[2023-03-18 22:34:59,283] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:34:59,283] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:34:59,283] [INFO] DQC Reference Directory: /var/lib/cwl/stg24fd1ef2-b30f-49c3-9514-eb2d1e63e24e/dqc_reference
[2023-03-18 22:35:00,377] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:35:00,378] [INFO] Task started: Prodigal
[2023-03-18 22:35:00,378] [INFO] Running command: cat /var/lib/cwl/stg5be250ce-7912-47b3-a8a8-383d028626b7/OceanDNA-a3226.fa | prodigal -d OceanDNA-a3226/cds.fna -a OceanDNA-a3226/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:35:05,090] [INFO] Task succeeded: Prodigal
[2023-03-18 22:35:05,090] [INFO] Task started: HMMsearch
[2023-03-18 22:35:05,090] [INFO] Running command: hmmsearch --tblout OceanDNA-a3226/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24fd1ef2-b30f-49c3-9514-eb2d1e63e24e/dqc_reference/reference_markers.hmm OceanDNA-a3226/protein.faa > /dev/null
[2023-03-18 22:35:05,196] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:35:05,197] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg5be250ce-7912-47b3-a8a8-383d028626b7/OceanDNA-a3226.fa]
[2023-03-18 22:35:05,204] [INFO] Query marker FASTA was written to OceanDNA-a3226/markers.fasta
[2023-03-18 22:35:05,204] [INFO] Task started: Blastn
[2023-03-18 22:35:05,204] [INFO] Running command: blastn -query OceanDNA-a3226/markers.fasta -db /var/lib/cwl/stg24fd1ef2-b30f-49c3-9514-eb2d1e63e24e/dqc_reference/reference_markers.fasta -out OceanDNA-a3226/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:35:05,727] [INFO] Task succeeded: Blastn
[2023-03-18 22:35:05,727] [INFO] Selected 0 target genomes.
[2023-03-18 22:35:05,727] [INFO] Target genome list was writen to OceanDNA-a3226/target_genomes.txt
[2023-03-18 22:35:05,727] [ERROR] File is empty. [OceanDNA-a3226/target_genomes.txt]
[2023-03-18 22:35:05,728] [ERROR] Task failed. No target genome found.
[2023-03-18 22:35:05,728] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:35:05,728] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24fd1ef2-b30f-49c3-9514-eb2d1e63e24e/dqc_reference/checkm_data
[2023-03-18 22:35:05,738] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:35:05,741] [INFO] Task started: CheckM
[2023-03-18 22:35:05,741] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3226/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3226/checkm_input OceanDNA-a3226/checkm_result
[2023-03-18 22:35:23,961] [INFO] Task succeeded: CheckM
[2023-03-18 22:35:23,961] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.36%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:35:23,962] [INFO] ===== Completeness check finished =====
[2023-03-18 22:35:23,962] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:35:23,963] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3226/markers.fasta)
[2023-03-18 22:35:23,964] [INFO] Task started: Blastn
[2023-03-18 22:35:23,964] [INFO] Running command: blastn -query OceanDNA-a3226/markers.fasta -db /var/lib/cwl/stg24fd1ef2-b30f-49c3-9514-eb2d1e63e24e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3226/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:35:24,460] [INFO] Task succeeded: Blastn
[2023-03-18 22:35:24,461] [INFO] Selected 4 target genomes.
[2023-03-18 22:35:24,461] [INFO] Target genome list was writen to OceanDNA-a3226/target_genomes_gtdb.txt
[2023-03-18 22:35:24,464] [INFO] Task started: fastANI
[2023-03-18 22:35:24,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg5be250ce-7912-47b3-a8a8-383d028626b7/OceanDNA-a3226.fa --refList OceanDNA-a3226/target_genomes_gtdb.txt --output OceanDNA-a3226/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:35:25,537] [INFO] Task succeeded: fastANI
[2023-03-18 22:35:25,541] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:35:25,541] [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_002712645.1	s__MGIIb-N1 sp002712645	91.1536	238	261	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002497295.1	s__MGIIb-N1 sp002497295	89.9254	249	261	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002504845.1	s__MGIIb-N1 sp002504845	88.9732	219	261	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	98.34	97.20	0.81	0.69	5	-
GCA_002170775.2	s__MGIIb-N1 sp002170775	88.907	238	261	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:35:25,541] [INFO] GTDB search result was written to OceanDNA-a3226/result_gtdb.tsv
[2023-03-18 22:35:25,541] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:35:25,542] [INFO] DFAST_QC result json was written to OceanDNA-a3226/dqc_result.json
[2023-03-18 22:35:25,542] [INFO] DFAST_QC completed!
[2023-03-18 22:35:25,542] [INFO] Total running time: 0h0m26s