[2023-03-15 03:14:16,605] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:14:16,605] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:14:16,605] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e7238eb-6a73-400a-b3b0-a3d0c67974bb/dqc_reference
[2023-03-15 03:14:17,736] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:14:17,737] [INFO] Task started: Prodigal
[2023-03-15 03:14:17,737] [INFO] Running command: cat /var/lib/cwl/stg6d987a1a-5b35-4dfa-ac47-2041cda4f1e2/OceanDNA-a908.fa | prodigal -d OceanDNA-a908/cds.fna -a OceanDNA-a908/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:14:20,750] [INFO] Task succeeded: Prodigal
[2023-03-15 03:14:20,750] [INFO] Task started: HMMsearch
[2023-03-15 03:14:20,750] [INFO] Running command: hmmsearch --tblout OceanDNA-a908/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e7238eb-6a73-400a-b3b0-a3d0c67974bb/dqc_reference/reference_markers.hmm OceanDNA-a908/protein.faa > /dev/null
[2023-03-15 03:14:20,916] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:14:20,917] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg6d987a1a-5b35-4dfa-ac47-2041cda4f1e2/OceanDNA-a908.fa]
[2023-03-15 03:14:20,943] [INFO] Query marker FASTA was written to OceanDNA-a908/markers.fasta
[2023-03-15 03:14:20,945] [INFO] Task started: Blastn
[2023-03-15 03:14:20,945] [INFO] Running command: blastn -query OceanDNA-a908/markers.fasta -db /var/lib/cwl/stg4e7238eb-6a73-400a-b3b0-a3d0c67974bb/dqc_reference/reference_markers.fasta -out OceanDNA-a908/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:14:21,422] [INFO] Task succeeded: Blastn
[2023-03-15 03:14:21,427] [INFO] Selected 0 target genomes.
[2023-03-15 03:14:21,428] [INFO] Target genome list was writen to OceanDNA-a908/target_genomes.txt
[2023-03-15 03:14:21,428] [ERROR] File is empty. [OceanDNA-a908/target_genomes.txt]
[2023-03-15 03:14:21,428] [ERROR] Task failed. No target genome found.
[2023-03-15 03:14:21,428] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:14:21,428] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e7238eb-6a73-400a-b3b0-a3d0c67974bb/dqc_reference/checkm_data
[2023-03-15 03:14:21,483] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:14:21,487] [INFO] Task started: CheckM
[2023-03-15 03:14:21,487] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a908/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a908/checkm_input OceanDNA-a908/checkm_result
[2023-03-15 03:14:37,923] [INFO] Task succeeded: CheckM
[2023-03-15 03:14:37,923] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.81%
Contamintation: 1.45%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-15 03:14:37,929] [INFO] ===== Completeness check finished =====
[2023-03-15 03:14:37,929] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:14:37,929] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a908/markers.fasta)
[2023-03-15 03:14:37,930] [INFO] Task started: Blastn
[2023-03-15 03:14:37,930] [INFO] Running command: blastn -query OceanDNA-a908/markers.fasta -db /var/lib/cwl/stg4e7238eb-6a73-400a-b3b0-a3d0c67974bb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a908/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:14:38,625] [INFO] Task succeeded: Blastn
[2023-03-15 03:14:38,633] [INFO] Selected 5 target genomes.
[2023-03-15 03:14:38,634] [INFO] Target genome list was writen to OceanDNA-a908/target_genomes_gtdb.txt
[2023-03-15 03:14:38,640] [INFO] Task started: fastANI
[2023-03-15 03:14:38,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d987a1a-5b35-4dfa-ac47-2041cda4f1e2/OceanDNA-a908.fa --refList OceanDNA-a908/target_genomes_gtdb.txt --output OceanDNA-a908/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:14:39,485] [INFO] Task succeeded: fastANI
[2023-03-15 03:14:39,488] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:14:39,488] [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_002495905.1	s__UBA57 sp002495905	88.3433	145	174	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__UBA57;g__UBA57	95.0	98.98	98.92	0.81	0.77	4	-
GCA_013378385.1	s__UBA57 sp013378385	83.5993	147	174	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__UBA57;g__UBA57	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:14:39,490] [INFO] GTDB search result was written to OceanDNA-a908/result_gtdb.tsv
[2023-03-15 03:14:39,492] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:14:39,494] [INFO] DFAST_QC result json was written to OceanDNA-a908/dqc_result.json
[2023-03-15 03:14:39,494] [INFO] DFAST_QC completed!
[2023-03-15 03:14:39,495] [INFO] Total running time: 0h0m23s