[2023-03-17 09:41:39,965] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:41:39,969] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:41:39,969] [INFO] DQC Reference Directory: /var/lib/cwl/stgde56c7ce-c138-4606-9037-ce5a1a189340/dqc_reference
[2023-03-17 09:41:41,756] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:41:41,757] [INFO] Task started: Prodigal
[2023-03-17 09:41:41,757] [INFO] Running command: cat /var/lib/cwl/stg07097028-0e7c-4cae-b132-1712801d232a/OceanDNA-b5161.fa | prodigal -d OceanDNA-b5161/cds.fna -a OceanDNA-b5161/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:41:49,728] [INFO] Task succeeded: Prodigal
[2023-03-17 09:41:49,728] [INFO] Task started: HMMsearch
[2023-03-17 09:41:49,728] [INFO] Running command: hmmsearch --tblout OceanDNA-b5161/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde56c7ce-c138-4606-9037-ce5a1a189340/dqc_reference/reference_markers.hmm OceanDNA-b5161/protein.faa > /dev/null
[2023-03-17 09:41:49,918] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:41:49,918] [INFO] Found 6/6 markers.
[2023-03-17 09:41:49,932] [INFO] Query marker FASTA was written to OceanDNA-b5161/markers.fasta
[2023-03-17 09:41:49,933] [INFO] Task started: Blastn
[2023-03-17 09:41:49,933] [INFO] Running command: blastn -query OceanDNA-b5161/markers.fasta -db /var/lib/cwl/stgde56c7ce-c138-4606-9037-ce5a1a189340/dqc_reference/reference_markers.fasta -out OceanDNA-b5161/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:41:50,495] [INFO] Task succeeded: Blastn
[2023-03-17 09:41:50,497] [INFO] Selected 25 target genomes.
[2023-03-17 09:41:50,498] [INFO] Target genome list was writen to OceanDNA-b5161/target_genomes.txt
[2023-03-17 09:41:50,673] [INFO] Task started: fastANI
[2023-03-17 09:41:50,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg07097028-0e7c-4cae-b132-1712801d232a/OceanDNA-b5161.fa --refList OceanDNA-b5161/target_genomes.txt --output OceanDNA-b5161/fastani_result.tsv --threads 1
[2023-03-17 09:42:04,275] [INFO] Task succeeded: fastANI
[2023-03-17 09:42:04,275] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde56c7ce-c138-4606-9037-ce5a1a189340/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:42:04,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde56c7ce-c138-4606-9037-ce5a1a189340/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:42:04,276] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:42:04,276] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:42:04,276] [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 09:42:04,276] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5161/tc_result.tsv
[2023-03-17 09:42:04,276] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:42:04,276] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:42:04,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde56c7ce-c138-4606-9037-ce5a1a189340/dqc_reference/checkm_data
[2023-03-17 09:42:04,279] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:42:04,342] [INFO] Task started: CheckM
[2023-03-17 09:42:04,342] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5161/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5161/checkm_input OceanDNA-b5161/checkm_result
[2023-03-17 09:42:29,345] [INFO] Task succeeded: CheckM
[2023-03-17 09:42:29,345] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 09:42:29,379] [INFO] ===== Completeness check finished =====
[2023-03-17 09:42:29,379] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:42:29,380] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5161/markers.fasta)
[2023-03-17 09:42:29,380] [INFO] Task started: Blastn
[2023-03-17 09:42:29,381] [INFO] Running command: blastn -query OceanDNA-b5161/markers.fasta -db /var/lib/cwl/stgde56c7ce-c138-4606-9037-ce5a1a189340/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5161/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:42:30,304] [INFO] Task succeeded: Blastn
[2023-03-17 09:42:30,308] [INFO] Selected 29 target genomes.
[2023-03-17 09:42:30,308] [INFO] Target genome list was writen to OceanDNA-b5161/target_genomes_gtdb.txt
[2023-03-17 09:42:30,762] [INFO] Task started: fastANI
[2023-03-17 09:42:30,762] [INFO] Running command: fastANI --query /var/lib/cwl/stg07097028-0e7c-4cae-b132-1712801d232a/OceanDNA-b5161.fa --refList OceanDNA-b5161/target_genomes_gtdb.txt --output OceanDNA-b5161/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:42:39,855] [INFO] Task succeeded: fastANI
[2023-03-17 09:42:39,858] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 09:42:39,858] [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_905181585.1	s__CAJIYG01 sp905181585	75.9128	60	440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__CAJIYG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478555.1	s__GCA-002697625 sp905478555	75.4968	52	440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	96.63	96.63	0.87	0.87	2	-
GCA_018652335.1	s__GCA-2683775 sp018652335	75.4873	50	440	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2683775	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:42:39,858] [INFO] GTDB search result was written to OceanDNA-b5161/result_gtdb.tsv
[2023-03-17 09:42:39,858] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:42:39,859] [INFO] DFAST_QC result json was written to OceanDNA-b5161/dqc_result.json
[2023-03-17 09:42:39,859] [INFO] DFAST_QC completed!
[2023-03-17 09:42:39,859] [INFO] Total running time: 0h0m60s