[2023-03-19 01:13:44,401] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:13:44,401] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:13:44,401] [INFO] DQC Reference Directory: /var/lib/cwl/stg699a1ad6-84dc-42d1-8a99-2959f0393037/dqc_reference
[2023-03-19 01:13:45,489] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:13:45,489] [INFO] Task started: Prodigal
[2023-03-19 01:13:45,490] [INFO] Running command: cat /var/lib/cwl/stgd05cb8f0-c3f1-40f1-ad29-4b180d34c5fe/OceanDNA-a2962.fa | prodigal -d OceanDNA-a2962/cds.fna -a OceanDNA-a2962/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:13:53,645] [INFO] Task succeeded: Prodigal
[2023-03-19 01:13:53,645] [INFO] Task started: HMMsearch
[2023-03-19 01:13:53,645] [INFO] Running command: hmmsearch --tblout OceanDNA-a2962/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg699a1ad6-84dc-42d1-8a99-2959f0393037/dqc_reference/reference_markers.hmm OceanDNA-a2962/protein.faa > /dev/null
[2023-03-19 01:13:53,806] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:13:53,807] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd05cb8f0-c3f1-40f1-ad29-4b180d34c5fe/OceanDNA-a2962.fa]
[2023-03-19 01:13:53,818] [INFO] Query marker FASTA was written to OceanDNA-a2962/markers.fasta
[2023-03-19 01:13:53,819] [INFO] Task started: Blastn
[2023-03-19 01:13:53,819] [INFO] Running command: blastn -query OceanDNA-a2962/markers.fasta -db /var/lib/cwl/stg699a1ad6-84dc-42d1-8a99-2959f0393037/dqc_reference/reference_markers.fasta -out OceanDNA-a2962/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:13:54,251] [INFO] Task succeeded: Blastn
[2023-03-19 01:13:54,251] [INFO] Selected 0 target genomes.
[2023-03-19 01:13:54,251] [INFO] Target genome list was writen to OceanDNA-a2962/target_genomes.txt
[2023-03-19 01:13:54,252] [ERROR] File is empty. [OceanDNA-a2962/target_genomes.txt]
[2023-03-19 01:13:54,252] [ERROR] Task failed. No target genome found.
[2023-03-19 01:13:54,252] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:13:54,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg699a1ad6-84dc-42d1-8a99-2959f0393037/dqc_reference/checkm_data
[2023-03-19 01:13:54,255] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:13:54,258] [INFO] Task started: CheckM
[2023-03-19 01:13:54,258] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2962/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2962/checkm_input OceanDNA-a2962/checkm_result
[2023-03-19 01:14:20,790] [INFO] Task succeeded: CheckM
[2023-03-19 01:14:20,790] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.88%
Contamintation: 0.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-19 01:14:20,792] [INFO] ===== Completeness check finished =====
[2023-03-19 01:14:20,792] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:14:20,792] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2962/markers.fasta)
[2023-03-19 01:14:20,794] [INFO] Task started: Blastn
[2023-03-19 01:14:20,794] [INFO] Running command: blastn -query OceanDNA-a2962/markers.fasta -db /var/lib/cwl/stg699a1ad6-84dc-42d1-8a99-2959f0393037/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2962/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:14:21,224] [INFO] Task succeeded: Blastn
[2023-03-19 01:14:21,225] [INFO] Selected 9 target genomes.
[2023-03-19 01:14:21,225] [INFO] Target genome list was writen to OceanDNA-a2962/target_genomes_gtdb.txt
[2023-03-19 01:14:21,233] [INFO] Task started: fastANI
[2023-03-19 01:14:21,233] [INFO] Running command: fastANI --query /var/lib/cwl/stgd05cb8f0-c3f1-40f1-ad29-4b180d34c5fe/OceanDNA-a2962.fa --refList OceanDNA-a2962/target_genomes_gtdb.txt --output OceanDNA-a2962/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:14:24,797] [INFO] Task succeeded: fastANI
[2023-03-19 01:14:24,801] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:14:24,801] [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_002722695.1	s__Poseidonia sp002722695	91.7466	323	384	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.22	99.22	0.79	0.79	3	-
GCA_002694525.1	s__Poseidonia sp002694525	81.1565	267	384	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002495645.1	s__Poseidonia sp002495645	78.1738	174	384	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.68	99.68	0.84	0.84	2	-
GCA_002689105.1	s__Poseidonia sp002689105	78.0759	149	384	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.72	96.72	0.80	0.80	2	-
GCA_002704515.1	s__Poseidonia sp002704515	77.9855	155	384	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:14:24,801] [INFO] GTDB search result was written to OceanDNA-a2962/result_gtdb.tsv
[2023-03-19 01:14:24,801] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:14:24,802] [INFO] DFAST_QC result json was written to OceanDNA-a2962/dqc_result.json
[2023-03-19 01:14:24,802] [INFO] DFAST_QC completed!
[2023-03-19 01:14:24,802] [INFO] Total running time: 0h0m40s