[2023-03-14 14:05:20,205] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:05:20,205] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:05:20,205] [INFO] DQC Reference Directory: /var/lib/cwl/stg14002aa9-7bab-4c16-a338-0c6c214a8dd3/dqc_reference
[2023-03-14 14:05:21,315] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:05:21,315] [INFO] Task started: Prodigal
[2023-03-14 14:05:21,315] [INFO] Running command: cat /var/lib/cwl/stgf1964cf1-309a-4aec-a12b-6f45fcf30c93/OceanDNA-b377.fa | prodigal -d OceanDNA-b377/cds.fna -a OceanDNA-b377/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:05:29,744] [INFO] Task succeeded: Prodigal
[2023-03-14 14:05:29,744] [INFO] Task started: HMMsearch
[2023-03-14 14:05:29,744] [INFO] Running command: hmmsearch --tblout OceanDNA-b377/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14002aa9-7bab-4c16-a338-0c6c214a8dd3/dqc_reference/reference_markers.hmm OceanDNA-b377/protein.faa > /dev/null
[2023-03-14 14:05:29,875] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:05:29,876] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf1964cf1-309a-4aec-a12b-6f45fcf30c93/OceanDNA-b377.fa]
[2023-03-14 14:05:29,886] [INFO] Query marker FASTA was written to OceanDNA-b377/markers.fasta
[2023-03-14 14:05:29,887] [INFO] Task started: Blastn
[2023-03-14 14:05:29,887] [INFO] Running command: blastn -query OceanDNA-b377/markers.fasta -db /var/lib/cwl/stg14002aa9-7bab-4c16-a338-0c6c214a8dd3/dqc_reference/reference_markers.fasta -out OceanDNA-b377/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:05:30,316] [INFO] Task succeeded: Blastn
[2023-03-14 14:05:30,316] [INFO] Selected 9 target genomes.
[2023-03-14 14:05:30,317] [INFO] Target genome list was writen to OceanDNA-b377/target_genomes.txt
[2023-03-14 14:05:30,321] [INFO] Task started: fastANI
[2023-03-14 14:05:30,321] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1964cf1-309a-4aec-a12b-6f45fcf30c93/OceanDNA-b377.fa --refList OceanDNA-b377/target_genomes.txt --output OceanDNA-b377/fastani_result.tsv --threads 1
[2023-03-14 14:05:35,455] [INFO] Task succeeded: fastANI
[2023-03-14 14:05:35,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14002aa9-7bab-4c16-a338-0c6c214a8dd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:05:35,456] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14002aa9-7bab-4c16-a338-0c6c214a8dd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:05:35,456] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:05:35,456] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 14:05:35,456] [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
--------------------------------------------------------------------------------
[2023-03-14 14:05:35,456] [INFO] DFAST Taxonomy check result was written to OceanDNA-b377/tc_result.tsv
[2023-03-14 14:05:35,456] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:05:35,457] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:05:35,457] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14002aa9-7bab-4c16-a338-0c6c214a8dd3/dqc_reference/checkm_data
[2023-03-14 14:05:35,459] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:05:35,462] [INFO] Task started: CheckM
[2023-03-14 14:05:35,462] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b377/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b377/checkm_input OceanDNA-b377/checkm_result
[2023-03-14 14:06:05,311] [INFO] Task succeeded: CheckM
[2023-03-14 14:06:05,311] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 0.84%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-14 14:06:05,313] [INFO] ===== Completeness check finished =====
[2023-03-14 14:06:05,313] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:06:05,313] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b377/markers.fasta)
[2023-03-14 14:06:05,314] [INFO] Task started: Blastn
[2023-03-14 14:06:05,314] [INFO] Running command: blastn -query OceanDNA-b377/markers.fasta -db /var/lib/cwl/stg14002aa9-7bab-4c16-a338-0c6c214a8dd3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b377/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:06:05,758] [INFO] Task succeeded: Blastn
[2023-03-14 14:06:05,759] [INFO] Selected 10 target genomes.
[2023-03-14 14:06:05,759] [INFO] Target genome list was writen to OceanDNA-b377/target_genomes_gtdb.txt
[2023-03-14 14:06:05,796] [INFO] Task started: fastANI
[2023-03-14 14:06:05,796] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1964cf1-309a-4aec-a12b-6f45fcf30c93/OceanDNA-b377.fa --refList OceanDNA-b377/target_genomes_gtdb.txt --output OceanDNA-b377/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:06:09,168] [INFO] Task succeeded: fastANI
[2023-03-14 14:06:09,174] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 14:06:09,174] [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_016463105.1	s__BACL27 sp016463105	97.2497	322	419	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014190295.1	s__BACL27 sp014190295	92.7591	353	419	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003569125.1	s__BACL27 sp003569125	80.2383	216	419	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016462185.1	s__BACL27 sp016462185	79.2912	161	419	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	98.92	98.92	0.88	0.88	2	-
GCA_009703975.1	s__BACL27 sp009703975	79.0153	169	419	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	97.18	96.93	0.73	0.69	4	-
GCA_002737635.1	s__BACL27 sp002737635	78.8499	120	419	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005805045.1	s__BACL27 sp005805045	78.5374	108	419	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	99.25	99.23	0.81	0.81	3	-
GCA_014190055.1	s__BACL27 sp014190055	78.2937	120	419	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	95.53	95.36	0.86	0.77	8	-
GCA_016870935.1	s__BACL27 sp016870935	77.0181	59	419	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__BACL27	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:06:09,174] [INFO] GTDB search result was written to OceanDNA-b377/result_gtdb.tsv
[2023-03-14 14:06:09,174] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:06:09,175] [INFO] DFAST_QC result json was written to OceanDNA-b377/dqc_result.json
[2023-03-14 14:06:09,175] [INFO] DFAST_QC completed!
[2023-03-14 14:06:09,175] [INFO] Total running time: 0h0m49s