[2023-03-18 10:24:55,191] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:24:55,191] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:24:55,191] [INFO] DQC Reference Directory: /var/lib/cwl/stgb85d2cd6-000e-4c29-9d22-a923179cdc04/dqc_reference
[2023-03-18 10:24:56,332] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:24:56,333] [INFO] Task started: Prodigal
[2023-03-18 10:24:56,333] [INFO] Running command: cat /var/lib/cwl/stg77c21887-886c-45be-a986-e5177c2b9792/OceanDNA-b22231.fa | prodigal -d OceanDNA-b22231/cds.fna -a OceanDNA-b22231/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:25:16,115] [INFO] Task succeeded: Prodigal
[2023-03-18 10:25:16,115] [INFO] Task started: HMMsearch
[2023-03-18 10:25:16,115] [INFO] Running command: hmmsearch --tblout OceanDNA-b22231/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb85d2cd6-000e-4c29-9d22-a923179cdc04/dqc_reference/reference_markers.hmm OceanDNA-b22231/protein.faa > /dev/null
[2023-03-18 10:25:16,324] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:25:16,325] [INFO] Found 6/6 markers.
[2023-03-18 10:25:16,345] [INFO] Query marker FASTA was written to OceanDNA-b22231/markers.fasta
[2023-03-18 10:25:16,346] [INFO] Task started: Blastn
[2023-03-18 10:25:16,346] [INFO] Running command: blastn -query OceanDNA-b22231/markers.fasta -db /var/lib/cwl/stgb85d2cd6-000e-4c29-9d22-a923179cdc04/dqc_reference/reference_markers.fasta -out OceanDNA-b22231/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:25:16,870] [INFO] Task succeeded: Blastn
[2023-03-18 10:25:16,871] [INFO] Selected 21 target genomes.
[2023-03-18 10:25:16,871] [INFO] Target genome list was writen to OceanDNA-b22231/target_genomes.txt
[2023-03-18 10:25:16,880] [INFO] Task started: fastANI
[2023-03-18 10:25:16,881] [INFO] Running command: fastANI --query /var/lib/cwl/stg77c21887-886c-45be-a986-e5177c2b9792/OceanDNA-b22231.fa --refList OceanDNA-b22231/target_genomes.txt --output OceanDNA-b22231/fastani_result.tsv --threads 1
[2023-03-18 10:25:31,935] [INFO] Task succeeded: fastANI
[2023-03-18 10:25:31,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb85d2cd6-000e-4c29-9d22-a923179cdc04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:25:31,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb85d2cd6-000e-4c29-9d22-a923179cdc04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:25:31,936] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:25:31,936] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:25:31,936] [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 10:25:31,936] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22231/tc_result.tsv
[2023-03-18 10:25:31,936] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:25:31,936] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:25:31,937] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb85d2cd6-000e-4c29-9d22-a923179cdc04/dqc_reference/checkm_data
[2023-03-18 10:25:31,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:25:32,068] [INFO] Task started: CheckM
[2023-03-18 10:25:32,068] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22231/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22231/checkm_input OceanDNA-b22231/checkm_result
[2023-03-18 10:26:24,413] [INFO] Task succeeded: CheckM
[2023-03-18 10:26:24,413] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:26:24,417] [INFO] ===== Completeness check finished =====
[2023-03-18 10:26:24,417] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:26:24,417] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22231/markers.fasta)
[2023-03-18 10:26:24,418] [INFO] Task started: Blastn
[2023-03-18 10:26:24,418] [INFO] Running command: blastn -query OceanDNA-b22231/markers.fasta -db /var/lib/cwl/stgb85d2cd6-000e-4c29-9d22-a923179cdc04/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22231/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:26:25,126] [INFO] Task succeeded: Blastn
[2023-03-18 10:26:25,129] [INFO] Selected 21 target genomes.
[2023-03-18 10:26:25,129] [INFO] Target genome list was writen to OceanDNA-b22231/target_genomes_gtdb.txt
[2023-03-18 10:26:25,143] [INFO] Task started: fastANI
[2023-03-18 10:26:25,143] [INFO] Running command: fastANI --query /var/lib/cwl/stg77c21887-886c-45be-a986-e5177c2b9792/OceanDNA-b22231.fa --refList OceanDNA-b22231/target_genomes_gtdb.txt --output OceanDNA-b22231/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:26:35,374] [INFO] Task succeeded: fastANI
[2023-03-18 10:26:35,379] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:26:35,379] [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_016764015.1	s__UBA1924 sp016764015	78.3064	267	1022	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	77.884	306	1022	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	77.0926	106	1022	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	76.9541	143	1022	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	99.92	99.89	0.95	0.91	4	-
GCA_002337545.1	s__UBA1924 sp002337545	76.7559	128	1022	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	98.57	98.49	0.90	0.89	3	-
GCA_016764895.1	s__UBA1924 sp016764895	76.699	98	1022	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642965.1	s__UBA1924 sp017642965	76.633	111	1022	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:26:35,382] [INFO] GTDB search result was written to OceanDNA-b22231/result_gtdb.tsv
[2023-03-18 10:26:35,385] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:26:35,389] [INFO] DFAST_QC result json was written to OceanDNA-b22231/dqc_result.json
[2023-03-18 10:26:35,389] [INFO] DFAST_QC completed!
[2023-03-18 10:26:35,390] [INFO] Total running time: 0h1m40s