[2023-03-14 11:26:25,351] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:26:25,356] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:26:25,356] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f30b496-9f77-4784-8c9f-42aa00f161d0/dqc_reference
[2023-03-14 11:26:27,359] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:26:27,360] [INFO] Task started: Prodigal
[2023-03-14 11:26:27,360] [INFO] Running command: cat /var/lib/cwl/stgcfefb988-f1c4-48c7-9f3a-b35f445dd0de/OceanDNA-b29381.fa | prodigal -d OceanDNA-b29381/cds.fna -a OceanDNA-b29381/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:26:38,774] [INFO] Task succeeded: Prodigal
[2023-03-14 11:26:38,775] [INFO] Task started: HMMsearch
[2023-03-14 11:26:38,775] [INFO] Running command: hmmsearch --tblout OceanDNA-b29381/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f30b496-9f77-4784-8c9f-42aa00f161d0/dqc_reference/reference_markers.hmm OceanDNA-b29381/protein.faa > /dev/null
[2023-03-14 11:26:38,966] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:26:38,967] [INFO] Found 6/6 markers.
[2023-03-14 11:26:39,024] [INFO] Query marker FASTA was written to OceanDNA-b29381/markers.fasta
[2023-03-14 11:26:39,024] [INFO] Task started: Blastn
[2023-03-14 11:26:39,024] [INFO] Running command: blastn -query OceanDNA-b29381/markers.fasta -db /var/lib/cwl/stg1f30b496-9f77-4784-8c9f-42aa00f161d0/dqc_reference/reference_markers.fasta -out OceanDNA-b29381/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:26:39,644] [INFO] Task succeeded: Blastn
[2023-03-14 11:26:39,658] [INFO] Selected 37 target genomes.
[2023-03-14 11:26:39,659] [INFO] Target genome list was writen to OceanDNA-b29381/target_genomes.txt
[2023-03-14 11:26:39,676] [INFO] Task started: fastANI
[2023-03-14 11:26:39,676] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfefb988-f1c4-48c7-9f3a-b35f445dd0de/OceanDNA-b29381.fa --refList OceanDNA-b29381/target_genomes.txt --output OceanDNA-b29381/fastani_result.tsv --threads 1
[2023-03-14 11:26:59,321] [INFO] Task succeeded: fastANI
[2023-03-14 11:26:59,322] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f30b496-9f77-4784-8c9f-42aa00f161d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:26:59,322] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f30b496-9f77-4784-8c9f-42aa00f161d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:26:59,322] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:26:59,322] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:26:59,322] [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 11:26:59,328] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29381/tc_result.tsv
[2023-03-14 11:26:59,337] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:26:59,337] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:26:59,337] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f30b496-9f77-4784-8c9f-42aa00f161d0/dqc_reference/checkm_data
[2023-03-14 11:26:59,342] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:26:59,357] [INFO] Task started: CheckM
[2023-03-14 11:26:59,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29381/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29381/checkm_input OceanDNA-b29381/checkm_result
[2023-03-14 11:27:32,163] [INFO] Task succeeded: CheckM
[2023-03-14 11:27:32,163] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:27:32,251] [INFO] ===== Completeness check finished =====
[2023-03-14 11:27:32,251] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:27:32,251] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29381/markers.fasta)
[2023-03-14 11:27:32,252] [INFO] Task started: Blastn
[2023-03-14 11:27:32,252] [INFO] Running command: blastn -query OceanDNA-b29381/markers.fasta -db /var/lib/cwl/stg1f30b496-9f77-4784-8c9f-42aa00f161d0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29381/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:27:33,305] [INFO] Task succeeded: Blastn
[2023-03-14 11:27:33,321] [INFO] Selected 24 target genomes.
[2023-03-14 11:27:33,321] [INFO] Target genome list was writen to OceanDNA-b29381/target_genomes_gtdb.txt
[2023-03-14 11:27:33,461] [INFO] Task started: fastANI
[2023-03-14 11:27:33,462] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfefb988-f1c4-48c7-9f3a-b35f445dd0de/OceanDNA-b29381.fa --refList OceanDNA-b29381/target_genomes_gtdb.txt --output OceanDNA-b29381/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:27:47,249] [INFO] Task succeeded: fastANI
[2023-03-14 11:27:47,253] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:27:47,253] [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_002726375.1	s__CABZJG01 sp002726375	98.4581	400	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CABZJG01	95.0	97.70	96.98	0.64	0.64	3	conclusive
GCA_902525995.1	s__CABZJG01 sp902525995	87.0871	275	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CABZJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512685.1	s__CABZJG01 sp902512685	85.1912	332	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CABZJG01	95.0	97.75	97.42	0.59	0.54	7	-
GCA_001642945.1	s__LGRT01 sp001642945	77.2637	64	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LGRT01	95.0	99.21	98.81	0.97	0.88	20	-
GCF_003352045.1	s__JL08 sp003352045	76.1655	50	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JL08	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:27:47,261] [INFO] GTDB search result was written to OceanDNA-b29381/result_gtdb.tsv
[2023-03-14 11:27:47,270] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:27:47,280] [INFO] DFAST_QC result json was written to OceanDNA-b29381/dqc_result.json
[2023-03-14 11:27:47,280] [INFO] DFAST_QC completed!
[2023-03-14 11:27:47,280] [INFO] Total running time: 0h1m22s