[2023-03-15 20:34:26,716] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:34:26,716] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:34:26,716] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bf5baac-4972-43cc-85a8-ce2bab8108f6/dqc_reference
[2023-03-15 20:34:28,459] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:34:28,460] [INFO] Task started: Prodigal
[2023-03-15 20:34:28,460] [INFO] Running command: cat /var/lib/cwl/stgee7fc4b5-5cf0-40e4-a3fa-cfa955dcecc3/OceanDNA-b30783.fa | prodigal -d OceanDNA-b30783/cds.fna -a OceanDNA-b30783/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:34:37,694] [INFO] Task succeeded: Prodigal
[2023-03-15 20:34:37,695] [INFO] Task started: HMMsearch
[2023-03-15 20:34:37,695] [INFO] Running command: hmmsearch --tblout OceanDNA-b30783/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bf5baac-4972-43cc-85a8-ce2bab8108f6/dqc_reference/reference_markers.hmm OceanDNA-b30783/protein.faa > /dev/null
[2023-03-15 20:34:37,842] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:34:37,842] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgee7fc4b5-5cf0-40e4-a3fa-cfa955dcecc3/OceanDNA-b30783.fa]
[2023-03-15 20:34:37,859] [INFO] Query marker FASTA was written to OceanDNA-b30783/markers.fasta
[2023-03-15 20:34:37,860] [INFO] Task started: Blastn
[2023-03-15 20:34:37,860] [INFO] Running command: blastn -query OceanDNA-b30783/markers.fasta -db /var/lib/cwl/stg4bf5baac-4972-43cc-85a8-ce2bab8108f6/dqc_reference/reference_markers.fasta -out OceanDNA-b30783/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:34:38,300] [INFO] Task succeeded: Blastn
[2023-03-15 20:34:38,301] [INFO] Selected 19 target genomes.
[2023-03-15 20:34:38,301] [INFO] Target genome list was writen to OceanDNA-b30783/target_genomes.txt
[2023-03-15 20:34:38,312] [INFO] Task started: fastANI
[2023-03-15 20:34:38,312] [INFO] Running command: fastANI --query /var/lib/cwl/stgee7fc4b5-5cf0-40e4-a3fa-cfa955dcecc3/OceanDNA-b30783.fa --refList OceanDNA-b30783/target_genomes.txt --output OceanDNA-b30783/fastani_result.tsv --threads 1
[2023-03-15 20:34:51,245] [INFO] Task succeeded: fastANI
[2023-03-15 20:34:51,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bf5baac-4972-43cc-85a8-ce2bab8108f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 20:34:51,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bf5baac-4972-43cc-85a8-ce2bab8108f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 20:34:51,246] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 20:34:51,246] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 20:34:51,246] [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
--------------------------------------------------------------------------------
[2023-03-15 20:34:51,247] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30783/tc_result.tsv
[2023-03-15 20:34:51,247] [INFO] ===== Taxonomy check completed =====
[2023-03-15 20:34:51,247] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:34:51,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bf5baac-4972-43cc-85a8-ce2bab8108f6/dqc_reference/checkm_data
[2023-03-15 20:34:51,250] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:34:51,253] [INFO] Task started: CheckM
[2023-03-15 20:34:51,253] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30783/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30783/checkm_input OceanDNA-b30783/checkm_result
[2023-03-15 20:35:19,086] [INFO] Task succeeded: CheckM
[2023-03-15 20:35:19,086] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.86%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 20:35:19,088] [INFO] ===== Completeness check finished =====
[2023-03-15 20:35:19,088] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:35:19,089] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30783/markers.fasta)
[2023-03-15 20:35:19,090] [INFO] Task started: Blastn
[2023-03-15 20:35:19,090] [INFO] Running command: blastn -query OceanDNA-b30783/markers.fasta -db /var/lib/cwl/stg4bf5baac-4972-43cc-85a8-ce2bab8108f6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30783/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:35:19,537] [INFO] Task succeeded: Blastn
[2023-03-15 20:35:19,538] [INFO] Selected 14 target genomes.
[2023-03-15 20:35:19,538] [INFO] Target genome list was writen to OceanDNA-b30783/target_genomes_gtdb.txt
[2023-03-15 20:35:19,945] [INFO] Task started: fastANI
[2023-03-15 20:35:19,945] [INFO] Running command: fastANI --query /var/lib/cwl/stgee7fc4b5-5cf0-40e4-a3fa-cfa955dcecc3/OceanDNA-b30783.fa --refList OceanDNA-b30783/target_genomes_gtdb.txt --output OceanDNA-b30783/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:35:27,138] [INFO] Task succeeded: fastANI
[2023-03-15 20:35:27,143] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 20:35:27,143] [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_016763915.1	s__Casp-alpha2 sp016763915	81.3508	174	453	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382345.1	s__Casp-alpha2 sp014382345	79.785	267	453	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_013204265.1	s__Casp-alpha2 sp013204265	79.5078	256	453	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001510075.1	s__Casp-alpha2 sp001510075	77.774	93	453	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002938075.1	s__Casp-alpha2 sp002938075	77.7387	126	453	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_002938315.1	s__Casp-alpha2 sp002938315	77.6469	150	453	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.33	99.24	0.87	0.79	4	-
GCA_013203955.1	s__Casp-alpha2 sp013203955	77.3742	143	453	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 20:35:27,143] [INFO] GTDB search result was written to OceanDNA-b30783/result_gtdb.tsv
[2023-03-15 20:35:27,143] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:35:27,144] [INFO] DFAST_QC result json was written to OceanDNA-b30783/dqc_result.json
[2023-03-15 20:35:27,144] [INFO] DFAST_QC completed!
[2023-03-15 20:35:27,144] [INFO] Total running time: 0h1m0s