[2023-03-17 11:57:19,285] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:57:19,285] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:57:19,285] [INFO] DQC Reference Directory: /var/lib/cwl/stg2814b0f4-2b92-41e7-906b-3960dfc9caaf/dqc_reference
[2023-03-17 11:57:20,888] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:57:20,888] [INFO] Task started: Prodigal
[2023-03-17 11:57:20,888] [INFO] Running command: cat /var/lib/cwl/stg1b3fb25a-092e-4ffc-8829-9bda3c9dcfc6/OceanDNA-b26751.fa | prodigal -d OceanDNA-b26751/cds.fna -a OceanDNA-b26751/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:57:31,634] [INFO] Task succeeded: Prodigal
[2023-03-17 11:57:31,634] [INFO] Task started: HMMsearch
[2023-03-17 11:57:31,634] [INFO] Running command: hmmsearch --tblout OceanDNA-b26751/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2814b0f4-2b92-41e7-906b-3960dfc9caaf/dqc_reference/reference_markers.hmm OceanDNA-b26751/protein.faa > /dev/null
[2023-03-17 11:57:31,800] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:57:31,801] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1b3fb25a-092e-4ffc-8829-9bda3c9dcfc6/OceanDNA-b26751.fa]
[2023-03-17 11:57:31,814] [INFO] Query marker FASTA was written to OceanDNA-b26751/markers.fasta
[2023-03-17 11:57:31,815] [INFO] Task started: Blastn
[2023-03-17 11:57:31,815] [INFO] Running command: blastn -query OceanDNA-b26751/markers.fasta -db /var/lib/cwl/stg2814b0f4-2b92-41e7-906b-3960dfc9caaf/dqc_reference/reference_markers.fasta -out OceanDNA-b26751/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:57:32,406] [INFO] Task succeeded: Blastn
[2023-03-17 11:57:32,407] [INFO] Selected 25 target genomes.
[2023-03-17 11:57:32,407] [INFO] Target genome list was writen to OceanDNA-b26751/target_genomes.txt
[2023-03-17 11:57:32,421] [INFO] Task started: fastANI
[2023-03-17 11:57:32,422] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b3fb25a-092e-4ffc-8829-9bda3c9dcfc6/OceanDNA-b26751.fa --refList OceanDNA-b26751/target_genomes.txt --output OceanDNA-b26751/fastani_result.tsv --threads 1
[2023-03-17 11:57:48,246] [INFO] Task succeeded: fastANI
[2023-03-17 11:57:48,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2814b0f4-2b92-41e7-906b-3960dfc9caaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:57:48,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2814b0f4-2b92-41e7-906b-3960dfc9caaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:57:48,246] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:57:48,246] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:57:48,246] [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 11:57:48,247] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26751/tc_result.tsv
[2023-03-17 11:57:48,247] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:57:48,247] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:57:48,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2814b0f4-2b92-41e7-906b-3960dfc9caaf/dqc_reference/checkm_data
[2023-03-17 11:57:48,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:57:48,253] [INFO] Task started: CheckM
[2023-03-17 11:57:48,253] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26751/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26751/checkm_input OceanDNA-b26751/checkm_result
[2023-03-17 11:58:20,171] [INFO] Task succeeded: CheckM
[2023-03-17 11:58:20,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 11:58:20,174] [INFO] ===== Completeness check finished =====
[2023-03-17 11:58:20,174] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:58:20,174] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26751/markers.fasta)
[2023-03-17 11:58:20,174] [INFO] Task started: Blastn
[2023-03-17 11:58:20,174] [INFO] Running command: blastn -query OceanDNA-b26751/markers.fasta -db /var/lib/cwl/stg2814b0f4-2b92-41e7-906b-3960dfc9caaf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26751/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:58:21,169] [INFO] Task succeeded: Blastn
[2023-03-17 11:58:21,170] [INFO] Selected 24 target genomes.
[2023-03-17 11:58:21,170] [INFO] Target genome list was writen to OceanDNA-b26751/target_genomes_gtdb.txt
[2023-03-17 11:58:21,351] [INFO] Task started: fastANI
[2023-03-17 11:58:21,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b3fb25a-092e-4ffc-8829-9bda3c9dcfc6/OceanDNA-b26751.fa --refList OceanDNA-b26751/target_genomes_gtdb.txt --output OceanDNA-b26751/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:58:35,497] [INFO] Task succeeded: fastANI
[2023-03-17 11:58:35,499] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:58:35,499] [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_017640685.1	s__HXMU1428-3 sp017640685	76.0059	73	570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__HXMU1428-3;g__HXMU1428-3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:58:35,500] [INFO] GTDB search result was written to OceanDNA-b26751/result_gtdb.tsv
[2023-03-17 11:58:35,500] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:58:35,500] [INFO] DFAST_QC result json was written to OceanDNA-b26751/dqc_result.json
[2023-03-17 11:58:35,500] [INFO] DFAST_QC completed!
[2023-03-17 11:58:35,500] [INFO] Total running time: 0h1m16s