[2023-03-19 02:05:11,578] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:05:11,578] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:05:11,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg2eb69d41-af5d-4570-981c-b6de1321a6d8/dqc_reference
[2023-03-19 02:05:13,268] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:05:13,268] [INFO] Task started: Prodigal
[2023-03-19 02:05:13,268] [INFO] Running command: cat /var/lib/cwl/stgf99a1e06-fc7a-4cd3-821b-7c6585281b1e/OceanDNA-a455.fa | prodigal -d OceanDNA-a455/cds.fna -a OceanDNA-a455/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:05:15,000] [INFO] Task succeeded: Prodigal
[2023-03-19 02:05:15,000] [INFO] Task started: HMMsearch
[2023-03-19 02:05:15,000] [INFO] Running command: hmmsearch --tblout OceanDNA-a455/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2eb69d41-af5d-4570-981c-b6de1321a6d8/dqc_reference/reference_markers.hmm OceanDNA-a455/protein.faa > /dev/null
[2023-03-19 02:05:15,120] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:05:15,121] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgf99a1e06-fc7a-4cd3-821b-7c6585281b1e/OceanDNA-a455.fa]
[2023-03-19 02:05:15,126] [INFO] Query marker FASTA was written to OceanDNA-a455/markers.fasta
[2023-03-19 02:05:15,128] [INFO] Task started: Blastn
[2023-03-19 02:05:15,128] [INFO] Running command: blastn -query OceanDNA-a455/markers.fasta -db /var/lib/cwl/stg2eb69d41-af5d-4570-981c-b6de1321a6d8/dqc_reference/reference_markers.fasta -out OceanDNA-a455/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:05:18,048] [INFO] Task succeeded: Blastn
[2023-03-19 02:05:18,049] [INFO] Selected 0 target genomes.
[2023-03-19 02:05:18,049] [INFO] Target genome list was writen to OceanDNA-a455/target_genomes.txt
[2023-03-19 02:05:18,049] [ERROR] File is empty. [OceanDNA-a455/target_genomes.txt]
[2023-03-19 02:05:18,049] [ERROR] Task failed. No target genome found.
[2023-03-19 02:05:18,050] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:05:18,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2eb69d41-af5d-4570-981c-b6de1321a6d8/dqc_reference/checkm_data
[2023-03-19 02:05:18,053] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:05:18,054] [INFO] Task started: CheckM
[2023-03-19 02:05:18,054] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a455/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a455/checkm_input OceanDNA-a455/checkm_result
[2023-03-19 02:05:30,557] [INFO] Task succeeded: CheckM
[2023-03-19 02:05:30,557] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.86%
Contamintation: 0.84%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 02:05:30,559] [INFO] ===== Completeness check finished =====
[2023-03-19 02:05:30,559] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:05:30,559] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a455/markers.fasta)
[2023-03-19 02:05:30,561] [INFO] Task started: Blastn
[2023-03-19 02:05:30,561] [INFO] Running command: blastn -query OceanDNA-a455/markers.fasta -db /var/lib/cwl/stg2eb69d41-af5d-4570-981c-b6de1321a6d8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a455/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:05:31,215] [INFO] Task succeeded: Blastn
[2023-03-19 02:05:31,216] [INFO] Selected 5 target genomes.
[2023-03-19 02:05:31,217] [INFO] Target genome list was writen to OceanDNA-a455/target_genomes_gtdb.txt
[2023-03-19 02:05:31,285] [INFO] Task started: fastANI
[2023-03-19 02:05:31,285] [INFO] Running command: fastANI --query /var/lib/cwl/stgf99a1e06-fc7a-4cd3-821b-7c6585281b1e/OceanDNA-a455.fa --refList OceanDNA-a455/target_genomes_gtdb.txt --output OceanDNA-a455/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:05:32,041] [INFO] Task succeeded: fastANI
[2023-03-19 02:05:32,044] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:05:32,044] [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_013390745.1	s__Nitrosopelagicus sp013390745	90.335	59	66	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018263495.1	s__Nitrosopelagicus sp018263495	88.3587	60	66	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013390785.1	s__Nitrosopelagicus sp013390785	87.0458	55	66	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:05:32,044] [INFO] GTDB search result was written to OceanDNA-a455/result_gtdb.tsv
[2023-03-19 02:05:32,045] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:05:32,045] [INFO] DFAST_QC result json was written to OceanDNA-a455/dqc_result.json
[2023-03-19 02:05:32,045] [INFO] DFAST_QC completed!
[2023-03-19 02:05:32,045] [INFO] Total running time: 0h0m20s