[2023-03-17 07:44:38,661] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:44:38,661] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:44:38,661] [INFO] DQC Reference Directory: /var/lib/cwl/stg163a9759-7e1a-43f9-8020-c2ed5794c197/dqc_reference
[2023-03-17 07:44:39,801] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:44:39,801] [INFO] Task started: Prodigal
[2023-03-17 07:44:39,801] [INFO] Running command: cat /var/lib/cwl/stge6e8e277-c8b6-474a-b678-7c80d7d5ade3/OceanDNA-b4882.fa | prodigal -d OceanDNA-b4882/cds.fna -a OceanDNA-b4882/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:44:44,146] [INFO] Task succeeded: Prodigal
[2023-03-17 07:44:44,146] [INFO] Task started: HMMsearch
[2023-03-17 07:44:44,146] [INFO] Running command: hmmsearch --tblout OceanDNA-b4882/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg163a9759-7e1a-43f9-8020-c2ed5794c197/dqc_reference/reference_markers.hmm OceanDNA-b4882/protein.faa > /dev/null
[2023-03-17 07:44:44,293] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:44:44,293] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge6e8e277-c8b6-474a-b678-7c80d7d5ade3/OceanDNA-b4882.fa]
[2023-03-17 07:44:44,302] [INFO] Query marker FASTA was written to OceanDNA-b4882/markers.fasta
[2023-03-17 07:44:44,302] [INFO] Task started: Blastn
[2023-03-17 07:44:44,302] [INFO] Running command: blastn -query OceanDNA-b4882/markers.fasta -db /var/lib/cwl/stg163a9759-7e1a-43f9-8020-c2ed5794c197/dqc_reference/reference_markers.fasta -out OceanDNA-b4882/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:44:45,370] [INFO] Task succeeded: Blastn
[2023-03-17 07:44:45,371] [INFO] Selected 15 target genomes.
[2023-03-17 07:44:45,371] [INFO] Target genome list was writen to OceanDNA-b4882/target_genomes.txt
[2023-03-17 07:44:45,400] [INFO] Task started: fastANI
[2023-03-17 07:44:45,400] [INFO] Running command: fastANI --query /var/lib/cwl/stge6e8e277-c8b6-474a-b678-7c80d7d5ade3/OceanDNA-b4882.fa --refList OceanDNA-b4882/target_genomes.txt --output OceanDNA-b4882/fastani_result.tsv --threads 1
[2023-03-17 07:44:53,308] [INFO] Task succeeded: fastANI
[2023-03-17 07:44:53,308] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg163a9759-7e1a-43f9-8020-c2ed5794c197/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:44:53,309] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg163a9759-7e1a-43f9-8020-c2ed5794c197/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:44:53,309] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:44:53,309] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:44:53,309] [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
--------------------------------------------------------------------------------
[2023-03-17 07:44:53,309] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4882/tc_result.tsv
[2023-03-17 07:44:53,309] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:44:53,309] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:44:53,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg163a9759-7e1a-43f9-8020-c2ed5794c197/dqc_reference/checkm_data
[2023-03-17 07:44:53,312] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:44:53,314] [INFO] Task started: CheckM
[2023-03-17 07:44:53,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4882/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4882/checkm_input OceanDNA-b4882/checkm_result
[2023-03-17 07:45:10,379] [INFO] Task succeeded: CheckM
[2023-03-17 07:45:10,380] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.26%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:45:10,381] [INFO] ===== Completeness check finished =====
[2023-03-17 07:45:10,381] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:45:10,382] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4882/markers.fasta)
[2023-03-17 07:45:10,382] [INFO] Task started: Blastn
[2023-03-17 07:45:10,382] [INFO] Running command: blastn -query OceanDNA-b4882/markers.fasta -db /var/lib/cwl/stg163a9759-7e1a-43f9-8020-c2ed5794c197/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4882/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:45:10,994] [INFO] Task succeeded: Blastn
[2023-03-17 07:45:10,994] [INFO] Selected 12 target genomes.
[2023-03-17 07:45:10,994] [INFO] Target genome list was writen to OceanDNA-b4882/target_genomes_gtdb.txt
[2023-03-17 07:45:11,016] [INFO] Task started: fastANI
[2023-03-17 07:45:11,016] [INFO] Running command: fastANI --query /var/lib/cwl/stge6e8e277-c8b6-474a-b678-7c80d7d5ade3/OceanDNA-b4882.fa --refList OceanDNA-b4882/target_genomes_gtdb.txt --output OceanDNA-b4882/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:45:14,141] [INFO] Task succeeded: fastANI
[2023-03-17 07:45:14,144] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:45:14,145] [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_002730985.1	s__BACL11 sp002730985	81.1027	116	183	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	97.22	97.22	0.84	0.84	2	-
GCA_002693745.1	s__BACL11 sp002693745	78.2379	63	183	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	98.58	98.58	0.90	0.90	2	-
GCA_905478185.1	s__UWMA-0277 sp905478185	76.8751	56	183	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	96.67	96.67	0.88	0.88	2	-
GCA_905478765.1	s__UWMA-0277 sp905478765	76.7114	67	183	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:45:14,145] [INFO] GTDB search result was written to OceanDNA-b4882/result_gtdb.tsv
[2023-03-17 07:45:14,145] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:45:14,146] [INFO] DFAST_QC result json was written to OceanDNA-b4882/dqc_result.json
[2023-03-17 07:45:14,146] [INFO] DFAST_QC completed!
[2023-03-17 07:45:14,146] [INFO] Total running time: 0h0m35s