[2023-03-16 10:06:33,503] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:06:33,503] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:06:33,503] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a865bdd-ef70-4b84-b7d3-a35b207b754a/dqc_reference
[2023-03-16 10:06:34,609] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:06:34,609] [INFO] Task started: Prodigal
[2023-03-16 10:06:34,609] [INFO] Running command: cat /var/lib/cwl/stg8b5f67fd-e181-450f-b56e-07df230c6b73/OceanDNA-b29639.fa | prodigal -d OceanDNA-b29639/cds.fna -a OceanDNA-b29639/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:06:44,529] [INFO] Task succeeded: Prodigal
[2023-03-16 10:06:44,530] [INFO] Task started: HMMsearch
[2023-03-16 10:06:44,530] [INFO] Running command: hmmsearch --tblout OceanDNA-b29639/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a865bdd-ef70-4b84-b7d3-a35b207b754a/dqc_reference/reference_markers.hmm OceanDNA-b29639/protein.faa > /dev/null
[2023-03-16 10:06:44,685] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:06:44,686] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8b5f67fd-e181-450f-b56e-07df230c6b73/OceanDNA-b29639.fa]
[2023-03-16 10:06:44,699] [INFO] Query marker FASTA was written to OceanDNA-b29639/markers.fasta
[2023-03-16 10:06:44,700] [INFO] Task started: Blastn
[2023-03-16 10:06:44,700] [INFO] Running command: blastn -query OceanDNA-b29639/markers.fasta -db /var/lib/cwl/stg6a865bdd-ef70-4b84-b7d3-a35b207b754a/dqc_reference/reference_markers.fasta -out OceanDNA-b29639/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:06:45,195] [INFO] Task succeeded: Blastn
[2023-03-16 10:06:45,196] [INFO] Selected 20 target genomes.
[2023-03-16 10:06:45,196] [INFO] Target genome list was writen to OceanDNA-b29639/target_genomes.txt
[2023-03-16 10:06:45,207] [INFO] Task started: fastANI
[2023-03-16 10:06:45,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b5f67fd-e181-450f-b56e-07df230c6b73/OceanDNA-b29639.fa --refList OceanDNA-b29639/target_genomes.txt --output OceanDNA-b29639/fastani_result.tsv --threads 1
[2023-03-16 10:06:56,768] [INFO] Task succeeded: fastANI
[2023-03-16 10:06:56,768] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a865bdd-ef70-4b84-b7d3-a35b207b754a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:06:56,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a865bdd-ef70-4b84-b7d3-a35b207b754a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:06:56,771] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:06:56,771] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:06:56,772] [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
Planktomarina temperata	strain=RCA23	GCA_000738435.1	1284658	1284658	type	True	76.9157	123	533	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:06:56,772] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29639/tc_result.tsv
[2023-03-16 10:06:56,772] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:06:56,772] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:06:56,772] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a865bdd-ef70-4b84-b7d3-a35b207b754a/dqc_reference/checkm_data
[2023-03-16 10:06:56,773] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:06:56,776] [INFO] Task started: CheckM
[2023-03-16 10:06:56,776] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29639/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29639/checkm_input OceanDNA-b29639/checkm_result
[2023-03-16 10:07:25,770] [INFO] Task succeeded: CheckM
[2023-03-16 10:07:25,770] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.40%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 10:07:25,772] [INFO] ===== Completeness check finished =====
[2023-03-16 10:07:25,772] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:07:25,773] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29639/markers.fasta)
[2023-03-16 10:07:25,774] [INFO] Task started: Blastn
[2023-03-16 10:07:25,774] [INFO] Running command: blastn -query OceanDNA-b29639/markers.fasta -db /var/lib/cwl/stg6a865bdd-ef70-4b84-b7d3-a35b207b754a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29639/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:07:26,454] [INFO] Task succeeded: Blastn
[2023-03-16 10:07:26,455] [INFO] Selected 16 target genomes.
[2023-03-16 10:07:26,455] [INFO] Target genome list was writen to OceanDNA-b29639/target_genomes_gtdb.txt
[2023-03-16 10:07:26,467] [INFO] Task started: fastANI
[2023-03-16 10:07:26,467] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b5f67fd-e181-450f-b56e-07df230c6b73/OceanDNA-b29639.fa --refList OceanDNA-b29639/target_genomes_gtdb.txt --output OceanDNA-b29639/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:07:33,787] [INFO] Task succeeded: fastANI
[2023-03-16 10:07:33,792] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:07:33,793] [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_905182195.1	s__Planktomarina sp905182195	99.38	520	533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905182535.1	s__Planktomarina sp905182535	80.7207	280	533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	98.42	98.42	0.82	0.82	2	-
GCA_000981705.1	s__Planktomarina sp000981705	79.6876	246	533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	98.80	98.80	0.86	0.86	2	-
GCA_905182455.1	s__Planktomarina sp905182455	79.4655	256	533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181815.1	s__Planktomarina sp905181815	77.2765	120	533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780825.1	s__Planktomarina sp016780825	76.9194	108	533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000738435.1	s__Planktomarina temperata	76.9157	123	533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	98.99	97.76	0.97	0.80	20	-
GCA_002683685.1	s__Planktomarina sp002683685	76.541	86	533	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	95.59	95.45	0.70	0.67	6	-
--------------------------------------------------------------------------------
[2023-03-16 10:07:33,793] [INFO] GTDB search result was written to OceanDNA-b29639/result_gtdb.tsv
[2023-03-16 10:07:33,793] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:07:33,794] [INFO] DFAST_QC result json was written to OceanDNA-b29639/dqc_result.json
[2023-03-16 10:07:33,794] [INFO] DFAST_QC completed!
[2023-03-16 10:07:33,794] [INFO] Total running time: 0h1m0s