[2023-03-17 09:05:02,541] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:05:02,541] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:05:02,541] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5a6685b-8eb2-4585-8378-aa9a406a9013/dqc_reference
[2023-03-17 09:05:03,729] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:05:03,729] [INFO] Task started: Prodigal
[2023-03-17 09:05:03,729] [INFO] Running command: cat /var/lib/cwl/stg541c7b74-35f8-4087-bf6a-602c78b6dc73/OceanDNA-b26362.fa | prodigal -d OceanDNA-b26362/cds.fna -a OceanDNA-b26362/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:05:12,161] [INFO] Task succeeded: Prodigal
[2023-03-17 09:05:12,162] [INFO] Task started: HMMsearch
[2023-03-17 09:05:12,162] [INFO] Running command: hmmsearch --tblout OceanDNA-b26362/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5a6685b-8eb2-4585-8378-aa9a406a9013/dqc_reference/reference_markers.hmm OceanDNA-b26362/protein.faa > /dev/null
[2023-03-17 09:05:12,330] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:05:12,330] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg541c7b74-35f8-4087-bf6a-602c78b6dc73/OceanDNA-b26362.fa]
[2023-03-17 09:05:12,343] [INFO] Query marker FASTA was written to OceanDNA-b26362/markers.fasta
[2023-03-17 09:05:12,344] [INFO] Task started: Blastn
[2023-03-17 09:05:12,344] [INFO] Running command: blastn -query OceanDNA-b26362/markers.fasta -db /var/lib/cwl/stgf5a6685b-8eb2-4585-8378-aa9a406a9013/dqc_reference/reference_markers.fasta -out OceanDNA-b26362/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:05:12,884] [INFO] Task succeeded: Blastn
[2023-03-17 09:05:12,884] [INFO] Selected 22 target genomes.
[2023-03-17 09:05:12,885] [INFO] Target genome list was writen to OceanDNA-b26362/target_genomes.txt
[2023-03-17 09:05:13,072] [INFO] Task started: fastANI
[2023-03-17 09:05:13,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg541c7b74-35f8-4087-bf6a-602c78b6dc73/OceanDNA-b26362.fa --refList OceanDNA-b26362/target_genomes.txt --output OceanDNA-b26362/fastani_result.tsv --threads 1
[2023-03-17 09:05:20,935] [INFO] Task succeeded: fastANI
[2023-03-17 09:05:20,935] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5a6685b-8eb2-4585-8378-aa9a406a9013/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:05:20,935] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5a6685b-8eb2-4585-8378-aa9a406a9013/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:05:20,936] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:05:20,936] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:05:20,936] [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
--------------------------------------------------------------------------------
[2023-03-17 09:05:20,936] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26362/tc_result.tsv
[2023-03-17 09:05:20,936] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:05:20,936] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:05:20,936] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5a6685b-8eb2-4585-8378-aa9a406a9013/dqc_reference/checkm_data
[2023-03-17 09:05:20,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:05:20,942] [INFO] Task started: CheckM
[2023-03-17 09:05:20,942] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26362/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26362/checkm_input OceanDNA-b26362/checkm_result
[2023-03-17 09:05:47,444] [INFO] Task succeeded: CheckM
[2023-03-17 09:05:47,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 09:05:47,446] [INFO] ===== Completeness check finished =====
[2023-03-17 09:05:47,446] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:05:47,446] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26362/markers.fasta)
[2023-03-17 09:05:47,447] [INFO] Task started: Blastn
[2023-03-17 09:05:47,448] [INFO] Running command: blastn -query OceanDNA-b26362/markers.fasta -db /var/lib/cwl/stgf5a6685b-8eb2-4585-8378-aa9a406a9013/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26362/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:05:48,269] [INFO] Task succeeded: Blastn
[2023-03-17 09:05:48,270] [INFO] Selected 19 target genomes.
[2023-03-17 09:05:48,270] [INFO] Target genome list was writen to OceanDNA-b26362/target_genomes_gtdb.txt
[2023-03-17 09:05:48,576] [INFO] Task started: fastANI
[2023-03-17 09:05:48,576] [INFO] Running command: fastANI --query /var/lib/cwl/stg541c7b74-35f8-4087-bf6a-602c78b6dc73/OceanDNA-b26362.fa --refList OceanDNA-b26362/target_genomes_gtdb.txt --output OceanDNA-b26362/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:05:54,402] [INFO] Task succeeded: fastANI
[2023-03-17 09:05:54,405] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 09:05:54,405] [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_002299005.1	s__UBA685 sp002299005	77.8951	130	467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA685	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526395.1	s__UBA685 sp011526395	77.787	121	467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA685	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524995.1	s__UBA685 sp011524995	77.4764	147	467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA685	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525265.1	s__UBA685 sp011525265	77.1251	122	467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA685	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:05:54,406] [INFO] GTDB search result was written to OceanDNA-b26362/result_gtdb.tsv
[2023-03-17 09:05:54,406] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:05:54,407] [INFO] DFAST_QC result json was written to OceanDNA-b26362/dqc_result.json
[2023-03-17 09:05:54,407] [INFO] DFAST_QC completed!
[2023-03-17 09:05:54,407] [INFO] Total running time: 0h0m52s