[2023-03-18 21:15:29,379] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:15:29,381] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:15:29,381] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bff449f-1eb1-41df-9921-5cb8d35aa7b5/dqc_reference
[2023-03-18 21:15:31,043] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:15:31,043] [INFO] Task started: Prodigal
[2023-03-18 21:15:31,043] [INFO] Running command: cat /var/lib/cwl/stg63b554df-a24b-442c-91d4-bff37c4c4da3/OceanDNA-b28261.fa | prodigal -d OceanDNA-b28261/cds.fna -a OceanDNA-b28261/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:15:36,276] [INFO] Task succeeded: Prodigal
[2023-03-18 21:15:36,276] [INFO] Task started: HMMsearch
[2023-03-18 21:15:36,276] [INFO] Running command: hmmsearch --tblout OceanDNA-b28261/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bff449f-1eb1-41df-9921-5cb8d35aa7b5/dqc_reference/reference_markers.hmm OceanDNA-b28261/protein.faa > /dev/null
[2023-03-18 21:15:36,436] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:15:36,436] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg63b554df-a24b-442c-91d4-bff37c4c4da3/OceanDNA-b28261.fa]
[2023-03-18 21:15:36,450] [INFO] Query marker FASTA was written to OceanDNA-b28261/markers.fasta
[2023-03-18 21:15:36,451] [INFO] Task started: Blastn
[2023-03-18 21:15:36,451] [INFO] Running command: blastn -query OceanDNA-b28261/markers.fasta -db /var/lib/cwl/stg2bff449f-1eb1-41df-9921-5cb8d35aa7b5/dqc_reference/reference_markers.fasta -out OceanDNA-b28261/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:15:37,193] [INFO] Task succeeded: Blastn
[2023-03-18 21:15:37,196] [INFO] Selected 16 target genomes.
[2023-03-18 21:15:37,197] [INFO] Target genome list was writen to OceanDNA-b28261/target_genomes.txt
[2023-03-18 21:15:37,207] [INFO] Task started: fastANI
[2023-03-18 21:15:37,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg63b554df-a24b-442c-91d4-bff37c4c4da3/OceanDNA-b28261.fa --refList OceanDNA-b28261/target_genomes.txt --output OceanDNA-b28261/fastani_result.tsv --threads 1
[2023-03-18 21:15:42,426] [INFO] Task succeeded: fastANI
[2023-03-18 21:15:42,427] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bff449f-1eb1-41df-9921-5cb8d35aa7b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:15:42,427] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bff449f-1eb1-41df-9921-5cb8d35aa7b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:15:42,427] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:15:42,427] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:15:42,427] [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
--------------------------------------------------------------------------------
[2023-03-18 21:15:42,428] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28261/tc_result.tsv
[2023-03-18 21:15:42,428] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:15:42,428] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:15:42,428] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bff449f-1eb1-41df-9921-5cb8d35aa7b5/dqc_reference/checkm_data
[2023-03-18 21:15:42,431] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:15:42,436] [INFO] Task started: CheckM
[2023-03-18 21:15:42,436] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28261/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28261/checkm_input OceanDNA-b28261/checkm_result
[2023-03-18 21:16:01,527] [INFO] Task succeeded: CheckM
[2023-03-18 21:16:01,528] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.15%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:16:01,537] [INFO] ===== Completeness check finished =====
[2023-03-18 21:16:01,537] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:16:01,537] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28261/markers.fasta)
[2023-03-18 21:16:01,538] [INFO] Task started: Blastn
[2023-03-18 21:16:01,538] [INFO] Running command: blastn -query OceanDNA-b28261/markers.fasta -db /var/lib/cwl/stg2bff449f-1eb1-41df-9921-5cb8d35aa7b5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28261/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:16:02,364] [INFO] Task succeeded: Blastn
[2023-03-18 21:16:02,365] [INFO] Selected 14 target genomes.
[2023-03-18 21:16:02,365] [INFO] Target genome list was writen to OceanDNA-b28261/target_genomes_gtdb.txt
[2023-03-18 21:16:02,384] [INFO] Task started: fastANI
[2023-03-18 21:16:02,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg63b554df-a24b-442c-91d4-bff37c4c4da3/OceanDNA-b28261.fa --refList OceanDNA-b28261/target_genomes_gtdb.txt --output OceanDNA-b28261/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:16:06,003] [INFO] Task succeeded: fastANI
[2023-03-18 21:16:06,008] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:16:06,008] [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_902578545.1	s__CACIIZ01 sp902578545	93.0525	278	359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	96.87	95.99	0.65	0.64	7	-
GCA_902573735.1	s__CACIIZ01 sp902573735	92.3308	229	359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902625475.1	s__CACIIZ01 sp902625475	92.2658	185	359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902562285.1	s__CACIIZ01 sp902562285	80.9782	186	359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902611605.1	s__CACIIZ01 sp902611605	80.9288	183	359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	96.35	96.35	0.51	0.51	2	-
GCA_902570265.1	s__CACIIZ01 sp902570265	80.4298	229	359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:16:06,009] [INFO] GTDB search result was written to OceanDNA-b28261/result_gtdb.tsv
[2023-03-18 21:16:06,010] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:16:06,012] [INFO] DFAST_QC result json was written to OceanDNA-b28261/dqc_result.json
[2023-03-18 21:16:06,012] [INFO] DFAST_QC completed!
[2023-03-18 21:16:06,012] [INFO] Total running time: 0h0m37s