[2023-03-14 10:55:58,922] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,922] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,922] [INFO] DQC Reference Directory: /var/lib/cwl/stg837b69d1-3edc-4da8-8a2e-e687c3e5bb13/dqc_reference
[2023-03-14 10:56:00,680] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,680] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,680] [INFO] Running command: cat /var/lib/cwl/stg915da912-b2a4-4693-8b6c-857b0bdaa6dc/OceanDNA-b42532.fa | prodigal -d OceanDNA-b42532/cds.fna -a OceanDNA-b42532/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:04,864] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:04,864] [INFO] Task started: HMMsearch
[2023-03-14 10:56:04,864] [INFO] Running command: hmmsearch --tblout OceanDNA-b42532/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg837b69d1-3edc-4da8-8a2e-e687c3e5bb13/dqc_reference/reference_markers.hmm OceanDNA-b42532/protein.faa > /dev/null
[2023-03-14 10:56:05,009] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:05,009] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg915da912-b2a4-4693-8b6c-857b0bdaa6dc/OceanDNA-b42532.fa]
[2023-03-14 10:56:05,017] [INFO] Query marker FASTA was written to OceanDNA-b42532/markers.fasta
[2023-03-14 10:56:05,017] [INFO] Task started: Blastn
[2023-03-14 10:56:05,017] [INFO] Running command: blastn -query OceanDNA-b42532/markers.fasta -db /var/lib/cwl/stg837b69d1-3edc-4da8-8a2e-e687c3e5bb13/dqc_reference/reference_markers.fasta -out OceanDNA-b42532/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:05,509] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:05,510] [INFO] Selected 17 target genomes.
[2023-03-14 10:56:05,510] [INFO] Target genome list was writen to OceanDNA-b42532/target_genomes.txt
[2023-03-14 10:56:05,519] [INFO] Task started: fastANI
[2023-03-14 10:56:05,519] [INFO] Running command: fastANI --query /var/lib/cwl/stg915da912-b2a4-4693-8b6c-857b0bdaa6dc/OceanDNA-b42532.fa --refList OceanDNA-b42532/target_genomes.txt --output OceanDNA-b42532/fastani_result.tsv --threads 1
[2023-03-14 10:56:12,293] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:12,294] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg837b69d1-3edc-4da8-8a2e-e687c3e5bb13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:12,294] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg837b69d1-3edc-4da8-8a2e-e687c3e5bb13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:12,294] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:12,294] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 10:56:12,294] [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
--------------------------------------------------------------------------------
[2023-03-14 10:56:12,295] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42532/tc_result.tsv
[2023-03-14 10:56:12,295] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:12,295] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:12,295] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg837b69d1-3edc-4da8-8a2e-e687c3e5bb13/dqc_reference/checkm_data
[2023-03-14 10:56:12,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:12,810] [INFO] Task started: CheckM
[2023-03-14 10:56:12,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42532/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42532/checkm_input OceanDNA-b42532/checkm_result
[2023-03-14 10:56:29,939] [INFO] Task succeeded: CheckM
[2023-03-14 10:56:29,939] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.63%
Contamintation: 4.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 10:56:29,941] [INFO] ===== Completeness check finished =====
[2023-03-14 10:56:29,941] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:56:29,941] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42532/markers.fasta)
[2023-03-14 10:56:29,941] [INFO] Task started: Blastn
[2023-03-14 10:56:29,942] [INFO] Running command: blastn -query OceanDNA-b42532/markers.fasta -db /var/lib/cwl/stg837b69d1-3edc-4da8-8a2e-e687c3e5bb13/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42532/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:30,371] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:30,372] [INFO] Selected 20 target genomes.
[2023-03-14 10:56:30,372] [INFO] Target genome list was writen to OceanDNA-b42532/target_genomes_gtdb.txt
[2023-03-14 10:56:30,403] [INFO] Task started: fastANI
[2023-03-14 10:56:30,403] [INFO] Running command: fastANI --query /var/lib/cwl/stg915da912-b2a4-4693-8b6c-857b0bdaa6dc/OceanDNA-b42532.fa --refList OceanDNA-b42532/target_genomes_gtdb.txt --output OceanDNA-b42532/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:56:37,261] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:37,267] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 10:56:37,267] [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_003212335.1	s__GCA-2707915 sp003212335	93.5299	223	263	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	96.12	95.05	0.82	0.77	11	-
GCA_004214065.1	s__GCA-2707915 sp004214065	78.7081	90	263	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	97.49	97.45	0.77	0.70	3	-
GCA_902574355.1	s__GCA-2707915 sp902574355	77.6945	107	263	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902604855.1	s__GCA-2707915 sp902604855	77.6273	91	263	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902542325.1	s__GCA-2707915 sp902542325	77.4945	90	263	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	99.62	99.62	0.80	0.80	2	-
GCA_902517565.1	s__GCA-2707915 sp902517565	77.4365	87	263	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902618945.1	s__GCA-2707915 sp902618945	77.3425	88	263	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	95.64	95.64	0.79	0.79	2	-
GCA_902630715.1	s__GCA-2707915 sp902630715	77.1774	62	263	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 10:56:37,267] [INFO] GTDB search result was written to OceanDNA-b42532/result_gtdb.tsv
[2023-03-14 10:56:37,267] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:56:37,268] [INFO] DFAST_QC result json was written to OceanDNA-b42532/dqc_result.json
[2023-03-14 10:56:37,268] [INFO] DFAST_QC completed!
[2023-03-14 10:56:37,268] [INFO] Total running time: 0h0m38s