[2023-03-18 09:53:10,267] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:53:10,267] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:53:10,267] [INFO] DQC Reference Directory: /var/lib/cwl/stgee5b97af-adbe-42c1-bcfa-0ee3cc43ba4f/dqc_reference
[2023-03-18 09:53:11,375] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:53:11,375] [INFO] Task started: Prodigal
[2023-03-18 09:53:11,375] [INFO] Running command: cat /var/lib/cwl/stg53e67321-0a5b-441b-a22f-ed7a294e8510/OceanDNA-b18597.fa | prodigal -d OceanDNA-b18597/cds.fna -a OceanDNA-b18597/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:53:16,739] [INFO] Task succeeded: Prodigal
[2023-03-18 09:53:16,739] [INFO] Task started: HMMsearch
[2023-03-18 09:53:16,739] [INFO] Running command: hmmsearch --tblout OceanDNA-b18597/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee5b97af-adbe-42c1-bcfa-0ee3cc43ba4f/dqc_reference/reference_markers.hmm OceanDNA-b18597/protein.faa > /dev/null
[2023-03-18 09:53:16,855] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:53:16,855] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg53e67321-0a5b-441b-a22f-ed7a294e8510/OceanDNA-b18597.fa]
[2023-03-18 09:53:16,866] [INFO] Query marker FASTA was written to OceanDNA-b18597/markers.fasta
[2023-03-18 09:53:16,867] [INFO] Task started: Blastn
[2023-03-18 09:53:16,867] [INFO] Running command: blastn -query OceanDNA-b18597/markers.fasta -db /var/lib/cwl/stgee5b97af-adbe-42c1-bcfa-0ee3cc43ba4f/dqc_reference/reference_markers.fasta -out OceanDNA-b18597/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:53:17,322] [INFO] Task succeeded: Blastn
[2023-03-18 09:53:17,323] [INFO] Selected 0 target genomes.
[2023-03-18 09:53:17,323] [INFO] Target genome list was writen to OceanDNA-b18597/target_genomes.txt
[2023-03-18 09:53:17,323] [ERROR] File is empty. [OceanDNA-b18597/target_genomes.txt]
[2023-03-18 09:53:17,323] [ERROR] Task failed. No target genome found.
[2023-03-18 09:53:17,324] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:53:17,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee5b97af-adbe-42c1-bcfa-0ee3cc43ba4f/dqc_reference/checkm_data
[2023-03-18 09:53:17,370] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:53:17,373] [INFO] Task started: CheckM
[2023-03-18 09:53:17,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18597/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18597/checkm_input OceanDNA-b18597/checkm_result
[2023-03-18 09:53:38,302] [INFO] Task succeeded: CheckM
[2023-03-18 09:53:38,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.97%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:53:38,304] [INFO] ===== Completeness check finished =====
[2023-03-18 09:53:38,305] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:53:38,305] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18597/markers.fasta)
[2023-03-18 09:53:38,306] [INFO] Task started: Blastn
[2023-03-18 09:53:38,306] [INFO] Running command: blastn -query OceanDNA-b18597/markers.fasta -db /var/lib/cwl/stgee5b97af-adbe-42c1-bcfa-0ee3cc43ba4f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18597/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:53:39,136] [INFO] Task succeeded: Blastn
[2023-03-18 09:53:39,137] [INFO] Selected 6 target genomes.
[2023-03-18 09:53:39,137] [INFO] Target genome list was writen to OceanDNA-b18597/target_genomes_gtdb.txt
[2023-03-18 09:53:39,143] [INFO] Task started: fastANI
[2023-03-18 09:53:39,143] [INFO] Running command: fastANI --query /var/lib/cwl/stg53e67321-0a5b-441b-a22f-ed7a294e8510/OceanDNA-b18597.fa --refList OceanDNA-b18597/target_genomes_gtdb.txt --output OceanDNA-b18597/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:53:40,714] [INFO] Task succeeded: fastANI
[2023-03-18 09:53:40,717] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:53:40,717] [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_002701785.1	s__GCA-002701945 sp002701785	85.0297	253	324	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__GCA-002701945	95.0	97.49	97.49	0.87	0.87	2	-
GCA_002701945.1	s__GCA-002701945 sp002701945	83.8313	212	324	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__GCA-002701945	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004321715.1	s__GCA-002701945 sp004321715	81.6775	207	324	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__GCA-002701945	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:53:40,717] [INFO] GTDB search result was written to OceanDNA-b18597/result_gtdb.tsv
[2023-03-18 09:53:40,718] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:53:40,718] [INFO] DFAST_QC result json was written to OceanDNA-b18597/dqc_result.json
[2023-03-18 09:53:40,718] [INFO] DFAST_QC completed!
[2023-03-18 09:53:40,718] [INFO] Total running time: 0h0m30s