-b42458/markers.fasta
[2023-03-15 23:07:07,038] [INFO] Task started: Blastn
[2023-03-15 23:07:07,038] [INFO] Running command: blastn -query OceanDNA-b42458/markers.fasta -db /var/lib/cwl/stgb1e10e92-443b-4938-8ca2-36c2160ca160/dqc_reference/reference_markers.fasta -out OceanDNA-b42458/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:07:07,819] [INFO] Task succeeded: Blastn
[2023-03-15 23:07:07,820] [INFO] Selected 19 target genomes.
[2023-03-15 23:07:07,820] [INFO] Target genome list was writen to OceanDNA-b42458/target_genomes.txt
[2023-03-15 23:07:07,880] [INFO] Task started: fastANI
[2023-03-15 23:07:07,880] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1b09936-6de5-4433-b39b-189632e2be3b/OceanDNA-b42458.fa --refList OceanDNA-b42458/target_genomes.txt --output OceanDNA-b42458/fastani_result.tsv --threads 1
[2023-03-15 23:07:16,276] [INFO] Task succeeded: fastANI
[2023-03-15 23:07:16,277] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1e10e92-443b-4938-8ca2-36c2160ca160/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:07:16,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1e10e92-443b-4938-8ca2-36c2160ca160/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:07:16,277] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:07:16,277] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:07:16,277] [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 23:07:16,277] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42458/tc_result.tsv
[2023-03-15 23:07:16,277] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:07:16,278] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:07:16,278] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1e10e92-443b-4938-8ca2-36c2160ca160/dqc_reference/checkm_data
[2023-03-15 23:07:16,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:07:16,283] [INFO] Task started: CheckM
[2023-03-15 23:07:16,283] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42458/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42458/checkm_input OceanDNA-b42458/checkm_result
[2023-03-15 23:07:31,853] [INFO] Task succeeded: CheckM
[2023-03-15 23:07:31,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:07:31,855] [INFO] ===== Completeness check finished =====
[2023-03-15 23:07:31,855] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:07:31,856] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42458/markers.fasta)
[2023-03-15 23:07:31,857] [INFO] Task started: Blastn
[2023-03-15 23:07:31,857] [INFO] Running command: blastn -query OceanDNA-b42458/markers.fasta -db /var/lib/cwl/stgb1e10e92-443b-4938-8ca2-36c2160ca160/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42458/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:07:33,331] [INFO] Task succeeded: Blastn
[2023-03-15 23:07:33,332] [INFO] Selected 25 target genomes.
[2023-03-15 23:07:33,333] [INFO] Target genome list was writen to OceanDNA-b42458/target_genomes_gtdb.txt
[2023-03-15 23:07:33,485] [INFO] Task started: fastANI
[2023-03-15 23:07:33,486] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1b09936-6de5-4433-b39b-189632e2be3b/OceanDNA-b42458.fa --refList OceanDNA-b42458/target_genomes_gtdb.txt --output OceanDNA-b42458/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:07:40,251] [INFO] Task succeeded: fastANI
[2023-03-15 23:07:40,253] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:07:40,254] [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_905182235.1	s__CAJJAM01 sp905182235	83.3848	116	181	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__CAJJAM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015660645.1	s__CAJJAM01 sp015660645	81.5666	124	181	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__CAJJAM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:07:40,254] [INFO] GTDB search result was written to OceanDNA-b42458/result_gtdb.tsv
[2023-03-15 23:07:40,254] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:07:40,254] [INFO] DFAST_QC result json was written to OceanDNA-b42458/dqc_result.json
[2023-03-15 23:07:40,255] [INFO] DFAST_QC completed!
[2023-03-15 23:07:40,255] [INFO] Total running time: 0h0m38s