[2023-03-18 00:28:55,436] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:28:55,436] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:28:55,436] [INFO] DQC Reference Directory: /var/lib/cwl/stg14d2f6f9-8f8e-4f5d-9bc8-17d00c0008d2/dqc_reference
[2023-03-18 00:28:56,525] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:28:56,525] [INFO] Task started: Prodigal
[2023-03-18 00:28:56,526] [INFO] Running command: cat /var/lib/cwl/stg41325e5e-d911-4ac3-814c-6468ce0403ef/OceanDNA-b26371.fa | prodigal -d OceanDNA-b26371/cds.fna -a OceanDNA-b26371/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:29:06,617] [INFO] Task succeeded: Prodigal
[2023-03-18 00:29:06,617] [INFO] Task started: HMMsearch
[2023-03-18 00:29:06,617] [INFO] Running command: hmmsearch --tblout OceanDNA-b26371/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14d2f6f9-8f8e-4f5d-9bc8-17d00c0008d2/dqc_reference/reference_markers.hmm OceanDNA-b26371/protein.faa > /dev/null
[2023-03-18 00:29:06,784] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:29:06,785] [INFO] Found 6/6 markers.
[2023-03-18 00:29:06,797] [INFO] Query marker FASTA was written to OceanDNA-b26371/markers.fasta
[2023-03-18 00:29:06,798] [INFO] Task started: Blastn
[2023-03-18 00:29:06,798] [INFO] Running command: blastn -query OceanDNA-b26371/markers.fasta -db /var/lib/cwl/stg14d2f6f9-8f8e-4f5d-9bc8-17d00c0008d2/dqc_reference/reference_markers.fasta -out OceanDNA-b26371/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:29:07,372] [INFO] Task succeeded: Blastn
[2023-03-18 00:29:07,373] [INFO] Selected 25 target genomes.
[2023-03-18 00:29:07,373] [INFO] Target genome list was writen to OceanDNA-b26371/target_genomes.txt
[2023-03-18 00:29:07,386] [INFO] Task started: fastANI
[2023-03-18 00:29:07,386] [INFO] Running command: fastANI --query /var/lib/cwl/stg41325e5e-d911-4ac3-814c-6468ce0403ef/OceanDNA-b26371.fa --refList OceanDNA-b26371/target_genomes.txt --output OceanDNA-b26371/fastani_result.tsv --threads 1
[2023-03-18 00:29:18,780] [INFO] Task succeeded: fastANI
[2023-03-18 00:29:18,780] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14d2f6f9-8f8e-4f5d-9bc8-17d00c0008d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:29:18,781] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14d2f6f9-8f8e-4f5d-9bc8-17d00c0008d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:29:18,781] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:29:18,781] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:29:18,781] [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 00:29:18,781] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26371/tc_result.tsv
[2023-03-18 00:29:18,781] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:29:18,781] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:29:18,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14d2f6f9-8f8e-4f5d-9bc8-17d00c0008d2/dqc_reference/checkm_data
[2023-03-18 00:29:18,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:29:18,796] [INFO] Task started: CheckM
[2023-03-18 00:29:18,796] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26371/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26371/checkm_input OceanDNA-b26371/checkm_result
[2023-03-18 00:29:48,575] [INFO] Task succeeded: CheckM
[2023-03-18 00:29:48,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:29:48,577] [INFO] ===== Completeness check finished =====
[2023-03-18 00:29:48,577] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:29:48,578] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26371/markers.fasta)
[2023-03-18 00:29:48,579] [INFO] Task started: Blastn
[2023-03-18 00:29:48,579] [INFO] Running command: blastn -query OceanDNA-b26371/markers.fasta -db /var/lib/cwl/stg14d2f6f9-8f8e-4f5d-9bc8-17d00c0008d2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26371/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:29:49,508] [INFO] Task succeeded: Blastn
[2023-03-18 00:29:49,509] [INFO] Selected 20 target genomes.
[2023-03-18 00:29:49,509] [INFO] Target genome list was writen to OceanDNA-b26371/target_genomes_gtdb.txt
[2023-03-18 00:29:49,605] [INFO] Task started: fastANI
[2023-03-18 00:29:49,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg41325e5e-d911-4ac3-814c-6468ce0403ef/OceanDNA-b26371.fa --refList OceanDNA-b26371/target_genomes_gtdb.txt --output OceanDNA-b26371/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:29:56,073] [INFO] Task succeeded: fastANI
[2023-03-18 00:29:56,077] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:29:56,077] [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_011524995.1	s__UBA685 sp011524995	87.0444	472	559	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA685	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002299005.1	s__UBA685 sp002299005	77.4794	149	559	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	77.4639	119	559	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	77.2255	103	559	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA685	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011522945.1	s__WTHY01 sp011522945	76.1689	53	559	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__WTHY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:29:56,078] [INFO] GTDB search result was written to OceanDNA-b26371/result_gtdb.tsv
[2023-03-18 00:29:56,078] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:29:56,078] [INFO] DFAST_QC result json was written to OceanDNA-b26371/dqc_result.json
[2023-03-18 00:29:56,078] [INFO] DFAST_QC completed!
[2023-03-18 00:29:56,078] [INFO] Total running time: 0h1m1s