[2023-03-16 08:10:35,264] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:10:35,266] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:10:35,266] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2fbc95f-6b59-4601-a381-c389366e9296/dqc_reference
[2023-03-16 08:10:36,368] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:10:36,368] [INFO] Task started: Prodigal
[2023-03-16 08:10:36,368] [INFO] Running command: cat /var/lib/cwl/stg42297676-53b5-4975-9363-c5594d47e0af/OceanDNA-b36617.fa | prodigal -d OceanDNA-b36617/cds.fna -a OceanDNA-b36617/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:10:56,121] [INFO] Task succeeded: Prodigal
[2023-03-16 08:10:56,122] [INFO] Task started: HMMsearch
[2023-03-16 08:10:56,122] [INFO] Running command: hmmsearch --tblout OceanDNA-b36617/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2fbc95f-6b59-4601-a381-c389366e9296/dqc_reference/reference_markers.hmm OceanDNA-b36617/protein.faa > /dev/null
[2023-03-16 08:10:56,358] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:10:56,359] [INFO] Found 6/6 markers.
[2023-03-16 08:10:56,432] [INFO] Query marker FASTA was written to OceanDNA-b36617/markers.fasta
[2023-03-16 08:10:56,432] [INFO] Task started: Blastn
[2023-03-16 08:10:56,432] [INFO] Running command: blastn -query OceanDNA-b36617/markers.fasta -db /var/lib/cwl/stgd2fbc95f-6b59-4601-a381-c389366e9296/dqc_reference/reference_markers.fasta -out OceanDNA-b36617/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:10:57,110] [INFO] Task succeeded: Blastn
[2023-03-16 08:10:57,120] [INFO] Selected 34 target genomes.
[2023-03-16 08:10:57,121] [INFO] Target genome list was writen to OceanDNA-b36617/target_genomes.txt
[2023-03-16 08:10:57,140] [INFO] Task started: fastANI
[2023-03-16 08:10:57,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg42297676-53b5-4975-9363-c5594d47e0af/OceanDNA-b36617.fa --refList OceanDNA-b36617/target_genomes.txt --output OceanDNA-b36617/fastani_result.tsv --threads 1
[2023-03-16 08:11:19,926] [INFO] Task succeeded: fastANI
[2023-03-16 08:11:19,927] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2fbc95f-6b59-4601-a381-c389366e9296/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:11:19,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2fbc95f-6b59-4601-a381-c389366e9296/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:11:19,931] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:11:19,931] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:11:19,931] [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
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	76.4778	68	1091	95	below_threshold
Alcanivorax pacificus	strain=W11-5	GCA_000299335.2	1306787	1306787	type	True	76.2582	72	1091	95	below_threshold
Alcanivorax borkumensis	strain=SK2	GCA_000009365.1	59754	59754	type	True	76.1087	56	1091	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:11:19,936] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36617/tc_result.tsv
[2023-03-16 08:11:19,942] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:11:19,942] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:11:19,942] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2fbc95f-6b59-4601-a381-c389366e9296/dqc_reference/checkm_data
[2023-03-16 08:11:19,943] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:11:19,975] [INFO] Task started: CheckM
[2023-03-16 08:11:19,975] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36617/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36617/checkm_input OceanDNA-b36617/checkm_result
[2023-03-16 08:12:10,285] [INFO] Task succeeded: CheckM
[2023-03-16 08:12:10,285] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:12:10,394] [INFO] ===== Completeness check finished =====
[2023-03-16 08:12:10,394] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:12:10,395] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36617/markers.fasta)
[2023-03-16 08:12:10,396] [INFO] Task started: Blastn
[2023-03-16 08:12:10,396] [INFO] Running command: blastn -query OceanDNA-b36617/markers.fasta -db /var/lib/cwl/stgd2fbc95f-6b59-4601-a381-c389366e9296/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36617/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:12:11,491] [INFO] Task succeeded: Blastn
[2023-03-16 08:12:11,524] [INFO] Selected 26 target genomes.
[2023-03-16 08:12:11,524] [INFO] Target genome list was writen to OceanDNA-b36617/target_genomes_gtdb.txt
[2023-03-16 08:12:11,545] [INFO] Task started: fastANI
[2023-03-16 08:12:11,545] [INFO] Running command: fastANI --query /var/lib/cwl/stg42297676-53b5-4975-9363-c5594d47e0af/OceanDNA-b36617.fa --refList OceanDNA-b36617/target_genomes_gtdb.txt --output OceanDNA-b36617/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:12:27,142] [INFO] Task succeeded: fastANI
[2023-03-16 08:12:27,146] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 08:12:27,147] [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_018067045.1	s__PGZG01 sp018067045	98.6787	1004	1091	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__PGZG01	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_009846755.1	s__Alcanivorax_A sp009846755	76.3754	67	1091	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840115.1	s__PGZG01 sp002840115	76.2793	52	1091	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__PGZG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299335.2	s__Alcanivorax_A pacificus	76.2582	72	1091	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000009365.1	s__Alcanivorax borkumensis	76.1087	56	1091	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.54	99.30	0.96	0.95	6	-
--------------------------------------------------------------------------------
[2023-03-16 08:12:27,150] [INFO] GTDB search result was written to OceanDNA-b36617/result_gtdb.tsv
[2023-03-16 08:12:27,161] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:12:27,167] [INFO] DFAST_QC result json was written to OceanDNA-b36617/dqc_result.json
[2023-03-16 08:12:27,167] [INFO] DFAST_QC completed!
[2023-03-16 08:12:27,167] [INFO] Total running time: 0h1m52s