[2023-03-19 00:22:37,638] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:22:37,639] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:22:37,639] [INFO] DQC Reference Directory: /var/lib/cwl/stg99a25785-e400-4013-b580-d2283d1f4e65/dqc_reference
[2023-03-19 00:22:38,757] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:22:38,758] [INFO] Task started: Prodigal
[2023-03-19 00:22:38,758] [INFO] Running command: cat /var/lib/cwl/stg5e817865-d2d1-4533-968c-a7654b7171e3/OceanDNA-b11068.fa | prodigal -d OceanDNA-b11068/cds.fna -a OceanDNA-b11068/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:22:48,560] [INFO] Task succeeded: Prodigal
[2023-03-19 00:22:48,561] [INFO] Task started: HMMsearch
[2023-03-19 00:22:48,561] [INFO] Running command: hmmsearch --tblout OceanDNA-b11068/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99a25785-e400-4013-b580-d2283d1f4e65/dqc_reference/reference_markers.hmm OceanDNA-b11068/protein.faa > /dev/null
[2023-03-19 00:22:48,747] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:22:48,747] [INFO] Found 6/6 markers.
[2023-03-19 00:22:48,757] [INFO] Query marker FASTA was written to OceanDNA-b11068/markers.fasta
[2023-03-19 00:22:48,759] [INFO] Task started: Blastn
[2023-03-19 00:22:48,759] [INFO] Running command: blastn -query OceanDNA-b11068/markers.fasta -db /var/lib/cwl/stg99a25785-e400-4013-b580-d2283d1f4e65/dqc_reference/reference_markers.fasta -out OceanDNA-b11068/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:22:49,370] [INFO] Task succeeded: Blastn
[2023-03-19 00:22:49,371] [INFO] Selected 27 target genomes.
[2023-03-19 00:22:49,371] [INFO] Target genome list was writen to OceanDNA-b11068/target_genomes.txt
[2023-03-19 00:22:49,456] [INFO] Task started: fastANI
[2023-03-19 00:22:49,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e817865-d2d1-4533-968c-a7654b7171e3/OceanDNA-b11068.fa --refList OceanDNA-b11068/target_genomes.txt --output OceanDNA-b11068/fastani_result.tsv --threads 1
[2023-03-19 00:23:03,473] [INFO] Task succeeded: fastANI
[2023-03-19 00:23:03,474] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99a25785-e400-4013-b580-d2283d1f4e65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:23:03,474] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99a25785-e400-4013-b580-d2283d1f4e65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:23:03,474] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:23:03,474] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:23:03,474] [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
--------------------------------------------------------------------------------
[2023-03-19 00:23:03,474] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11068/tc_result.tsv
[2023-03-19 00:23:03,474] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:23:03,474] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:23:03,475] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99a25785-e400-4013-b580-d2283d1f4e65/dqc_reference/checkm_data
[2023-03-19 00:23:03,525] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:23:03,528] [INFO] Task started: CheckM
[2023-03-19 00:23:03,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11068/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11068/checkm_input OceanDNA-b11068/checkm_result
[2023-03-19 00:23:34,980] [INFO] Task succeeded: CheckM
[2023-03-19 00:23:34,980] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.26%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:23:34,982] [INFO] ===== Completeness check finished =====
[2023-03-19 00:23:34,982] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:23:34,982] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11068/markers.fasta)
[2023-03-19 00:23:34,984] [INFO] Task started: Blastn
[2023-03-19 00:23:34,984] [INFO] Running command: blastn -query OceanDNA-b11068/markers.fasta -db /var/lib/cwl/stg99a25785-e400-4013-b580-d2283d1f4e65/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11068/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:23:36,189] [INFO] Task succeeded: Blastn
[2023-03-19 00:23:36,189] [INFO] Selected 6 target genomes.
[2023-03-19 00:23:36,189] [INFO] Target genome list was writen to OceanDNA-b11068/target_genomes_gtdb.txt
[2023-03-19 00:23:36,265] [INFO] Task started: fastANI
[2023-03-19 00:23:36,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e817865-d2d1-4533-968c-a7654b7171e3/OceanDNA-b11068.fa --refList OceanDNA-b11068/target_genomes_gtdb.txt --output OceanDNA-b11068/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:23:38,172] [INFO] Task succeeded: fastANI
[2023-03-19 00:23:38,176] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:23:38,177] [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_009886265.1	s__UBA7446 sp009886265	99.2496	327	388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002862705.1	s__UBA7446 sp002862705	91.183	338	388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.06	98.27	0.87	0.83	14	-
GCA_002313325.1	s__UBA7446 sp002313325	89.1157	253	388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.90	99.90	0.92	0.92	2	-
GCA_002698745.1	s__UBA7446 sp002698745	86.0725	274	388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862645.1	s__UBA7446 sp002862645	85.8483	304	388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	95.15	95.15	0.79	0.79	2	-
GCA_009937085.1	s__UBA7446 sp009937085	78.799	140	388	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:23:38,177] [INFO] GTDB search result was written to OceanDNA-b11068/result_gtdb.tsv
[2023-03-19 00:23:38,177] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:23:38,177] [INFO] DFAST_QC result json was written to OceanDNA-b11068/dqc_result.json
[2023-03-19 00:23:38,178] [INFO] DFAST_QC completed!
[2023-03-19 00:23:38,178] [INFO] Total running time: 0h1m1s