[2023-03-14 12:57:46,114] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:57:46,115] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:57:46,115] [INFO] DQC Reference Directory: /var/lib/cwl/stg45bfb9b0-0c2e-44d6-b362-585363b175e8/dqc_reference
[2023-03-14 12:57:48,865] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:57:48,865] [INFO] Task started: Prodigal
[2023-03-14 12:57:48,865] [INFO] Running command: cat /var/lib/cwl/stgb78edda5-20aa-4edf-86a1-40f15a61963c/OceanDNA-b23836.fa | prodigal -d OceanDNA-b23836/cds.fna -a OceanDNA-b23836/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:58:05,874] [INFO] Task succeeded: Prodigal
[2023-03-14 12:58:05,874] [INFO] Task started: HMMsearch
[2023-03-14 12:58:05,874] [INFO] Running command: hmmsearch --tblout OceanDNA-b23836/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45bfb9b0-0c2e-44d6-b362-585363b175e8/dqc_reference/reference_markers.hmm OceanDNA-b23836/protein.faa > /dev/null
[2023-03-14 12:58:06,419] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:58:06,419] [INFO] Found 6/6 markers.
[2023-03-14 12:58:06,450] [INFO] Query marker FASTA was written to OceanDNA-b23836/markers.fasta
[2023-03-14 12:58:06,454] [INFO] Task started: Blastn
[2023-03-14 12:58:06,454] [INFO] Running command: blastn -query OceanDNA-b23836/markers.fasta -db /var/lib/cwl/stg45bfb9b0-0c2e-44d6-b362-585363b175e8/dqc_reference/reference_markers.fasta -out OceanDNA-b23836/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:58:08,621] [INFO] Task succeeded: Blastn
[2023-03-14 12:58:08,623] [INFO] Selected 28 target genomes.
[2023-03-14 12:58:08,623] [INFO] Target genome list was writen to OceanDNA-b23836/target_genomes.txt
[2023-03-14 12:58:08,643] [INFO] Task started: fastANI
[2023-03-14 12:58:08,643] [INFO] Running command: fastANI --query /var/lib/cwl/stgb78edda5-20aa-4edf-86a1-40f15a61963c/OceanDNA-b23836.fa --refList OceanDNA-b23836/target_genomes.txt --output OceanDNA-b23836/fastani_result.tsv --threads 1
[2023-03-14 12:58:32,245] [INFO] Task succeeded: fastANI
[2023-03-14 12:58:32,245] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45bfb9b0-0c2e-44d6-b362-585363b175e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:58:32,245] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45bfb9b0-0c2e-44d6-b362-585363b175e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:58:32,251] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:58:32,252] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:58:32,252] [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
Litorimonas taeanensis	strain=DSM 22008	GCA_003634015.1	568099	568099	type	True	77.3276	104	833	95	below_threshold
Robiginitomaculum antarcticum	strain=DSM 21748	GCA_000365025.1	437507	437507	type	True	76.5203	65	833	95	below_threshold
Hellea balneolensis	strain=DSM 19091	GCA_000428525.1	287478	287478	type	True	76.4747	93	833	95	below_threshold
Algimonas arctica	strain=KCTC 32513	GCA_014652695.1	1479486	1479486	type	True	76.4028	52	833	95	below_threshold
Litorimonas cladophorae	strain=KCTC 23968	GCA_014652455.1	1220491	1220491	type	True	76.1865	65	833	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:58:32,252] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23836/tc_result.tsv
[2023-03-14 12:58:32,252] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:58:32,253] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:58:32,253] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45bfb9b0-0c2e-44d6-b362-585363b175e8/dqc_reference/checkm_data
[2023-03-14 12:58:32,254] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:58:32,265] [INFO] Task started: CheckM
[2023-03-14 12:58:32,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23836/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23836/checkm_input OceanDNA-b23836/checkm_result
[2023-03-14 12:59:24,202] [INFO] Task succeeded: CheckM
[2023-03-14 12:59:24,203] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:59:24,205] [INFO] ===== Completeness check finished =====
[2023-03-14 12:59:24,206] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:59:24,206] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23836/markers.fasta)
[2023-03-14 12:59:24,208] [INFO] Task started: Blastn
[2023-03-14 12:59:24,208] [INFO] Running command: blastn -query OceanDNA-b23836/markers.fasta -db /var/lib/cwl/stg45bfb9b0-0c2e-44d6-b362-585363b175e8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23836/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:59:25,484] [INFO] Task succeeded: Blastn
[2023-03-14 12:59:25,485] [INFO] Selected 29 target genomes.
[2023-03-14 12:59:25,485] [INFO] Target genome list was writen to OceanDNA-b23836/target_genomes_gtdb.txt
[2023-03-14 12:59:25,617] [INFO] Task started: fastANI
[2023-03-14 12:59:25,617] [INFO] Running command: fastANI --query /var/lib/cwl/stgb78edda5-20aa-4edf-86a1-40f15a61963c/OceanDNA-b23836.fa --refList OceanDNA-b23836/target_genomes_gtdb.txt --output OceanDNA-b23836/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:59:45,421] [INFO] Task succeeded: fastANI
[2023-03-14 12:59:45,425] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:59:45,426] [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
GCF_003634015.1	s__Litorimonas taeanensis	77.3276	104	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Litorimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000365025.1	s__Robiginitomaculum antarcticum	76.5203	65	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Robiginitomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428525.1	s__Hellea balneolensis	76.4747	93	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hellea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652695.1	s__Litorimonas arctica	76.4403	51	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Litorimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002305.1	s__JACOMS01 sp013002305	76.4228	56	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__JACOMS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652455.1	s__Litorimonas cladophorae	76.1865	65	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Litorimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:59:45,426] [INFO] GTDB search result was written to OceanDNA-b23836/result_gtdb.tsv
[2023-03-14 12:59:45,426] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:59:45,427] [INFO] DFAST_QC result json was written to OceanDNA-b23836/dqc_result.json
[2023-03-14 12:59:45,427] [INFO] DFAST_QC completed!
[2023-03-14 12:59:45,427] [INFO] Total running time: 0h1m59s