[2023-03-18 01:24:39,915] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:24:39,915] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:24:39,915] [INFO] DQC Reference Directory: /var/lib/cwl/stg68caed2f-819c-432f-a69a-d23c934479f7/dqc_reference
[2023-03-18 01:24:41,207] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:24:41,208] [INFO] Task started: Prodigal
[2023-03-18 01:24:41,208] [INFO] Running command: cat /var/lib/cwl/stgc4e322bb-6331-4458-bf8e-fe37e49d3385/OceanDNA-a2935.fa | prodigal -d OceanDNA-a2935/cds.fna -a OceanDNA-a2935/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:24:49,048] [INFO] Task succeeded: Prodigal
[2023-03-18 01:24:49,049] [INFO] Task started: HMMsearch
[2023-03-18 01:24:49,049] [INFO] Running command: hmmsearch --tblout OceanDNA-a2935/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68caed2f-819c-432f-a69a-d23c934479f7/dqc_reference/reference_markers.hmm OceanDNA-a2935/protein.faa > /dev/null
[2023-03-18 01:24:49,205] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:24:49,205] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgc4e322bb-6331-4458-bf8e-fe37e49d3385/OceanDNA-a2935.fa]
[2023-03-18 01:24:49,217] [INFO] Query marker FASTA was written to OceanDNA-a2935/markers.fasta
[2023-03-18 01:24:49,218] [INFO] Task started: Blastn
[2023-03-18 01:24:49,218] [INFO] Running command: blastn -query OceanDNA-a2935/markers.fasta -db /var/lib/cwl/stg68caed2f-819c-432f-a69a-d23c934479f7/dqc_reference/reference_markers.fasta -out OceanDNA-a2935/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:24:49,643] [INFO] Task succeeded: Blastn
[2023-03-18 01:24:49,643] [INFO] Selected 0 target genomes.
[2023-03-18 01:24:49,644] [INFO] Target genome list was writen to OceanDNA-a2935/target_genomes.txt
[2023-03-18 01:24:49,644] [ERROR] File is empty. [OceanDNA-a2935/target_genomes.txt]
[2023-03-18 01:24:49,644] [ERROR] Task failed. No target genome found.
[2023-03-18 01:24:49,644] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:24:49,644] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68caed2f-819c-432f-a69a-d23c934479f7/dqc_reference/checkm_data
[2023-03-18 01:24:49,711] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:24:49,714] [INFO] Task started: CheckM
[2023-03-18 01:24:49,714] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2935/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2935/checkm_input OceanDNA-a2935/checkm_result
[2023-03-18 01:25:17,242] [INFO] Task succeeded: CheckM
[2023-03-18 01:25:17,243] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:25:17,244] [INFO] ===== Completeness check finished =====
[2023-03-18 01:25:17,245] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:25:17,245] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2935/markers.fasta)
[2023-03-18 01:25:17,246] [INFO] Task started: Blastn
[2023-03-18 01:25:17,247] [INFO] Running command: blastn -query OceanDNA-a2935/markers.fasta -db /var/lib/cwl/stg68caed2f-819c-432f-a69a-d23c934479f7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2935/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:25:17,910] [INFO] Task succeeded: Blastn
[2023-03-18 01:25:17,910] [INFO] Selected 5 target genomes.
[2023-03-18 01:25:17,911] [INFO] Target genome list was writen to OceanDNA-a2935/target_genomes_gtdb.txt
[2023-03-18 01:25:17,946] [INFO] Task started: fastANI
[2023-03-18 01:25:17,946] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4e322bb-6331-4458-bf8e-fe37e49d3385/OceanDNA-a2935.fa --refList OceanDNA-a2935/target_genomes_gtdb.txt --output OceanDNA-a2935/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:25:19,456] [INFO] Task succeeded: fastANI
[2023-03-18 01:25:19,460] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:25:19,460] [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_002502295.1	s__Poseidonia sp002502295	91.7309	356	384	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013330155.1	s__Poseidonia sp8339u	79.7942	205	384	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.08	98.16	0.89	0.82	3	-
GCA_002495645.1	s__Poseidonia sp002495645	77.6293	130	384	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.68	99.68	0.84	0.84	2	-
GCA_902625885.1	s__Poseidonia sp902625885	77.3203	111	384	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:25:19,460] [INFO] GTDB search result was written to OceanDNA-a2935/result_gtdb.tsv
[2023-03-18 01:25:19,460] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:25:19,461] [INFO] DFAST_QC result json was written to OceanDNA-a2935/dqc_result.json
[2023-03-18 01:25:19,461] [INFO] DFAST_QC completed!
[2023-03-18 01:25:19,461] [INFO] Total running time: 0h0m40s