[2023-03-18 09:41:07,203] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:41:07,203] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:41:07,203] [INFO] DQC Reference Directory: /var/lib/cwl/stgf541de55-54a9-4971-8915-027c4a73a5d1/dqc_reference
[2023-03-18 09:41:08,290] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:41:08,290] [INFO] Task started: Prodigal
[2023-03-18 09:41:08,291] [INFO] Running command: cat /var/lib/cwl/stgb808bb0e-43b0-44c5-bdd0-00a729cebd5e/OceanDNA-b10524.fa | prodigal -d OceanDNA-b10524/cds.fna -a OceanDNA-b10524/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:41:14,204] [INFO] Task succeeded: Prodigal
[2023-03-18 09:41:14,204] [INFO] Task started: HMMsearch
[2023-03-18 09:41:14,204] [INFO] Running command: hmmsearch --tblout OceanDNA-b10524/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf541de55-54a9-4971-8915-027c4a73a5d1/dqc_reference/reference_markers.hmm OceanDNA-b10524/protein.faa > /dev/null
[2023-03-18 09:41:14,364] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:41:14,364] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb808bb0e-43b0-44c5-bdd0-00a729cebd5e/OceanDNA-b10524.fa]
[2023-03-18 09:41:14,377] [INFO] Query marker FASTA was written to OceanDNA-b10524/markers.fasta
[2023-03-18 09:41:14,377] [INFO] Task started: Blastn
[2023-03-18 09:41:14,377] [INFO] Running command: blastn -query OceanDNA-b10524/markers.fasta -db /var/lib/cwl/stgf541de55-54a9-4971-8915-027c4a73a5d1/dqc_reference/reference_markers.fasta -out OceanDNA-b10524/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:14,835] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:14,836] [INFO] Selected 29 target genomes.
[2023-03-18 09:41:14,837] [INFO] Target genome list was writen to OceanDNA-b10524/target_genomes.txt
[2023-03-18 09:41:14,852] [INFO] Task started: fastANI
[2023-03-18 09:41:14,852] [INFO] Running command: fastANI --query /var/lib/cwl/stgb808bb0e-43b0-44c5-bdd0-00a729cebd5e/OceanDNA-b10524.fa --refList OceanDNA-b10524/target_genomes.txt --output OceanDNA-b10524/fastani_result.tsv --threads 1
[2023-03-18 09:41:31,540] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:31,541] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf541de55-54a9-4971-8915-027c4a73a5d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:41:31,541] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf541de55-54a9-4971-8915-027c4a73a5d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:41:31,541] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:41:31,541] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:41:31,541] [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
--------------------------------------------------------------------------------
[2023-03-18 09:41:31,541] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10524/tc_result.tsv
[2023-03-18 09:41:31,541] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:41:31,542] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:41:31,542] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf541de55-54a9-4971-8915-027c4a73a5d1/dqc_reference/checkm_data
[2023-03-18 09:41:31,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:41:31,547] [INFO] Task started: CheckM
[2023-03-18 09:41:31,547] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10524/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10524/checkm_input OceanDNA-b10524/checkm_result
[2023-03-18 09:41:52,668] [INFO] Task succeeded: CheckM
[2023-03-18 09:41:52,669] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.65%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 09:41:52,670] [INFO] ===== Completeness check finished =====
[2023-03-18 09:41:52,671] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:41:52,671] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10524/markers.fasta)
[2023-03-18 09:41:52,671] [INFO] Task started: Blastn
[2023-03-18 09:41:52,671] [INFO] Running command: blastn -query OceanDNA-b10524/markers.fasta -db /var/lib/cwl/stgf541de55-54a9-4971-8915-027c4a73a5d1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10524/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:53,147] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:53,148] [INFO] Selected 19 target genomes.
[2023-03-18 09:41:53,148] [INFO] Target genome list was writen to OceanDNA-b10524/target_genomes_gtdb.txt
[2023-03-18 09:41:53,164] [INFO] Task started: fastANI
[2023-03-18 09:41:53,165] [INFO] Running command: fastANI --query /var/lib/cwl/stgb808bb0e-43b0-44c5-bdd0-00a729cebd5e/OceanDNA-b10524.fa --refList OceanDNA-b10524/target_genomes_gtdb.txt --output OceanDNA-b10524/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:42:00,383] [INFO] Task succeeded: fastANI
[2023-03-18 09:42:00,387] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:42:00,387] [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_002690085.1	s__UBA3537 sp002690085	92.9376	123	174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684355.1	s__UBA3537 sp002684355	92.6654	147	174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	96.40	96.15	0.80	0.77	3	-
GCA_002709185.1	s__UBA3537 sp002709185	87.877	90	174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	98.67	98.67	0.76	0.76	2	-
GCA_002698705.1	s__UBA3537 sp002698705	79.7945	74	174	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	78.0322	66	174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	96.56	95.66	0.77	0.72	3	-
--------------------------------------------------------------------------------
[2023-03-18 09:42:00,387] [INFO] GTDB search result was written to OceanDNA-b10524/result_gtdb.tsv
[2023-03-18 09:42:00,387] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:42:00,388] [INFO] DFAST_QC result json was written to OceanDNA-b10524/dqc_result.json
[2023-03-18 09:42:00,388] [INFO] DFAST_QC completed!
[2023-03-18 09:42:00,388] [INFO] Total running time: 0h0m53s