[2023-03-14 12:19:39,437] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:19:39,439] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:19:39,439] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbbd2d1d-67a0-4f8a-8572-6fc5e9f099e4/dqc_reference
[2023-03-14 12:19:40,534] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:19:40,535] [INFO] Task started: Prodigal
[2023-03-14 12:19:40,535] [INFO] Running command: cat /var/lib/cwl/stg457e748e-50b3-4ea8-a425-d0372a8d44a6/OceanDNA-b22278.fa | prodigal -d OceanDNA-b22278/cds.fna -a OceanDNA-b22278/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:19:46,043] [INFO] Task succeeded: Prodigal
[2023-03-14 12:19:46,043] [INFO] Task started: HMMsearch
[2023-03-14 12:19:46,043] [INFO] Running command: hmmsearch --tblout OceanDNA-b22278/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbbd2d1d-67a0-4f8a-8572-6fc5e9f099e4/dqc_reference/reference_markers.hmm OceanDNA-b22278/protein.faa > /dev/null
[2023-03-14 12:19:46,174] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:19:46,175] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg457e748e-50b3-4ea8-a425-d0372a8d44a6/OceanDNA-b22278.fa]
[2023-03-14 12:19:46,221] [INFO] Query marker FASTA was written to OceanDNA-b22278/markers.fasta
[2023-03-14 12:19:46,222] [INFO] Task started: Blastn
[2023-03-14 12:19:46,222] [INFO] Running command: blastn -query OceanDNA-b22278/markers.fasta -db /var/lib/cwl/stgcbbd2d1d-67a0-4f8a-8572-6fc5e9f099e4/dqc_reference/reference_markers.fasta -out OceanDNA-b22278/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:19:46,716] [INFO] Task succeeded: Blastn
[2023-03-14 12:19:46,733] [INFO] Selected 0 target genomes.
[2023-03-14 12:19:46,733] [INFO] Target genome list was writen to OceanDNA-b22278/target_genomes.txt
[2023-03-14 12:19:46,733] [ERROR] File is empty. [OceanDNA-b22278/target_genomes.txt]
[2023-03-14 12:19:46,733] [ERROR] Task failed. No target genome found.
[2023-03-14 12:19:46,734] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:19:46,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbbd2d1d-67a0-4f8a-8572-6fc5e9f099e4/dqc_reference/checkm_data
[2023-03-14 12:19:46,769] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:19:46,774] [INFO] Task started: CheckM
[2023-03-14 12:19:46,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22278/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22278/checkm_input OceanDNA-b22278/checkm_result
[2023-03-14 12:20:07,943] [INFO] Task succeeded: CheckM
[2023-03-14 12:20:07,944] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.47%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:20:07,962] [INFO] ===== Completeness check finished =====
[2023-03-14 12:20:07,962] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:20:07,962] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22278/markers.fasta)
[2023-03-14 12:20:07,972] [INFO] Task started: Blastn
[2023-03-14 12:20:07,972] [INFO] Running command: blastn -query OceanDNA-b22278/markers.fasta -db /var/lib/cwl/stgcbbd2d1d-67a0-4f8a-8572-6fc5e9f099e4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22278/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:20:08,847] [INFO] Task succeeded: Blastn
[2023-03-14 12:20:08,864] [INFO] Selected 6 target genomes.
[2023-03-14 12:20:08,864] [INFO] Target genome list was writen to OceanDNA-b22278/target_genomes_gtdb.txt
[2023-03-14 12:20:08,876] [INFO] Task started: fastANI
[2023-03-14 12:20:08,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg457e748e-50b3-4ea8-a425-d0372a8d44a6/OceanDNA-b22278.fa --refList OceanDNA-b22278/target_genomes_gtdb.txt --output OceanDNA-b22278/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:20:11,484] [INFO] Task succeeded: fastANI
[2023-03-14 12:20:11,487] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:20:11,488] [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_002168105.2	s__UBA8653 sp002168105	85.6741	189	203	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA8653	95.0	99.39	99.39	0.92	0.92	2	-
GCA_004213555.1	s__UBA8653 sp002862275	83.3239	171	203	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA8653	95.0	98.78	97.23	0.90	0.87	4	-
GCA_002705085.1	s__UBA8653 sp002705085	82.2322	149	203	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA8653	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:20:11,493] [INFO] GTDB search result was written to OceanDNA-b22278/result_gtdb.tsv
[2023-03-14 12:20:11,501] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:20:11,504] [INFO] DFAST_QC result json was written to OceanDNA-b22278/dqc_result.json
[2023-03-14 12:20:11,504] [INFO] DFAST_QC completed!
[2023-03-14 12:20:11,504] [INFO] Total running time: 0h0m32s