[2023-03-15 03:56:21,753] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:56:21,753] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:56:21,754] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e0a1258-5bc8-43ab-9b43-f7258af120a8/dqc_reference
[2023-03-15 03:56:23,405] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:56:23,406] [INFO] Task started: Prodigal
[2023-03-15 03:56:23,406] [INFO] Running command: cat /var/lib/cwl/stg3a92c3dd-94b7-44ec-9a12-5dd804eba276/OceanDNA-a4215.fa | prodigal -d OceanDNA-a4215/cds.fna -a OceanDNA-a4215/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:56:27,229] [INFO] Task succeeded: Prodigal
[2023-03-15 03:56:27,230] [INFO] Task started: HMMsearch
[2023-03-15 03:56:27,230] [INFO] Running command: hmmsearch --tblout OceanDNA-a4215/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e0a1258-5bc8-43ab-9b43-f7258af120a8/dqc_reference/reference_markers.hmm OceanDNA-a4215/protein.faa > /dev/null
[2023-03-15 03:56:27,343] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:56:27,344] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg3a92c3dd-94b7-44ec-9a12-5dd804eba276/OceanDNA-a4215.fa]
[2023-03-15 03:56:27,349] [INFO] Query marker FASTA was written to OceanDNA-a4215/markers.fasta
[2023-03-15 03:56:27,349] [INFO] Task started: Blastn
[2023-03-15 03:56:27,350] [INFO] Running command: blastn -query OceanDNA-a4215/markers.fasta -db /var/lib/cwl/stg5e0a1258-5bc8-43ab-9b43-f7258af120a8/dqc_reference/reference_markers.fasta -out OceanDNA-a4215/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:56:29,073] [INFO] Task succeeded: Blastn
[2023-03-15 03:56:29,073] [INFO] Selected 0 target genomes.
[2023-03-15 03:56:29,074] [INFO] Target genome list was writen to OceanDNA-a4215/target_genomes.txt
[2023-03-15 03:56:29,074] [ERROR] File is empty. [OceanDNA-a4215/target_genomes.txt]
[2023-03-15 03:56:29,074] [ERROR] Task failed. No target genome found.
[2023-03-15 03:56:29,074] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:56:29,074] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e0a1258-5bc8-43ab-9b43-f7258af120a8/dqc_reference/checkm_data
[2023-03-15 03:56:29,084] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:56:29,086] [INFO] Task started: CheckM
[2023-03-15 03:56:29,086] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4215/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4215/checkm_input OceanDNA-a4215/checkm_result
[2023-03-15 03:56:47,802] [INFO] Task succeeded: CheckM
[2023-03-15 03:56:47,803] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.32%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:56:47,804] [INFO] ===== Completeness check finished =====
[2023-03-15 03:56:47,804] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:56:47,804] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4215/markers.fasta)
[2023-03-15 03:56:47,806] [INFO] Task started: Blastn
[2023-03-15 03:56:47,806] [INFO] Running command: blastn -query OceanDNA-a4215/markers.fasta -db /var/lib/cwl/stg5e0a1258-5bc8-43ab-9b43-f7258af120a8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4215/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:56:48,438] [INFO] Task succeeded: Blastn
[2023-03-15 03:56:48,439] [INFO] Selected 5 target genomes.
[2023-03-15 03:56:48,439] [INFO] Target genome list was writen to OceanDNA-a4215/target_genomes_gtdb.txt
[2023-03-15 03:56:48,446] [INFO] Task started: fastANI
[2023-03-15 03:56:48,446] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a92c3dd-94b7-44ec-9a12-5dd804eba276/OceanDNA-a4215.fa --refList OceanDNA-a4215/target_genomes_gtdb.txt --output OceanDNA-a4215/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:56:49,638] [INFO] Task succeeded: fastANI
[2023-03-15 03:56:49,642] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:56:49,642] [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_002723045.1	s__MGIIb-O3 sp002723045	78.5217	60	221	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004195615.1	s__MGIIb-O3 sp004195615	77.6888	107	221	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.94	99.91	0.95	0.93	3	-
GCA_014239955.1	s__MGIIb-O3 sp014239955	77.6555	96	221	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:56:49,642] [INFO] GTDB search result was written to OceanDNA-a4215/result_gtdb.tsv
[2023-03-15 03:56:49,642] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:56:49,643] [INFO] DFAST_QC result json was written to OceanDNA-a4215/dqc_result.json
[2023-03-15 03:56:49,643] [INFO] DFAST_QC completed!
[2023-03-15 03:56:49,643] [INFO] Total running time: 0h0m28s