[2023-03-16 21:13:50,690] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:13:50,690] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:13:50,690] [INFO] DQC Reference Directory: /var/lib/cwl/stgf828d122-ed62-43d6-bcfd-5593573565e4/dqc_reference
[2023-03-16 21:13:52,415] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:13:52,416] [INFO] Task started: Prodigal
[2023-03-16 21:13:52,416] [INFO] Running command: cat /var/lib/cwl/stg245e9268-21ca-4192-9a06-05e8628c7ee8/OceanDNA-a3349.fa | prodigal -d OceanDNA-a3349/cds.fna -a OceanDNA-a3349/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:13:58,311] [INFO] Task succeeded: Prodigal
[2023-03-16 21:13:58,311] [INFO] Task started: HMMsearch
[2023-03-16 21:13:58,311] [INFO] Running command: hmmsearch --tblout OceanDNA-a3349/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf828d122-ed62-43d6-bcfd-5593573565e4/dqc_reference/reference_markers.hmm OceanDNA-a3349/protein.faa > /dev/null
[2023-03-16 21:13:58,456] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:13:58,457] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg245e9268-21ca-4192-9a06-05e8628c7ee8/OceanDNA-a3349.fa]
[2023-03-16 21:13:58,468] [INFO] Query marker FASTA was written to OceanDNA-a3349/markers.fasta
[2023-03-16 21:13:58,468] [INFO] Task started: Blastn
[2023-03-16 21:13:58,469] [INFO] Running command: blastn -query OceanDNA-a3349/markers.fasta -db /var/lib/cwl/stgf828d122-ed62-43d6-bcfd-5593573565e4/dqc_reference/reference_markers.fasta -out OceanDNA-a3349/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:13:58,905] [INFO] Task succeeded: Blastn
[2023-03-16 21:13:58,906] [INFO] Selected 0 target genomes.
[2023-03-16 21:13:58,906] [INFO] Target genome list was writen to OceanDNA-a3349/target_genomes.txt
[2023-03-16 21:13:58,906] [ERROR] File is empty. [OceanDNA-a3349/target_genomes.txt]
[2023-03-16 21:13:58,906] [ERROR] Task failed. No target genome found.
[2023-03-16 21:13:58,906] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:13:58,906] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf828d122-ed62-43d6-bcfd-5593573565e4/dqc_reference/checkm_data
[2023-03-16 21:13:58,959] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:13:58,962] [INFO] Task started: CheckM
[2023-03-16 21:13:58,962] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3349/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3349/checkm_input OceanDNA-a3349/checkm_result
[2023-03-16 21:14:23,171] [INFO] Task succeeded: CheckM
[2023-03-16 21:14:23,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.47%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 21:14:23,174] [INFO] ===== Completeness check finished =====
[2023-03-16 21:14:23,174] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:14:23,174] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3349/markers.fasta)
[2023-03-16 21:14:23,176] [INFO] Task started: Blastn
[2023-03-16 21:14:23,176] [INFO] Running command: blastn -query OceanDNA-a3349/markers.fasta -db /var/lib/cwl/stgf828d122-ed62-43d6-bcfd-5593573565e4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3349/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:14:23,928] [INFO] Task succeeded: Blastn
[2023-03-16 21:14:23,929] [INFO] Selected 4 target genomes.
[2023-03-16 21:14:23,929] [INFO] Target genome list was writen to OceanDNA-a3349/target_genomes_gtdb.txt
[2023-03-16 21:14:23,934] [INFO] Task started: fastANI
[2023-03-16 21:14:23,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg245e9268-21ca-4192-9a06-05e8628c7ee8/OceanDNA-a3349.fa --refList OceanDNA-a3349/target_genomes_gtdb.txt --output OceanDNA-a3349/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:14:25,156] [INFO] Task succeeded: fastANI
[2023-03-16 21:14:25,159] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 21:14:25,160] [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_002712285.1	s__MGIIb-N2 sp002712285	83.5675	215	266	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	98.10	96.52	0.84	0.79	3	-
GCA_002497905.1	s__MGIIb-N2 sp002497905	81.4386	218	266	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	99.55	99.55	0.87	0.87	3	-
GCA_002713585.1	s__MGIIb-N2 sp002713585	81.1386	214	266	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	98.11	98.05	0.86	0.82	4	-
--------------------------------------------------------------------------------
[2023-03-16 21:14:25,160] [INFO] GTDB search result was written to OceanDNA-a3349/result_gtdb.tsv
[2023-03-16 21:14:25,160] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:14:25,160] [INFO] DFAST_QC result json was written to OceanDNA-a3349/dqc_result.json
[2023-03-16 21:14:25,160] [INFO] DFAST_QC completed!
[2023-03-16 21:14:25,161] [INFO] Total running time: 0h0m34s