[2023-03-15 18:39:12,233] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:39:12,233] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:39:12,233] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c4d9a24-a83f-493a-b89f-69bebe2b3e49/dqc_reference
[2023-03-15 18:39:13,656] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:39:13,656] [INFO] Task started: Prodigal
[2023-03-15 18:39:13,656] [INFO] Running command: cat /var/lib/cwl/stgcff97107-e25b-4d73-88b8-890cbe8e5c1d/OceanDNA-a3214.fa | prodigal -d OceanDNA-a3214/cds.fna -a OceanDNA-a3214/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:39:20,461] [INFO] Task succeeded: Prodigal
[2023-03-15 18:39:20,462] [INFO] Task started: HMMsearch
[2023-03-15 18:39:20,462] [INFO] Running command: hmmsearch --tblout OceanDNA-a3214/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c4d9a24-a83f-493a-b89f-69bebe2b3e49/dqc_reference/reference_markers.hmm OceanDNA-a3214/protein.faa > /dev/null
[2023-03-15 18:39:20,585] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:39:20,586] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgcff97107-e25b-4d73-88b8-890cbe8e5c1d/OceanDNA-a3214.fa]
[2023-03-15 18:39:20,596] [INFO] Query marker FASTA was written to OceanDNA-a3214/markers.fasta
[2023-03-15 18:39:20,596] [INFO] Task started: Blastn
[2023-03-15 18:39:20,596] [INFO] Running command: blastn -query OceanDNA-a3214/markers.fasta -db /var/lib/cwl/stg6c4d9a24-a83f-493a-b89f-69bebe2b3e49/dqc_reference/reference_markers.fasta -out OceanDNA-a3214/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:21,002] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:21,002] [INFO] Selected 0 target genomes.
[2023-03-15 18:39:21,002] [INFO] Target genome list was writen to OceanDNA-a3214/target_genomes.txt
[2023-03-15 18:39:21,002] [ERROR] File is empty. [OceanDNA-a3214/target_genomes.txt]
[2023-03-15 18:39:21,003] [ERROR] Task failed. No target genome found.
[2023-03-15 18:39:21,003] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:39:21,003] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c4d9a24-a83f-493a-b89f-69bebe2b3e49/dqc_reference/checkm_data
[2023-03-15 18:39:21,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:39:21,357] [INFO] Task started: CheckM
[2023-03-15 18:39:21,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3214/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3214/checkm_input OceanDNA-a3214/checkm_result
[2023-03-15 18:39:47,171] [INFO] Task succeeded: CheckM
[2023-03-15 18:39:47,171] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.66%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:39:47,173] [INFO] ===== Completeness check finished =====
[2023-03-15 18:39:47,173] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:39:47,173] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3214/markers.fasta)
[2023-03-15 18:39:47,174] [INFO] Task started: Blastn
[2023-03-15 18:39:47,174] [INFO] Running command: blastn -query OceanDNA-a3214/markers.fasta -db /var/lib/cwl/stg6c4d9a24-a83f-493a-b89f-69bebe2b3e49/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3214/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:49,168] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:49,168] [INFO] Selected 4 target genomes.
[2023-03-15 18:39:49,168] [INFO] Target genome list was writen to OceanDNA-a3214/target_genomes_gtdb.txt
[2023-03-15 18:39:49,313] [INFO] Task started: fastANI
[2023-03-15 18:39:49,313] [INFO] Running command: fastANI --query /var/lib/cwl/stgcff97107-e25b-4d73-88b8-890cbe8e5c1d/OceanDNA-a3214.fa --refList OceanDNA-a3214/target_genomes_gtdb.txt --output OceanDNA-a3214/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:39:50,905] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:50,908] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 18:39:50,909] [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_012964335.1	s__MGIIb-Q1 sp012964335	93.3974	379	393	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	99.77	99.71	0.95	0.94	8	-
GCA_012959435.1	s__MGIIb-Q1 sp012959435	87.3032	350	393	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384685.1	s__MGIIb-Q1 sp014384685	84.4981	216	393	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845345.1	s__MGIIb-Q1 sp016845345	82.8718	336	393	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 18:39:50,909] [INFO] GTDB search result was written to OceanDNA-a3214/result_gtdb.tsv
[2023-03-15 18:39:50,909] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:39:50,909] [INFO] DFAST_QC result json was written to OceanDNA-a3214/dqc_result.json
[2023-03-15 18:39:50,909] [INFO] DFAST_QC completed!
[2023-03-15 18:39:50,910] [INFO] Total running time: 0h0m39s