[2023-03-16 06:03:26,031] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:03:26,031] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:03:26,031] [INFO] DQC Reference Directory: /var/lib/cwl/stg10676266-2329-442c-9f2d-e106c2f5f316/dqc_reference
[2023-03-16 06:03:27,131] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:03:27,131] [INFO] Task started: Prodigal
[2023-03-16 06:03:27,132] [INFO] Running command: cat /var/lib/cwl/stgfff45849-03f3-470c-92c7-2a6206c4b531/OceanDNA-a956.fa | prodigal -d OceanDNA-a956/cds.fna -a OceanDNA-a956/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:03:30,948] [INFO] Task succeeded: Prodigal
[2023-03-16 06:03:30,948] [INFO] Task started: HMMsearch
[2023-03-16 06:03:30,948] [INFO] Running command: hmmsearch --tblout OceanDNA-a956/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10676266-2329-442c-9f2d-e106c2f5f316/dqc_reference/reference_markers.hmm OceanDNA-a956/protein.faa > /dev/null
[2023-03-16 06:03:31,076] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:03:31,076] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgfff45849-03f3-470c-92c7-2a6206c4b531/OceanDNA-a956.fa]
[2023-03-16 06:03:31,083] [INFO] Query marker FASTA was written to OceanDNA-a956/markers.fasta
[2023-03-16 06:03:31,084] [INFO] Task started: Blastn
[2023-03-16 06:03:31,084] [INFO] Running command: blastn -query OceanDNA-a956/markers.fasta -db /var/lib/cwl/stg10676266-2329-442c-9f2d-e106c2f5f316/dqc_reference/reference_markers.fasta -out OceanDNA-a956/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:03:31,561] [INFO] Task succeeded: Blastn
[2023-03-16 06:03:31,562] [INFO] Selected 0 target genomes.
[2023-03-16 06:03:31,562] [INFO] Target genome list was writen to OceanDNA-a956/target_genomes.txt
[2023-03-16 06:03:31,562] [ERROR] File is empty. [OceanDNA-a956/target_genomes.txt]
[2023-03-16 06:03:31,562] [ERROR] Task failed. No target genome found.
[2023-03-16 06:03:31,562] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:03:31,562] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10676266-2329-442c-9f2d-e106c2f5f316/dqc_reference/checkm_data
[2023-03-16 06:03:31,573] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:03:31,575] [INFO] Task started: CheckM
[2023-03-16 06:03:31,575] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a956/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a956/checkm_input OceanDNA-a956/checkm_result
[2023-03-16 06:03:47,859] [INFO] Task succeeded: CheckM
[2023-03-16 06:03:47,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:03:47,861] [INFO] ===== Completeness check finished =====
[2023-03-16 06:03:47,861] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:03:47,861] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a956/markers.fasta)
[2023-03-16 06:03:47,863] [INFO] Task started: Blastn
[2023-03-16 06:03:47,863] [INFO] Running command: blastn -query OceanDNA-a956/markers.fasta -db /var/lib/cwl/stg10676266-2329-442c-9f2d-e106c2f5f316/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a956/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:03:48,399] [INFO] Task succeeded: Blastn
[2023-03-16 06:03:48,400] [INFO] Selected 5 target genomes.
[2023-03-16 06:03:48,400] [INFO] Target genome list was writen to OceanDNA-a956/target_genomes_gtdb.txt
[2023-03-16 06:03:48,409] [INFO] Task started: fastANI
[2023-03-16 06:03:48,409] [INFO] Running command: fastANI --query /var/lib/cwl/stgfff45849-03f3-470c-92c7-2a6206c4b531/OceanDNA-a956.fa --refList OceanDNA-a956/target_genomes_gtdb.txt --output OceanDNA-a956/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:03:49,353] [INFO] Task succeeded: fastANI
[2023-03-16 06:03:49,356] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:03:49,356] [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_002693165.1	s__UBA57 sp002693165	99.039	178	246	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__UBA57;g__UBA57	95.0	98.59	98.59	0.69	0.69	2	conclusive
GCA_013306035.1	s__UBA57 sp002494565	79.2198	129	246	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__UBA57;g__UBA57	95.0	98.92	96.91	0.92	0.82	6	-
GCA_013378385.1	s__UBA57 sp013378385	78.8387	135	246	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__UBA57;g__UBA57	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:03:49,356] [INFO] GTDB search result was written to OceanDNA-a956/result_gtdb.tsv
[2023-03-16 06:03:49,357] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:03:49,357] [INFO] DFAST_QC result json was written to OceanDNA-a956/dqc_result.json
[2023-03-16 06:03:49,357] [INFO] DFAST_QC completed!
[2023-03-16 06:03:49,357] [INFO] Total running time: 0h0m23s