[2023-03-17 07:28:31,297] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:28:31,297] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:28:31,297] [INFO] DQC Reference Directory: /var/lib/cwl/stg48173d70-d095-455d-8d23-21b7c412a515/dqc_reference
[2023-03-17 07:28:33,079] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:28:33,079] [INFO] Task started: Prodigal
[2023-03-17 07:28:33,079] [INFO] Running command: cat /var/lib/cwl/stg1873ba7c-9a1e-486d-8281-78d3cc79523b/OceanDNA-b10525.fa | prodigal -d OceanDNA-b10525/cds.fna -a OceanDNA-b10525/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:28:39,438] [INFO] Task succeeded: Prodigal
[2023-03-17 07:28:39,438] [INFO] Task started: HMMsearch
[2023-03-17 07:28:39,438] [INFO] Running command: hmmsearch --tblout OceanDNA-b10525/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48173d70-d095-455d-8d23-21b7c412a515/dqc_reference/reference_markers.hmm OceanDNA-b10525/protein.faa > /dev/null
[2023-03-17 07:28:39,588] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:28:39,589] [INFO] Found 6/6 markers.
[2023-03-17 07:28:39,600] [INFO] Query marker FASTA was written to OceanDNA-b10525/markers.fasta
[2023-03-17 07:28:39,600] [INFO] Task started: Blastn
[2023-03-17 07:28:39,600] [INFO] Running command: blastn -query OceanDNA-b10525/markers.fasta -db /var/lib/cwl/stg48173d70-d095-455d-8d23-21b7c412a515/dqc_reference/reference_markers.fasta -out OceanDNA-b10525/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:28:40,168] [INFO] Task succeeded: Blastn
[2023-03-17 07:28:40,169] [INFO] Selected 36 target genomes.
[2023-03-17 07:28:40,169] [INFO] Target genome list was writen to OceanDNA-b10525/target_genomes.txt
[2023-03-17 07:28:40,188] [INFO] Task started: fastANI
[2023-03-17 07:28:40,188] [INFO] Running command: fastANI --query /var/lib/cwl/stg1873ba7c-9a1e-486d-8281-78d3cc79523b/OceanDNA-b10525.fa --refList OceanDNA-b10525/target_genomes.txt --output OceanDNA-b10525/fastani_result.tsv --threads 1
[2023-03-17 07:29:04,426] [INFO] Task succeeded: fastANI
[2023-03-17 07:29:04,426] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48173d70-d095-455d-8d23-21b7c412a515/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:29:04,426] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48173d70-d095-455d-8d23-21b7c412a515/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:29:04,427] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:29:04,427] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:29:04,427] [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 07:29:04,427] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10525/tc_result.tsv
[2023-03-17 07:29:04,427] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:29:04,427] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:29:04,427] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48173d70-d095-455d-8d23-21b7c412a515/dqc_reference/checkm_data
[2023-03-17 07:29:04,430] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:29:04,433] [INFO] Task started: CheckM
[2023-03-17 07:29:04,433] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10525/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10525/checkm_input OceanDNA-b10525/checkm_result
[2023-03-17 07:29:26,769] [INFO] Task succeeded: CheckM
[2023-03-17 07:29:26,770] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.17%
Contamintation: 5.56%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 07:29:26,772] [INFO] ===== Completeness check finished =====
[2023-03-17 07:29:26,772] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:29:26,772] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10525/markers.fasta)
[2023-03-17 07:29:26,772] [INFO] Task started: Blastn
[2023-03-17 07:29:26,772] [INFO] Running command: blastn -query OceanDNA-b10525/markers.fasta -db /var/lib/cwl/stg48173d70-d095-455d-8d23-21b7c412a515/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10525/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:29:27,637] [INFO] Task succeeded: Blastn
[2023-03-17 07:29:27,638] [INFO] Selected 22 target genomes.
[2023-03-17 07:29:27,638] [INFO] Target genome list was writen to OceanDNA-b10525/target_genomes_gtdb.txt
[2023-03-17 07:29:27,801] [INFO] Task started: fastANI
[2023-03-17 07:29:27,801] [INFO] Running command: fastANI --query /var/lib/cwl/stg1873ba7c-9a1e-486d-8281-78d3cc79523b/OceanDNA-b10525.fa --refList OceanDNA-b10525/target_genomes_gtdb.txt --output OceanDNA-b10525/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:29:37,951] [INFO] Task succeeded: fastANI
[2023-03-17 07:29:37,955] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:29:37,956] [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_002684355.1	s__UBA3537 sp002684355	91.6663	168	202	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	96.40	96.15	0.80	0.77	3	-
GCA_002690085.1	s__UBA3537 sp002690085	91.2767	143	202	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709185.1	s__UBA3537 sp002709185	87.6907	110	202	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	98.67	98.67	0.76	0.76	2	-
GCA_902516685.1	s__UBA3537 sp902516685	82.1103	54	202	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002725015.1	s__UBA3537 sp002725015	77.6972	76	202	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	96.56	95.66	0.77	0.72	3	-
GCF_001735715.1	s__GCA001735715 sp001735715	77.4988	54	202	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA001735715	95.0	98.19	98.19	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-17 07:29:37,956] [INFO] GTDB search result was written to OceanDNA-b10525/result_gtdb.tsv
[2023-03-17 07:29:37,956] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:29:37,957] [INFO] DFAST_QC result json was written to OceanDNA-b10525/dqc_result.json
[2023-03-17 07:29:37,957] [INFO] DFAST_QC completed!
[2023-03-17 07:29:37,957] [INFO] Total running time: 0h1m7s