[2023-03-16 18:27:22,232] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:27:22,232] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:27:22,232] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4732cfe-4f57-425c-b609-6742b739cf98/dqc_reference
[2023-03-16 18:27:24,388] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:27:24,392] [INFO] Task started: Prodigal
[2023-03-16 18:27:24,392] [INFO] Running command: cat /var/lib/cwl/stgf4421a65-a541-41a4-8024-31f35c7661f0/OceanDNA-b30736.fa | prodigal -d OceanDNA-b30736/cds.fna -a OceanDNA-b30736/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:27:35,944] [INFO] Task succeeded: Prodigal
[2023-03-16 18:27:35,945] [INFO] Task started: HMMsearch
[2023-03-16 18:27:35,945] [INFO] Running command: hmmsearch --tblout OceanDNA-b30736/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4732cfe-4f57-425c-b609-6742b739cf98/dqc_reference/reference_markers.hmm OceanDNA-b30736/protein.faa > /dev/null
[2023-03-16 18:27:36,133] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:27:36,134] [INFO] Found 6/6 markers.
[2023-03-16 18:27:36,161] [INFO] Query marker FASTA was written to OceanDNA-b30736/markers.fasta
[2023-03-16 18:27:36,161] [INFO] Task started: Blastn
[2023-03-16 18:27:36,161] [INFO] Running command: blastn -query OceanDNA-b30736/markers.fasta -db /var/lib/cwl/stgd4732cfe-4f57-425c-b609-6742b739cf98/dqc_reference/reference_markers.fasta -out OceanDNA-b30736/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:27:36,886] [INFO] Task succeeded: Blastn
[2023-03-16 18:27:36,887] [INFO] Selected 32 target genomes.
[2023-03-16 18:27:36,887] [INFO] Target genome list was writen to OceanDNA-b30736/target_genomes.txt
[2023-03-16 18:27:36,901] [INFO] Task started: fastANI
[2023-03-16 18:27:36,902] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4421a65-a541-41a4-8024-31f35c7661f0/OceanDNA-b30736.fa --refList OceanDNA-b30736/target_genomes.txt --output OceanDNA-b30736/fastani_result.tsv --threads 1
[2023-03-16 18:28:06,366] [INFO] Task succeeded: fastANI
[2023-03-16 18:28:06,367] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4732cfe-4f57-425c-b609-6742b739cf98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:28:06,367] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4732cfe-4f57-425c-b609-6742b739cf98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:28:06,371] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:28:06,371] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:28:06,371] [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
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	75.7307	52	426	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	75.5883	54	426	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:28:06,371] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30736/tc_result.tsv
[2023-03-16 18:28:06,371] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:28:06,371] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:28:06,371] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4732cfe-4f57-425c-b609-6742b739cf98/dqc_reference/checkm_data
[2023-03-16 18:28:06,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:28:06,375] [INFO] Task started: CheckM
[2023-03-16 18:28:06,375] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30736/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30736/checkm_input OceanDNA-b30736/checkm_result
[2023-03-16 18:28:34,020] [INFO] Task succeeded: CheckM
[2023-03-16 18:28:34,021] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 18:28:34,022] [INFO] ===== Completeness check finished =====
[2023-03-16 18:28:34,022] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:28:34,023] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30736/markers.fasta)
[2023-03-16 18:28:34,023] [INFO] Task started: Blastn
[2023-03-16 18:28:34,023] [INFO] Running command: blastn -query OceanDNA-b30736/markers.fasta -db /var/lib/cwl/stgd4732cfe-4f57-425c-b609-6742b739cf98/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30736/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:28:35,298] [INFO] Task succeeded: Blastn
[2023-03-16 18:28:35,299] [INFO] Selected 23 target genomes.
[2023-03-16 18:28:35,299] [INFO] Target genome list was writen to OceanDNA-b30736/target_genomes_gtdb.txt
[2023-03-16 18:28:35,321] [INFO] Task started: fastANI
[2023-03-16 18:28:35,321] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4421a65-a541-41a4-8024-31f35c7661f0/OceanDNA-b30736.fa --refList OceanDNA-b30736/target_genomes_gtdb.txt --output OceanDNA-b30736/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:28:48,102] [INFO] Task succeeded: fastANI
[2023-03-16 18:28:48,108] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 18:28:48,108] [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_002725625.1	s__GCA-2725625 sp002725625	96.5401	65	426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__GCA-2725625	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013349695.1	s__GCA-2686765 sp013349695	87.0182	298	426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16;g__GCA-2686765	95.0	98.27	95.45	0.83	0.65	4	-
GCA_002686255.1	s__Casp-alpha2 sp002686255	76.6337	81	426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.76	99.74	0.90	0.88	3	-
GCA_002938075.1	s__Casp-alpha2 sp002938075	76.2341	59	426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	98.70	98.63	0.78	0.77	3	-
GCA_014859895.1	s__JACZKS01 sp014859895	76.2187	64	426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JACZKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382345.1	s__Casp-alpha2 sp014382345	75.981	57	426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.86	99.86	0.92	0.92	2	-
GCA_001830425.1	s__2-02-FULL-58-16 sp001830425	75.9572	59	426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16;g__2-02-FULL-58-16	95.0	99.96	99.96	0.97	0.97	2	-
GCA_016187325.1	s__JACPJY01 sp016187325	75.8627	58	426	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:28:48,108] [INFO] GTDB search result was written to OceanDNA-b30736/result_gtdb.tsv
[2023-03-16 18:28:48,108] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:28:48,109] [INFO] DFAST_QC result json was written to OceanDNA-b30736/dqc_result.json
[2023-03-16 18:28:48,109] [INFO] DFAST_QC completed!
[2023-03-16 18:28:48,109] [INFO] Total running time: 0h1m26s