[2023-03-15 09:25:29,132] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:25:29,132] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:25:29,132] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b67a7b6-997f-462a-bf4a-a2d0b1fd01fa/dqc_reference
[2023-03-15 09:25:30,382] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:25:30,382] [INFO] Task started: Prodigal
[2023-03-15 09:25:30,382] [INFO] Running command: cat /var/lib/cwl/stgd386f9e9-158f-49e7-983f-30a5bacfb86b/OceanDNA-a4647.fa | prodigal -d OceanDNA-a4647/cds.fna -a OceanDNA-a4647/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:25:38,451] [INFO] Task succeeded: Prodigal
[2023-03-15 09:25:38,452] [INFO] Task started: HMMsearch
[2023-03-15 09:25:38,452] [INFO] Running command: hmmsearch --tblout OceanDNA-a4647/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b67a7b6-997f-462a-bf4a-a2d0b1fd01fa/dqc_reference/reference_markers.hmm OceanDNA-a4647/protein.faa > /dev/null
[2023-03-15 09:25:38,637] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:25:38,637] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd386f9e9-158f-49e7-983f-30a5bacfb86b/OceanDNA-a4647.fa]
[2023-03-15 09:25:38,647] [INFO] Query marker FASTA was written to OceanDNA-a4647/markers.fasta
[2023-03-15 09:25:38,647] [INFO] Task started: Blastn
[2023-03-15 09:25:38,647] [INFO] Running command: blastn -query OceanDNA-a4647/markers.fasta -db /var/lib/cwl/stg3b67a7b6-997f-462a-bf4a-a2d0b1fd01fa/dqc_reference/reference_markers.fasta -out OceanDNA-a4647/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:25:39,064] [INFO] Task succeeded: Blastn
[2023-03-15 09:25:39,064] [INFO] Selected 0 target genomes.
[2023-03-15 09:25:39,064] [INFO] Target genome list was writen to OceanDNA-a4647/target_genomes.txt
[2023-03-15 09:25:39,064] [ERROR] File is empty. [OceanDNA-a4647/target_genomes.txt]
[2023-03-15 09:25:39,064] [ERROR] Task failed. No target genome found.
[2023-03-15 09:25:39,065] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:25:39,065] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b67a7b6-997f-462a-bf4a-a2d0b1fd01fa/dqc_reference/checkm_data
[2023-03-15 09:25:39,265] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:25:39,268] [INFO] Task started: CheckM
[2023-03-15 09:25:39,268] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4647/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4647/checkm_input OceanDNA-a4647/checkm_result
[2023-03-15 09:26:06,405] [INFO] Task succeeded: CheckM
[2023-03-15 09:26:06,405] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:26:06,407] [INFO] ===== Completeness check finished =====
[2023-03-15 09:26:06,407] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:26:06,407] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4647/markers.fasta)
[2023-03-15 09:26:06,408] [INFO] Task started: Blastn
[2023-03-15 09:26:06,408] [INFO] Running command: blastn -query OceanDNA-a4647/markers.fasta -db /var/lib/cwl/stg3b67a7b6-997f-462a-bf4a-a2d0b1fd01fa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4647/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:26:07,847] [INFO] Task succeeded: Blastn
[2023-03-15 09:26:07,847] [INFO] Selected 6 target genomes.
[2023-03-15 09:26:07,847] [INFO] Target genome list was writen to OceanDNA-a4647/target_genomes_gtdb.txt
[2023-03-15 09:26:08,172] [INFO] Task started: fastANI
[2023-03-15 09:26:08,172] [INFO] Running command: fastANI --query /var/lib/cwl/stgd386f9e9-158f-49e7-983f-30a5bacfb86b/OceanDNA-a4647.fa --refList OceanDNA-a4647/target_genomes_gtdb.txt --output OceanDNA-a4647/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:26:09,850] [INFO] Task succeeded: fastANI
[2023-03-15 09:26:09,853] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 09:26:09,853] [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_002505775.1	s__MGIIb-O5 sp002505775	99.8718	417	457	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.25	97.62	0.92	0.83	5	conclusive
GCA_002501605.1	s__MGIIb-O5 sp002501605	92.7426	369	457	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.05	98.72	0.89	0.86	6	-
GCA_002730095.1	s__MGIIb-O5 sp002730095	79.7892	253	457	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	98.71	97.66	0.85	0.80	5	-
--------------------------------------------------------------------------------
[2023-03-15 09:26:09,853] [INFO] GTDB search result was written to OceanDNA-a4647/result_gtdb.tsv
[2023-03-15 09:26:09,853] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:26:09,854] [INFO] DFAST_QC result json was written to OceanDNA-a4647/dqc_result.json
[2023-03-15 09:26:09,854] [INFO] DFAST_QC completed!
[2023-03-15 09:26:09,854] [INFO] Total running time: 0h0m41s