[2023-03-18 09:15:00,469] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:15:00,469] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:15:00,469] [INFO] DQC Reference Directory: /var/lib/cwl/stg35a7d0bc-d500-4179-ae15-a91c6834dde1/dqc_reference
[2023-03-18 09:15:02,034] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:15:02,034] [INFO] Task started: Prodigal
[2023-03-18 09:15:02,034] [INFO] Running command: cat /var/lib/cwl/stg98d6d992-e5ee-4fb6-aa14-9723b3ae5ab6/OceanDNA-a3372.fa | prodigal -d OceanDNA-a3372/cds.fna -a OceanDNA-a3372/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:15:11,401] [INFO] Task succeeded: Prodigal
[2023-03-18 09:15:11,401] [INFO] Task started: HMMsearch
[2023-03-18 09:15:11,401] [INFO] Running command: hmmsearch --tblout OceanDNA-a3372/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35a7d0bc-d500-4179-ae15-a91c6834dde1/dqc_reference/reference_markers.hmm OceanDNA-a3372/protein.faa > /dev/null
[2023-03-18 09:15:11,570] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:15:11,570] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg98d6d992-e5ee-4fb6-aa14-9723b3ae5ab6/OceanDNA-a3372.fa]
[2023-03-18 09:15:11,584] [INFO] Query marker FASTA was written to OceanDNA-a3372/markers.fasta
[2023-03-18 09:15:11,585] [INFO] Task started: Blastn
[2023-03-18 09:15:11,585] [INFO] Running command: blastn -query OceanDNA-a3372/markers.fasta -db /var/lib/cwl/stg35a7d0bc-d500-4179-ae15-a91c6834dde1/dqc_reference/reference_markers.fasta -out OceanDNA-a3372/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:15:12,019] [INFO] Task succeeded: Blastn
[2023-03-18 09:15:12,019] [INFO] Selected 0 target genomes.
[2023-03-18 09:15:12,020] [INFO] Target genome list was writen to OceanDNA-a3372/target_genomes.txt
[2023-03-18 09:15:12,020] [ERROR] File is empty. [OceanDNA-a3372/target_genomes.txt]
[2023-03-18 09:15:12,020] [ERROR] Task failed. No target genome found.
[2023-03-18 09:15:12,020] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:15:12,020] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35a7d0bc-d500-4179-ae15-a91c6834dde1/dqc_reference/checkm_data
[2023-03-18 09:15:12,023] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:15:12,027] [INFO] Task started: CheckM
[2023-03-18 09:15:12,027] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3372/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3372/checkm_input OceanDNA-a3372/checkm_result
[2023-03-18 09:15:40,412] [INFO] Task succeeded: CheckM
[2023-03-18 09:15:40,413] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:15:40,531] [INFO] ===== Completeness check finished =====
[2023-03-18 09:15:40,532] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:15:40,532] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3372/markers.fasta)
[2023-03-18 09:15:40,533] [INFO] Task started: Blastn
[2023-03-18 09:15:40,533] [INFO] Running command: blastn -query OceanDNA-a3372/markers.fasta -db /var/lib/cwl/stg35a7d0bc-d500-4179-ae15-a91c6834dde1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3372/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:15:40,978] [INFO] Task succeeded: Blastn
[2023-03-18 09:15:40,979] [INFO] Selected 10 target genomes.
[2023-03-18 09:15:40,979] [INFO] Target genome list was writen to OceanDNA-a3372/target_genomes_gtdb.txt
[2023-03-18 09:15:40,990] [INFO] Task started: fastANI
[2023-03-18 09:15:40,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg98d6d992-e5ee-4fb6-aa14-9723b3ae5ab6/OceanDNA-a3372.fa --refList OceanDNA-a3372/target_genomes_gtdb.txt --output OceanDNA-a3372/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:15:44,362] [INFO] Task succeeded: fastANI
[2023-03-18 09:15:44,367] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:15:44,368] [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_002502625.1	s__MGIIb-N2 sp002502625	99.641	505	571	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	99.71	99.70	0.87	0.83	3	conclusive
GCA_002708015.1	s__MGIIb-N2 sp002708015	90.8338	444	571	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702985.1	s__MGIIb-N2 sp002702985	89.9781	394	571	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002697105.1	s__MGIIb-N2 sp002697105	88.1765	363	571	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	96.01	96.01	0.68	0.68	2	-
GCA_002708695.1	s__MGIIb-N2 sp002708695	80.9662	339	571	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002503665.1	s__MGIIb-N2 sp002503665	79.0182	153	571	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713585.1	s__MGIIb-N2 sp002713585	77.0642	58	571	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	98.11	98.05	0.86	0.82	4	-
GCA_002506875.1	s__MGIIb-N2 sp002506875	76.1432	50	571	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	97.18	97.18	0.84	0.84	3	-
--------------------------------------------------------------------------------
[2023-03-18 09:15:44,419] [INFO] GTDB search result was written to OceanDNA-a3372/result_gtdb.tsv
[2023-03-18 09:15:44,419] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:15:44,420] [INFO] DFAST_QC result json was written to OceanDNA-a3372/dqc_result.json
[2023-03-18 09:15:44,420] [INFO] DFAST_QC completed!
[2023-03-18 09:15:44,420] [INFO] Total running time: 0h0m44s