[2023-03-16 06:57:27,877] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:57:27,877] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:57:27,877] [INFO] DQC Reference Directory: /var/lib/cwl/stg01e08c23-2204-481f-a6ba-1667562a9767/dqc_reference
[2023-03-16 06:57:28,969] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:57:28,969] [INFO] Task started: Prodigal
[2023-03-16 06:57:28,969] [INFO] Running command: cat /var/lib/cwl/stg5055676b-cc6f-4663-b03d-be5520acc287/OceanDNA-b15784.fa | prodigal -d OceanDNA-b15784/cds.fna -a OceanDNA-b15784/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:57:38,075] [INFO] Task succeeded: Prodigal
[2023-03-16 06:57:38,075] [INFO] Task started: HMMsearch
[2023-03-16 06:57:38,075] [INFO] Running command: hmmsearch --tblout OceanDNA-b15784/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01e08c23-2204-481f-a6ba-1667562a9767/dqc_reference/reference_markers.hmm OceanDNA-b15784/protein.faa > /dev/null
[2023-03-16 06:57:38,270] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:57:38,271] [INFO] Found 6/6 markers.
[2023-03-16 06:57:38,288] [INFO] Query marker FASTA was written to OceanDNA-b15784/markers.fasta
[2023-03-16 06:57:38,289] [INFO] Task started: Blastn
[2023-03-16 06:57:38,289] [INFO] Running command: blastn -query OceanDNA-b15784/markers.fasta -db /var/lib/cwl/stg01e08c23-2204-481f-a6ba-1667562a9767/dqc_reference/reference_markers.fasta -out OceanDNA-b15784/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:57:38,920] [INFO] Task succeeded: Blastn
[2023-03-16 06:57:38,921] [INFO] Selected 17 target genomes.
[2023-03-16 06:57:38,921] [INFO] Target genome list was writen to OceanDNA-b15784/target_genomes.txt
[2023-03-16 06:57:38,936] [INFO] Task started: fastANI
[2023-03-16 06:57:38,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg5055676b-cc6f-4663-b03d-be5520acc287/OceanDNA-b15784.fa --refList OceanDNA-b15784/target_genomes.txt --output OceanDNA-b15784/fastani_result.tsv --threads 1
[2023-03-16 06:57:52,885] [INFO] Task succeeded: fastANI
[2023-03-16 06:57:52,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01e08c23-2204-481f-a6ba-1667562a9767/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:57:52,886] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01e08c23-2204-481f-a6ba-1667562a9767/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:57:52,886] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:57:52,886] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:57:52,886] [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
--------------------------------------------------------------------------------
[2023-03-16 06:57:52,886] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15784/tc_result.tsv
[2023-03-16 06:57:52,886] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:57:52,886] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:57:52,886] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01e08c23-2204-481f-a6ba-1667562a9767/dqc_reference/checkm_data
[2023-03-16 06:57:52,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:57:53,147] [INFO] Task started: CheckM
[2023-03-16 06:57:53,147] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15784/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15784/checkm_input OceanDNA-b15784/checkm_result
[2023-03-16 06:58:22,677] [INFO] Task succeeded: CheckM
[2023-03-16 06:58:22,677] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.44%
Contamintation: 2.37%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-16 06:58:22,680] [INFO] ===== Completeness check finished =====
[2023-03-16 06:58:22,680] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:58:22,680] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15784/markers.fasta)
[2023-03-16 06:58:22,681] [INFO] Task started: Blastn
[2023-03-16 06:58:22,681] [INFO] Running command: blastn -query OceanDNA-b15784/markers.fasta -db /var/lib/cwl/stg01e08c23-2204-481f-a6ba-1667562a9767/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15784/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:58:23,650] [INFO] Task succeeded: Blastn
[2023-03-16 06:58:23,651] [INFO] Selected 22 target genomes.
[2023-03-16 06:58:23,651] [INFO] Target genome list was writen to OceanDNA-b15784/target_genomes_gtdb.txt
[2023-03-16 06:58:23,687] [INFO] Task started: fastANI
[2023-03-16 06:58:23,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg5055676b-cc6f-4663-b03d-be5520acc287/OceanDNA-b15784.fa --refList OceanDNA-b15784/target_genomes_gtdb.txt --output OceanDNA-b15784/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:58:34,477] [INFO] Task succeeded: fastANI
[2023-03-16 06:58:34,483] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:58:34,483] [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_002697005.1	s__UBA9611 sp002697005	98.4343	268	395	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009392095.1	s__UBA9611 sp009391975	78.3316	148	395	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	98.46	97.52	0.83	0.73	9	-
GCA_002328185.1	s__UBA9611 sp002328185	78.2434	189	395	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.09	98.06	0.94	0.90	6	-
GCA_002746355.1	s__UBA9611 sp002746355	77.6037	194	395	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.11	98.97	0.93	0.85	6	-
GCA_002816575.1	s__UBA9611 sp002816575	77.5464	87	395	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009392075.1	s__UBA9611 sp009392075	77.5035	116	395	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	96.71	96.71	0.58	0.58	2	-
GCA_002721995.1	s__UBA9611 sp002721995	77.2088	112	395	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.09	98.66	0.88	0.85	7	-
GCA_002816585.1	s__UBA9611 sp002816585	77.1016	80	395	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959605.1	s__UBA9611 sp012959605	76.9477	116	395	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.56	99.56	0.90	0.90	2	-
GCA_002730485.1	s__UBA9611 sp002730485	76.8738	111	395	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:58:34,483] [INFO] GTDB search result was written to OceanDNA-b15784/result_gtdb.tsv
[2023-03-16 06:58:34,484] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:58:34,484] [INFO] DFAST_QC result json was written to OceanDNA-b15784/dqc_result.json
[2023-03-16 06:58:34,484] [INFO] DFAST_QC completed!
[2023-03-16 06:58:34,485] [INFO] Total running time: 0h1m7s