[2023-03-17 23:20:46,556] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:20:46,566] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:20:46,566] [INFO] DQC Reference Directory: /var/lib/cwl/stg08c7a3ee-a4dd-437f-bb18-f124a75baf4b/dqc_reference
[2023-03-17 23:20:48,697] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:20:48,698] [INFO] Task started: Prodigal
[2023-03-17 23:20:48,698] [INFO] Running command: cat /var/lib/cwl/stgbd927041-ac47-4165-b2a7-7ffdfe2647ae/OceanDNA-a4473.fa | prodigal -d OceanDNA-a4473/cds.fna -a OceanDNA-a4473/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:20:53,828] [INFO] Task succeeded: Prodigal
[2023-03-17 23:20:53,828] [INFO] Task started: HMMsearch
[2023-03-17 23:20:53,828] [INFO] Running command: hmmsearch --tblout OceanDNA-a4473/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08c7a3ee-a4dd-437f-bb18-f124a75baf4b/dqc_reference/reference_markers.hmm OceanDNA-a4473/protein.faa > /dev/null
[2023-03-17 23:20:53,969] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:20:53,969] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgbd927041-ac47-4165-b2a7-7ffdfe2647ae/OceanDNA-a4473.fa]
[2023-03-17 23:20:54,045] [INFO] Query marker FASTA was written to OceanDNA-a4473/markers.fasta
[2023-03-17 23:20:54,045] [INFO] Task started: Blastn
[2023-03-17 23:20:54,046] [INFO] Running command: blastn -query OceanDNA-a4473/markers.fasta -db /var/lib/cwl/stg08c7a3ee-a4dd-437f-bb18-f124a75baf4b/dqc_reference/reference_markers.fasta -out OceanDNA-a4473/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:20:56,385] [INFO] Task succeeded: Blastn
[2023-03-17 23:20:56,415] [INFO] Selected 0 target genomes.
[2023-03-17 23:20:56,415] [INFO] Target genome list was writen to OceanDNA-a4473/target_genomes.txt
[2023-03-17 23:20:56,415] [ERROR] File is empty. [OceanDNA-a4473/target_genomes.txt]
[2023-03-17 23:20:56,415] [ERROR] Task failed. No target genome found.
[2023-03-17 23:20:56,415] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:20:56,416] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08c7a3ee-a4dd-437f-bb18-f124a75baf4b/dqc_reference/checkm_data
[2023-03-17 23:20:56,466] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:20:56,469] [INFO] Task started: CheckM
[2023-03-17 23:20:56,469] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4473/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4473/checkm_input OceanDNA-a4473/checkm_result
[2023-03-17 23:21:19,443] [INFO] Task succeeded: CheckM
[2023-03-17 23:21:19,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.66%
Contamintation: 5.59%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:21:19,593] [INFO] ===== Completeness check finished =====
[2023-03-17 23:21:19,593] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:21:19,594] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4473/markers.fasta)
[2023-03-17 23:21:19,595] [INFO] Task started: Blastn
[2023-03-17 23:21:19,595] [INFO] Running command: blastn -query OceanDNA-a4473/markers.fasta -db /var/lib/cwl/stg08c7a3ee-a4dd-437f-bb18-f124a75baf4b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4473/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:21:20,439] [INFO] Task succeeded: Blastn
[2023-03-17 23:21:20,446] [INFO] Selected 6 target genomes.
[2023-03-17 23:21:20,446] [INFO] Target genome list was writen to OceanDNA-a4473/target_genomes_gtdb.txt
[2023-03-17 23:21:20,478] [INFO] Task started: fastANI
[2023-03-17 23:21:20,478] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd927041-ac47-4165-b2a7-7ffdfe2647ae/OceanDNA-a4473.fa --refList OceanDNA-a4473/target_genomes_gtdb.txt --output OceanDNA-a4473/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:21:21,934] [INFO] Task succeeded: fastANI
[2023-03-17 23:21:21,938] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:21:21,938] [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_002502095.1	s__MGIIb-O5 sp002502095	94.0553	128	142	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.50	98.52	0.89	0.78	6	-
GCA_002501805.1	s__MGIIb-O5 sp002501805	93.1555	128	142	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	97.49	96.31	0.90	0.85	5	-
GCA_002499865.1	s__MGIIb-O5 sp002499865	89.9656	120	142	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.65	99.57	0.89	0.88	3	-
GCA_002499325.1	s__MGIIb-O5 sp002499325	89.86	111	142	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.30	99.30	0.84	0.84	2	-
GCA_002506825.1	s__MGIIb-O5 sp002506825	81.5005	110	142	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	98.02	97.97	0.86	0.84	3	-
--------------------------------------------------------------------------------
[2023-03-17 23:21:21,940] [INFO] GTDB search result was written to OceanDNA-a4473/result_gtdb.tsv
[2023-03-17 23:21:21,942] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:21:21,945] [INFO] DFAST_QC result json was written to OceanDNA-a4473/dqc_result.json
[2023-03-17 23:21:21,945] [INFO] DFAST_QC completed!
[2023-03-17 23:21:21,945] [INFO] Total running time: 0h0m35s