[2023-06-13 07:31:58,340] [INFO] DFAST_QC pipeline started.
[2023-06-13 07:31:58,346] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 07:31:58,346] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1b24921-b26f-4a4e-a235-2a89a73c6dae/dqc_reference
[2023-06-13 07:31:59,622] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 07:31:59,623] [INFO] Task started: Prodigal
[2023-06-13 07:31:59,623] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b808f42-4cc6-4751-b104-e98e6ace02f3/GCA_022425345.1_ASM2242534v1_genomic.fna.gz | prodigal -d GCA_022425345.1_ASM2242534v1_genomic.fna/cds.fna -a GCA_022425345.1_ASM2242534v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 07:32:03,946] [INFO] Task succeeded: Prodigal
[2023-06-13 07:32:03,947] [INFO] Task started: HMMsearch
[2023-06-13 07:32:03,947] [INFO] Running command: hmmsearch --tblout GCA_022425345.1_ASM2242534v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1b24921-b26f-4a4e-a235-2a89a73c6dae/dqc_reference/reference_markers.hmm GCA_022425345.1_ASM2242534v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 07:32:04,150] [INFO] Task succeeded: HMMsearch
[2023-06-13 07:32:04,151] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg3b808f42-4cc6-4751-b104-e98e6ace02f3/GCA_022425345.1_ASM2242534v1_genomic.fna.gz]
[2023-06-13 07:32:04,186] [INFO] Query marker FASTA was written to GCA_022425345.1_ASM2242534v1_genomic.fna/markers.fasta
[2023-06-13 07:32:04,186] [INFO] Task started: Blastn
[2023-06-13 07:32:04,187] [INFO] Running command: blastn -query GCA_022425345.1_ASM2242534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1b24921-b26f-4a4e-a235-2a89a73c6dae/dqc_reference/reference_markers.fasta -out GCA_022425345.1_ASM2242534v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 07:32:04,680] [INFO] Task succeeded: Blastn
[2023-06-13 07:32:04,684] [INFO] Selected 14 target genomes.
[2023-06-13 07:32:04,685] [INFO] Target genome list was writen to GCA_022425345.1_ASM2242534v1_genomic.fna/target_genomes.txt
[2023-06-13 07:32:04,687] [INFO] Task started: fastANI
[2023-06-13 07:32:04,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b808f42-4cc6-4751-b104-e98e6ace02f3/GCA_022425345.1_ASM2242534v1_genomic.fna.gz --refList GCA_022425345.1_ASM2242534v1_genomic.fna/target_genomes.txt --output GCA_022425345.1_ASM2242534v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 07:32:12,684] [INFO] Task succeeded: fastANI
[2023-06-13 07:32:12,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1b24921-b26f-4a4e-a235-2a89a73c6dae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 07:32:12,686] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1b24921-b26f-4a4e-a235-2a89a73c6dae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 07:32:12,692] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 07:32:12,693] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 07:32:12,693] [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	97.2851	394	406	95	conclusive
--------------------------------------------------------------------------------
[2023-06-13 07:32:12,695] [INFO] DFAST Taxonomy check result was written to GCA_022425345.1_ASM2242534v1_genomic.fna/tc_result.tsv
[2023-06-13 07:32:12,696] [INFO] ===== Taxonomy check completed =====
[2023-06-13 07:32:12,696] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 07:32:12,696] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1b24921-b26f-4a4e-a235-2a89a73c6dae/dqc_reference/checkm_data
[2023-06-13 07:32:12,698] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 07:32:12,721] [INFO] Task started: CheckM
[2023-06-13 07:32:12,721] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022425345.1_ASM2242534v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022425345.1_ASM2242534v1_genomic.fna/checkm_input GCA_022425345.1_ASM2242534v1_genomic.fna/checkm_result
[2023-06-13 07:32:32,770] [INFO] Task succeeded: CheckM
[2023-06-13 07:32:32,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 07:32:32,792] [INFO] ===== Completeness check finished =====
[2023-06-13 07:32:32,792] [INFO] ===== Start GTDB Search =====
[2023-06-13 07:32:32,793] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022425345.1_ASM2242534v1_genomic.fna/markers.fasta)
[2023-06-13 07:32:32,793] [INFO] Task started: Blastn
[2023-06-13 07:32:32,793] [INFO] Running command: blastn -query GCA_022425345.1_ASM2242534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1b24921-b26f-4a4e-a235-2a89a73c6dae/dqc_reference/reference_markers_gtdb.fasta -out GCA_022425345.1_ASM2242534v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 07:32:33,278] [INFO] Task succeeded: Blastn
[2023-06-13 07:32:33,283] [INFO] Selected 9 target genomes.
[2023-06-13 07:32:33,283] [INFO] Target genome list was writen to GCA_022425345.1_ASM2242534v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 07:32:33,288] [INFO] Task started: fastANI
[2023-06-13 07:32:33,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b808f42-4cc6-4751-b104-e98e6ace02f3/GCA_022425345.1_ASM2242534v1_genomic.fna.gz --refList GCA_022425345.1_ASM2242534v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022425345.1_ASM2242534v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 07:32:38,153] [INFO] Task succeeded: fastANI
[2023-06-13 07:32:38,163] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 07:32:38,163] [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_000738435.1	s__Planktomarina temperata	97.2851	394	406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	98.99	97.76	0.97	0.80	20	conclusive
GCA_016780825.1	s__Planktomarina sp016780825	90.0361	354	406	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	89.5426	363	406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683685.1	s__Planktomarina sp002683685	86.4179	296	406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	95.59	95.45	0.70	0.67	6	-
GCA_905182455.1	s__Planktomarina sp905182455	77.4257	149	406	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 07:32:38,165] [INFO] GTDB search result was written to GCA_022425345.1_ASM2242534v1_genomic.fna/result_gtdb.tsv
[2023-06-13 07:32:38,165] [INFO] ===== GTDB Search completed =====
[2023-06-13 07:32:38,168] [INFO] DFAST_QC result json was written to GCA_022425345.1_ASM2242534v1_genomic.fna/dqc_result.json
[2023-06-13 07:32:38,168] [INFO] DFAST_QC completed!
[2023-06-13 07:32:38,168] [INFO] Total running time: 0h0m40s