[2023-03-15 15:55:16,218] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:55:16,218] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:55:16,218] [INFO] DQC Reference Directory: /var/lib/cwl/stge223ceb6-dcd0-4ed8-a319-4db5a0212960/dqc_reference
[2023-03-15 15:55:17,918] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:55:17,920] [INFO] Task started: Prodigal
[2023-03-15 15:55:17,921] [INFO] Running command: cat /var/lib/cwl/stgc9ff0e0e-9e0c-4474-acba-02aa001ece76/OceanDNA-b22108.fa | prodigal -d OceanDNA-b22108/cds.fna -a OceanDNA-b22108/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:55:37,373] [INFO] Task succeeded: Prodigal
[2023-03-15 15:55:37,374] [INFO] Task started: HMMsearch
[2023-03-15 15:55:37,374] [INFO] Running command: hmmsearch --tblout OceanDNA-b22108/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge223ceb6-dcd0-4ed8-a319-4db5a0212960/dqc_reference/reference_markers.hmm OceanDNA-b22108/protein.faa > /dev/null
[2023-03-15 15:55:37,567] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:55:37,568] [INFO] Found 6/6 markers.
[2023-03-15 15:55:37,586] [INFO] Query marker FASTA was written to OceanDNA-b22108/markers.fasta
[2023-03-15 15:55:37,587] [INFO] Task started: Blastn
[2023-03-15 15:55:37,587] [INFO] Running command: blastn -query OceanDNA-b22108/markers.fasta -db /var/lib/cwl/stge223ceb6-dcd0-4ed8-a319-4db5a0212960/dqc_reference/reference_markers.fasta -out OceanDNA-b22108/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:55:38,150] [INFO] Task succeeded: Blastn
[2023-03-15 15:55:38,151] [INFO] Selected 26 target genomes.
[2023-03-15 15:55:38,151] [INFO] Target genome list was writen to OceanDNA-b22108/target_genomes.txt
[2023-03-15 15:55:38,169] [INFO] Task started: fastANI
[2023-03-15 15:55:38,169] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9ff0e0e-9e0c-4474-acba-02aa001ece76/OceanDNA-b22108.fa --refList OceanDNA-b22108/target_genomes.txt --output OceanDNA-b22108/fastani_result.tsv --threads 1
[2023-03-15 15:55:57,663] [INFO] Task succeeded: fastANI
[2023-03-15 15:55:57,664] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge223ceb6-dcd0-4ed8-a319-4db5a0212960/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:55:57,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge223ceb6-dcd0-4ed8-a319-4db5a0212960/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:55:57,664] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:55:57,664] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:55:57,664] [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 15:55:57,664] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22108/tc_result.tsv
[2023-03-15 15:55:57,665] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:55:57,665] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:55:57,665] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge223ceb6-dcd0-4ed8-a319-4db5a0212960/dqc_reference/checkm_data
[2023-03-15 15:55:57,668] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:55:57,672] [INFO] Task started: CheckM
[2023-03-15 15:55:57,673] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22108/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22108/checkm_input OceanDNA-b22108/checkm_result
[2023-03-15 15:56:50,305] [INFO] Task succeeded: CheckM
[2023-03-15 15:56:50,305] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:56:50,307] [INFO] ===== Completeness check finished =====
[2023-03-15 15:56:50,308] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:56:50,308] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22108/markers.fasta)
[2023-03-15 15:56:50,308] [INFO] Task started: Blastn
[2023-03-15 15:56:50,308] [INFO] Running command: blastn -query OceanDNA-b22108/markers.fasta -db /var/lib/cwl/stge223ceb6-dcd0-4ed8-a319-4db5a0212960/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22108/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:56:51,071] [INFO] Task succeeded: Blastn
[2023-03-15 15:56:51,072] [INFO] Selected 11 target genomes.
[2023-03-15 15:56:51,072] [INFO] Target genome list was writen to OceanDNA-b22108/target_genomes_gtdb.txt
[2023-03-15 15:56:51,084] [INFO] Task started: fastANI
[2023-03-15 15:56:51,085] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9ff0e0e-9e0c-4474-acba-02aa001ece76/OceanDNA-b22108.fa --refList OceanDNA-b22108/target_genomes_gtdb.txt --output OceanDNA-b22108/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:56:56,770] [INFO] Task succeeded: fastANI
[2023-03-15 15:56:56,777] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:56:56,777] [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_009827215.1	s__UBA1924 sp009827215	80.7605	428	997	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640485.1	s__UBA1924 sp017640485	80.3487	487	997	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764895.1	s__UBA1924 sp016764895	79.5221	387	997	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364005.1	s__UBA1924 sp002364005	77.1198	216	997	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	99.92	99.89	0.95	0.91	4	-
GCA_017642965.1	s__UBA1924 sp017642965	77.0075	191	997	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487555.1	s__UBA1924 sp015487555	76.8945	191	997	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337545.1	s__UBA1924 sp002337545	76.8691	187	997	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	98.57	98.49	0.90	0.89	3	-
GCA_016763115.1	s__UBA1924 sp016763115	76.6565	99	997	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696675.1	s__UBA6054 sp003696675	76.6338	113	997	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002429045.1	s__UBA6054 sp002429045	76.4767	123	997	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764015.1	s__UBA1924 sp016764015	76.3166	126	997	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 15:56:56,777] [INFO] GTDB search result was written to OceanDNA-b22108/result_gtdb.tsv
[2023-03-15 15:56:56,777] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:56:56,778] [INFO] DFAST_QC result json was written to OceanDNA-b22108/dqc_result.json
[2023-03-15 15:56:56,778] [INFO] DFAST_QC completed!
[2023-03-15 15:56:56,778] [INFO] Total running time: 0h1m41s