[2023-03-15 04:10:27,901] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:10:27,901] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:10:27,902] [INFO] DQC Reference Directory: /var/lib/cwl/stgafef67d9-feeb-4198-acd7-5c5bbf08121c/dqc_reference
[2023-03-15 04:10:28,996] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:10:28,996] [INFO] Task started: Prodigal
[2023-03-15 04:10:28,997] [INFO] Running command: cat /var/lib/cwl/stg2b3ec642-5270-4b30-889b-2e787df14de2/OceanDNA-a4323.fa | prodigal -d OceanDNA-a4323/cds.fna -a OceanDNA-a4323/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:10:35,762] [INFO] Task succeeded: Prodigal
[2023-03-15 04:10:35,762] [INFO] Task started: HMMsearch
[2023-03-15 04:10:35,762] [INFO] Running command: hmmsearch --tblout OceanDNA-a4323/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgafef67d9-feeb-4198-acd7-5c5bbf08121c/dqc_reference/reference_markers.hmm OceanDNA-a4323/protein.faa > /dev/null
[2023-03-15 04:10:35,927] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:10:35,927] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2b3ec642-5270-4b30-889b-2e787df14de2/OceanDNA-a4323.fa]
[2023-03-15 04:10:35,944] [INFO] Query marker FASTA was written to OceanDNA-a4323/markers.fasta
[2023-03-15 04:10:35,945] [INFO] Task started: Blastn
[2023-03-15 04:10:35,945] [INFO] Running command: blastn -query OceanDNA-a4323/markers.fasta -db /var/lib/cwl/stgafef67d9-feeb-4198-acd7-5c5bbf08121c/dqc_reference/reference_markers.fasta -out OceanDNA-a4323/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:10:36,373] [INFO] Task succeeded: Blastn
[2023-03-15 04:10:36,380] [INFO] Selected 4 target genomes.
[2023-03-15 04:10:36,381] [INFO] Target genome list was writen to OceanDNA-a4323/target_genomes.txt
[2023-03-15 04:10:36,383] [INFO] Task started: fastANI
[2023-03-15 04:10:36,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b3ec642-5270-4b30-889b-2e787df14de2/OceanDNA-a4323.fa --refList OceanDNA-a4323/target_genomes.txt --output OceanDNA-a4323/fastani_result.tsv --threads 1
[2023-03-15 04:10:38,214] [INFO] Task succeeded: fastANI
[2023-03-15 04:10:38,214] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgafef67d9-feeb-4198-acd7-5c5bbf08121c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:10:38,214] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgafef67d9-feeb-4198-acd7-5c5bbf08121c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:10:38,215] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:10:38,215] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 04:10:38,215] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-15 04:10:38,218] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4323/tc_result.tsv
[2023-03-15 04:10:38,220] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:10:38,220] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:10:38,220] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgafef67d9-feeb-4198-acd7-5c5bbf08121c/dqc_reference/checkm_data
[2023-03-15 04:10:38,223] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:10:38,231] [INFO] Task started: CheckM
[2023-03-15 04:10:38,231] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4323/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4323/checkm_input OceanDNA-a4323/checkm_result
[2023-03-15 04:11:00,740] [INFO] Task succeeded: CheckM
[2023-03-15 04:11:00,741] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 04:11:00,750] [INFO] ===== Completeness check finished =====
[2023-03-15 04:11:00,750] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:11:00,751] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4323/markers.fasta)
[2023-03-15 04:11:00,752] [INFO] Task started: Blastn
[2023-03-15 04:11:00,752] [INFO] Running command: blastn -query OceanDNA-a4323/markers.fasta -db /var/lib/cwl/stgafef67d9-feeb-4198-acd7-5c5bbf08121c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4323/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:11:01,166] [INFO] Task succeeded: Blastn
[2023-03-15 04:11:01,170] [INFO] Selected 7 target genomes.
[2023-03-15 04:11:01,170] [INFO] Target genome list was writen to OceanDNA-a4323/target_genomes_gtdb.txt
[2023-03-15 04:11:01,185] [INFO] Task started: fastANI
[2023-03-15 04:11:01,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b3ec642-5270-4b30-889b-2e787df14de2/OceanDNA-a4323.fa --refList OceanDNA-a4323/target_genomes_gtdb.txt --output OceanDNA-a4323/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:11:03,511] [INFO] Task succeeded: fastANI
[2023-03-15 04:11:03,516] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 04:11:03,516] [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_002172375.1	s__MGIIb-O3 sp002172375	97.3307	300	422	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002712575.1	s__MGIIb-O3 sp002712575	89.5826	327	422	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602595.1	s__MGIIb-O3 sp003602595	89.2551	335	422	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719615.1	s__MGIIb-O3 sp002719615	89.0535	384	422	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002731195.1	s__MGIIb-O3 sp002731195	83.0323	275	422	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457145.1	s__MGIIb-O3 sp002457145	79.847	304	422	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.76	99.72	0.89	0.85	3	-
--------------------------------------------------------------------------------
[2023-03-15 04:11:03,518] [INFO] GTDB search result was written to OceanDNA-a4323/result_gtdb.tsv
[2023-03-15 04:11:03,518] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:11:03,520] [INFO] DFAST_QC result json was written to OceanDNA-a4323/dqc_result.json
[2023-03-15 04:11:03,520] [INFO] DFAST_QC completed!
[2023-03-15 04:11:03,521] [INFO] Total running time: 0h0m36s