[2023-03-15 07:29:11,757] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:29:11,757] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:29:11,757] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0c65f3b-5c00-4fbf-b3ed-ba436d30e00f/dqc_reference
[2023-03-15 07:29:13,589] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:29:13,590] [INFO] Task started: Prodigal
[2023-03-15 07:29:13,590] [INFO] Running command: cat /var/lib/cwl/stg8226f4fe-9dc3-45de-b4b3-b163becee837/OceanDNA-b32469.fa | prodigal -d OceanDNA-b32469/cds.fna -a OceanDNA-b32469/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:29:19,282] [INFO] Task succeeded: Prodigal
[2023-03-15 07:29:19,282] [INFO] Task started: HMMsearch
[2023-03-15 07:29:19,282] [INFO] Running command: hmmsearch --tblout OceanDNA-b32469/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0c65f3b-5c00-4fbf-b3ed-ba436d30e00f/dqc_reference/reference_markers.hmm OceanDNA-b32469/protein.faa > /dev/null
[2023-03-15 07:29:19,439] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:29:19,440] [INFO] Found 6/6 markers.
[2023-03-15 07:29:19,450] [INFO] Query marker FASTA was written to OceanDNA-b32469/markers.fasta
[2023-03-15 07:29:19,451] [INFO] Task started: Blastn
[2023-03-15 07:29:19,451] [INFO] Running command: blastn -query OceanDNA-b32469/markers.fasta -db /var/lib/cwl/stgb0c65f3b-5c00-4fbf-b3ed-ba436d30e00f/dqc_reference/reference_markers.fasta -out OceanDNA-b32469/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:29:19,948] [INFO] Task succeeded: Blastn
[2023-03-15 07:29:19,949] [INFO] Selected 14 target genomes.
[2023-03-15 07:29:19,949] [INFO] Target genome list was writen to OceanDNA-b32469/target_genomes.txt
[2023-03-15 07:29:19,959] [INFO] Task started: fastANI
[2023-03-15 07:29:19,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg8226f4fe-9dc3-45de-b4b3-b163becee837/OceanDNA-b32469.fa --refList OceanDNA-b32469/target_genomes.txt --output OceanDNA-b32469/fastani_result.tsv --threads 1
[2023-03-15 07:29:25,896] [INFO] Task succeeded: fastANI
[2023-03-15 07:29:25,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0c65f3b-5c00-4fbf-b3ed-ba436d30e00f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:29:25,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0c65f3b-5c00-4fbf-b3ed-ba436d30e00f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:29:25,898] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:29:25,898] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:29:25,898] [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 07:29:25,898] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32469/tc_result.tsv
[2023-03-15 07:29:25,898] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:29:25,898] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:29:25,899] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0c65f3b-5c00-4fbf-b3ed-ba436d30e00f/dqc_reference/checkm_data
[2023-03-15 07:29:25,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:29:25,905] [INFO] Task started: CheckM
[2023-03-15 07:29:25,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32469/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32469/checkm_input OceanDNA-b32469/checkm_result
[2023-03-15 07:29:46,212] [INFO] Task succeeded: CheckM
[2023-03-15 07:29:46,212] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:29:46,214] [INFO] ===== Completeness check finished =====
[2023-03-15 07:29:46,214] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:29:46,214] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32469/markers.fasta)
[2023-03-15 07:29:46,215] [INFO] Task started: Blastn
[2023-03-15 07:29:46,215] [INFO] Running command: blastn -query OceanDNA-b32469/markers.fasta -db /var/lib/cwl/stgb0c65f3b-5c00-4fbf-b3ed-ba436d30e00f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32469/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:29:46,918] [INFO] Task succeeded: Blastn
[2023-03-15 07:29:46,919] [INFO] Selected 18 target genomes.
[2023-03-15 07:29:46,919] [INFO] Target genome list was writen to OceanDNA-b32469/target_genomes_gtdb.txt
[2023-03-15 07:29:46,930] [INFO] Task started: fastANI
[2023-03-15 07:29:46,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg8226f4fe-9dc3-45de-b4b3-b163becee837/OceanDNA-b32469.fa --refList OceanDNA-b32469/target_genomes_gtdb.txt --output OceanDNA-b32469/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:29:50,459] [INFO] Task succeeded: fastANI
[2023-03-15 07:29:50,464] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:29:50,464] [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_002715505.1	s__GCA-2715505 sp002715505	80.2772	301	393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__GCA-2715505	95.0	99.85	99.85	0.95	0.95	2	-
GCA_002732015.1	s__GCA-2732015 sp002732015	77.7918	188	393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__GCA-2732015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171495.2	s__GCA-2732015 sp002171495	77.7878	168	393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__GCA-2732015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902579545.1	s__CACHHO01 sp902579545	76.5851	54	393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__CACHHO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002170595.1	s__TMED62 sp002170595	75.8255	65	393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__TMED62	95.0	99.91	99.91	0.92	0.92	2	-
GCA_002720125.1	s__GCA-2720125 sp002720125	75.7376	57	393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__GCA-2720125	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:29:50,464] [INFO] GTDB search result was written to OceanDNA-b32469/result_gtdb.tsv
[2023-03-15 07:29:50,464] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:29:50,465] [INFO] DFAST_QC result json was written to OceanDNA-b32469/dqc_result.json
[2023-03-15 07:29:50,465] [INFO] DFAST_QC completed!
[2023-03-15 07:29:50,465] [INFO] Total running time: 0h0m39s