[2023-03-18 00:05:54,481] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:05:54,481] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:05:54,481] [INFO] DQC Reference Directory: /var/lib/cwl/stg88a438e5-ce1c-4dd9-b022-453629804277/dqc_reference
[2023-03-18 00:05:55,682] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:05:55,682] [INFO] Task started: Prodigal
[2023-03-18 00:05:55,682] [INFO] Running command: cat /var/lib/cwl/stga46c813b-1d60-45df-af15-5a1ffc9bc7b8/OceanDNA-b42501.fa | prodigal -d OceanDNA-b42501/cds.fna -a OceanDNA-b42501/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:06:01,403] [INFO] Task succeeded: Prodigal
[2023-03-18 00:06:01,403] [INFO] Task started: HMMsearch
[2023-03-18 00:06:01,403] [INFO] Running command: hmmsearch --tblout OceanDNA-b42501/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88a438e5-ce1c-4dd9-b022-453629804277/dqc_reference/reference_markers.hmm OceanDNA-b42501/protein.faa > /dev/null
[2023-03-18 00:06:01,618] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:06:01,618] [INFO] Found 6/6 markers.
[2023-03-18 00:06:01,627] [INFO] Query marker FASTA was written to OceanDNA-b42501/markers.fasta
[2023-03-18 00:06:01,628] [INFO] Task started: Blastn
[2023-03-18 00:06:01,628] [INFO] Running command: blastn -query OceanDNA-b42501/markers.fasta -db /var/lib/cwl/stg88a438e5-ce1c-4dd9-b022-453629804277/dqc_reference/reference_markers.fasta -out OceanDNA-b42501/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:06:02,168] [INFO] Task succeeded: Blastn
[2023-03-18 00:06:02,169] [INFO] Selected 12 target genomes.
[2023-03-18 00:06:02,169] [INFO] Target genome list was writen to OceanDNA-b42501/target_genomes.txt
[2023-03-18 00:06:02,176] [INFO] Task started: fastANI
[2023-03-18 00:06:02,176] [INFO] Running command: fastANI --query /var/lib/cwl/stga46c813b-1d60-45df-af15-5a1ffc9bc7b8/OceanDNA-b42501.fa --refList OceanDNA-b42501/target_genomes.txt --output OceanDNA-b42501/fastani_result.tsv --threads 1
[2023-03-18 00:06:07,166] [INFO] Task succeeded: fastANI
[2023-03-18 00:06:07,166] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88a438e5-ce1c-4dd9-b022-453629804277/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:06:07,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88a438e5-ce1c-4dd9-b022-453629804277/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:06:07,166] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:06:07,166] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:06:07,166] [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
--------------------------------------------------------------------------------
[2023-03-18 00:06:07,167] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42501/tc_result.tsv
[2023-03-18 00:06:07,167] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:06:07,167] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:06:07,167] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88a438e5-ce1c-4dd9-b022-453629804277/dqc_reference/checkm_data
[2023-03-18 00:06:07,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:06:07,262] [INFO] Task started: CheckM
[2023-03-18 00:06:07,262] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42501/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42501/checkm_input OceanDNA-b42501/checkm_result
[2023-03-18 00:06:27,447] [INFO] Task succeeded: CheckM
[2023-03-18 00:06:27,448] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.38%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 00:06:27,458] [INFO] ===== Completeness check finished =====
[2023-03-18 00:06:27,458] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:06:27,458] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42501/markers.fasta)
[2023-03-18 00:06:27,458] [INFO] Task started: Blastn
[2023-03-18 00:06:27,458] [INFO] Running command: blastn -query OceanDNA-b42501/markers.fasta -db /var/lib/cwl/stg88a438e5-ce1c-4dd9-b022-453629804277/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42501/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:06:28,357] [INFO] Task succeeded: Blastn
[2023-03-18 00:06:28,358] [INFO] Selected 28 target genomes.
[2023-03-18 00:06:28,358] [INFO] Target genome list was writen to OceanDNA-b42501/target_genomes_gtdb.txt
[2023-03-18 00:06:28,423] [INFO] Task started: fastANI
[2023-03-18 00:06:28,423] [INFO] Running command: fastANI --query /var/lib/cwl/stga46c813b-1d60-45df-af15-5a1ffc9bc7b8/OceanDNA-b42501.fa --refList OceanDNA-b42501/target_genomes_gtdb.txt --output OceanDNA-b42501/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:06:36,034] [INFO] Task succeeded: fastANI
[2023-03-18 00:06:36,037] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:06:36,037] [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_001628005.1	s__AEGEAN-183 sp001628005	78.133	156	383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__AEGEAN-183	95.0	99.32	99.31	0.88	0.87	3	-
GCA_012965075.1	s__AEGEAN-183 sp012965075	77.2278	105	383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__AEGEAN-183	95.0	98.73	98.73	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-03-18 00:06:36,039] [INFO] GTDB search result was written to OceanDNA-b42501/result_gtdb.tsv
[2023-03-18 00:06:36,043] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:06:36,045] [INFO] DFAST_QC result json was written to OceanDNA-b42501/dqc_result.json
[2023-03-18 00:06:36,045] [INFO] DFAST_QC completed!
[2023-03-18 00:06:36,045] [INFO] Total running time: 0h0m42s