[2023-03-19 02:29:22,701] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:29:22,702] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:29:22,702] [INFO] DQC Reference Directory: /var/lib/cwl/stg583bc30a-6507-45af-892e-b6cf6853d55f/dqc_reference
[2023-03-19 02:29:23,824] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:29:23,824] [INFO] Task started: Prodigal
[2023-03-19 02:29:23,824] [INFO] Running command: cat /var/lib/cwl/stg874865b0-6044-4784-8592-29d70b156c12/OceanDNA-a4085.fa | prodigal -d OceanDNA-a4085/cds.fna -a OceanDNA-a4085/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:29:27,933] [INFO] Task succeeded: Prodigal
[2023-03-19 02:29:27,934] [INFO] Task started: HMMsearch
[2023-03-19 02:29:27,934] [INFO] Running command: hmmsearch --tblout OceanDNA-a4085/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg583bc30a-6507-45af-892e-b6cf6853d55f/dqc_reference/reference_markers.hmm OceanDNA-a4085/protein.faa > /dev/null
[2023-03-19 02:29:28,051] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:29:28,051] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg874865b0-6044-4784-8592-29d70b156c12/OceanDNA-a4085.fa]
[2023-03-19 02:29:28,058] [INFO] Query marker FASTA was written to OceanDNA-a4085/markers.fasta
[2023-03-19 02:29:28,060] [INFO] Task started: Blastn
[2023-03-19 02:29:28,060] [INFO] Running command: blastn -query OceanDNA-a4085/markers.fasta -db /var/lib/cwl/stg583bc30a-6507-45af-892e-b6cf6853d55f/dqc_reference/reference_markers.fasta -out OceanDNA-a4085/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:29:28,529] [INFO] Task succeeded: Blastn
[2023-03-19 02:29:28,532] [INFO] Selected 0 target genomes.
[2023-03-19 02:29:28,532] [INFO] Target genome list was writen to OceanDNA-a4085/target_genomes.txt
[2023-03-19 02:29:28,532] [ERROR] File is empty. [OceanDNA-a4085/target_genomes.txt]
[2023-03-19 02:29:28,532] [ERROR] Task failed. No target genome found.
[2023-03-19 02:29:28,532] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:29:28,532] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg583bc30a-6507-45af-892e-b6cf6853d55f/dqc_reference/checkm_data
[2023-03-19 02:29:28,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:29:28,588] [INFO] Task started: CheckM
[2023-03-19 02:29:28,588] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4085/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4085/checkm_input OceanDNA-a4085/checkm_result
[2023-03-19 02:29:48,288] [INFO] Task succeeded: CheckM
[2023-03-19 02:29:48,289] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.43%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 02:29:48,316] [INFO] ===== Completeness check finished =====
[2023-03-19 02:29:48,316] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:29:48,316] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4085/markers.fasta)
[2023-03-19 02:29:48,317] [INFO] Task started: Blastn
[2023-03-19 02:29:48,318] [INFO] Running command: blastn -query OceanDNA-a4085/markers.fasta -db /var/lib/cwl/stg583bc30a-6507-45af-892e-b6cf6853d55f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4085/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:29:48,907] [INFO] Task succeeded: Blastn
[2023-03-19 02:29:48,908] [INFO] Selected 3 target genomes.
[2023-03-19 02:29:48,908] [INFO] Target genome list was writen to OceanDNA-a4085/target_genomes_gtdb.txt
[2023-03-19 02:29:48,912] [INFO] Task started: fastANI
[2023-03-19 02:29:48,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg874865b0-6044-4784-8592-29d70b156c12/OceanDNA-a4085.fa --refList OceanDNA-a4085/target_genomes_gtdb.txt --output OceanDNA-a4085/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:29:49,575] [INFO] Task succeeded: fastANI
[2023-03-19 02:29:49,578] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:29:49,578] [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_902573115.1	s__MGIIb-O3 sp902573115	90.7545	139	238	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_002506755.1	s__MGIIb-O3 sp002506755	90.293	218	238	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.90	99.90	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-19 02:29:49,578] [INFO] GTDB search result was written to OceanDNA-a4085/result_gtdb.tsv
[2023-03-19 02:29:49,578] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:29:49,580] [INFO] DFAST_QC result json was written to OceanDNA-a4085/dqc_result.json
[2023-03-19 02:29:49,580] [INFO] DFAST_QC completed!
[2023-03-19 02:29:49,580] [INFO] Total running time: 0h0m27s