[2023-03-18 23:45:35,839] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:45:35,840] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:45:35,840] [INFO] DQC Reference Directory: /var/lib/cwl/stgc410b836-8b83-4a43-a5af-63ada688188c/dqc_reference
[2023-03-18 23:45:37,731] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:45:37,732] [INFO] Task started: Prodigal
[2023-03-18 23:45:37,732] [INFO] Running command: cat /var/lib/cwl/stgc6706ce4-601b-4acc-a057-790aec669b26/OceanDNA-b28607.fa | prodigal -d OceanDNA-b28607/cds.fna -a OceanDNA-b28607/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:45:46,701] [INFO] Task succeeded: Prodigal
[2023-03-18 23:45:46,701] [INFO] Task started: HMMsearch
[2023-03-18 23:45:46,701] [INFO] Running command: hmmsearch --tblout OceanDNA-b28607/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc410b836-8b83-4a43-a5af-63ada688188c/dqc_reference/reference_markers.hmm OceanDNA-b28607/protein.faa > /dev/null
[2023-03-18 23:45:46,893] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:45:46,894] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc6706ce4-601b-4acc-a057-790aec669b26/OceanDNA-b28607.fa]
[2023-03-18 23:45:46,912] [INFO] Query marker FASTA was written to OceanDNA-b28607/markers.fasta
[2023-03-18 23:45:46,914] [INFO] Task started: Blastn
[2023-03-18 23:45:46,914] [INFO] Running command: blastn -query OceanDNA-b28607/markers.fasta -db /var/lib/cwl/stgc410b836-8b83-4a43-a5af-63ada688188c/dqc_reference/reference_markers.fasta -out OceanDNA-b28607/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:45:49,820] [INFO] Task succeeded: Blastn
[2023-03-18 23:45:49,821] [INFO] Selected 20 target genomes.
[2023-03-18 23:45:49,821] [INFO] Target genome list was writen to OceanDNA-b28607/target_genomes.txt
[2023-03-18 23:45:49,832] [INFO] Task started: fastANI
[2023-03-18 23:45:49,832] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6706ce4-601b-4acc-a057-790aec669b26/OceanDNA-b28607.fa --refList OceanDNA-b28607/target_genomes.txt --output OceanDNA-b28607/fastani_result.tsv --threads 1
[2023-03-18 23:46:01,844] [INFO] Task succeeded: fastANI
[2023-03-18 23:46:01,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc410b836-8b83-4a43-a5af-63ada688188c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:46:01,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc410b836-8b83-4a43-a5af-63ada688188c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:46:01,844] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:46:01,844] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:46:01,844] [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 23:46:02,206] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28607/tc_result.tsv
[2023-03-18 23:46:02,206] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:46:02,206] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:46:02,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc410b836-8b83-4a43-a5af-63ada688188c/dqc_reference/checkm_data
[2023-03-18 23:46:02,210] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:46:02,284] [INFO] Task started: CheckM
[2023-03-18 23:46:02,285] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28607/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28607/checkm_input OceanDNA-b28607/checkm_result
[2023-03-18 23:46:31,859] [INFO] Task succeeded: CheckM
[2023-03-18 23:46:31,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:46:31,862] [INFO] ===== Completeness check finished =====
[2023-03-18 23:46:31,862] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:46:31,862] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28607/markers.fasta)
[2023-03-18 23:46:31,863] [INFO] Task started: Blastn
[2023-03-18 23:46:31,864] [INFO] Running command: blastn -query OceanDNA-b28607/markers.fasta -db /var/lib/cwl/stgc410b836-8b83-4a43-a5af-63ada688188c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28607/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:46:32,352] [INFO] Task succeeded: Blastn
[2023-03-18 23:46:32,353] [INFO] Selected 20 target genomes.
[2023-03-18 23:46:32,353] [INFO] Target genome list was writen to OceanDNA-b28607/target_genomes_gtdb.txt
[2023-03-18 23:46:32,372] [INFO] Task started: fastANI
[2023-03-18 23:46:32,372] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6706ce4-601b-4acc-a057-790aec669b26/OceanDNA-b28607.fa --refList OceanDNA-b28607/target_genomes_gtdb.txt --output OceanDNA-b28607/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:46:44,044] [INFO] Task succeeded: fastANI
[2023-03-18 23:46:44,046] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:46:44,046] [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_002336405.1	s__CPC320 sp002336405	77.6454	93	295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CPC320	95.0	98.74	97.78	0.79	0.51	9	-
GCA_002684375.1	s__CPC320 sp002684375	77.5113	90	295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CPC320	95.0	98.52	98.26	0.79	0.72	8	-
--------------------------------------------------------------------------------
[2023-03-18 23:46:44,047] [INFO] GTDB search result was written to OceanDNA-b28607/result_gtdb.tsv
[2023-03-18 23:46:44,047] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:46:44,047] [INFO] DFAST_QC result json was written to OceanDNA-b28607/dqc_result.json
[2023-03-18 23:46:44,047] [INFO] DFAST_QC completed!
[2023-03-18 23:46:44,047] [INFO] Total running time: 0h1m8s