[2023-03-15 10:21:46,236] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:21:46,236] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:21:46,236] [INFO] DQC Reference Directory: /var/lib/cwl/stgac179bcd-cd71-4cc0-b381-236a9cff63af/dqc_reference
[2023-03-15 10:21:47,931] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:21:47,934] [INFO] Task started: Prodigal
[2023-03-15 10:21:47,934] [INFO] Running command: cat /var/lib/cwl/stg390a736d-f3a0-4f50-918a-5cfe5f62efb8/OceanDNA-b32501.fa | prodigal -d OceanDNA-b32501/cds.fna -a OceanDNA-b32501/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:21:54,705] [INFO] Task succeeded: Prodigal
[2023-03-15 10:21:54,706] [INFO] Task started: HMMsearch
[2023-03-15 10:21:54,706] [INFO] Running command: hmmsearch --tblout OceanDNA-b32501/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac179bcd-cd71-4cc0-b381-236a9cff63af/dqc_reference/reference_markers.hmm OceanDNA-b32501/protein.faa > /dev/null
[2023-03-15 10:21:54,893] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:21:54,894] [INFO] Found 6/6 markers.
[2023-03-15 10:21:54,905] [INFO] Query marker FASTA was written to OceanDNA-b32501/markers.fasta
[2023-03-15 10:21:54,905] [INFO] Task started: Blastn
[2023-03-15 10:21:54,906] [INFO] Running command: blastn -query OceanDNA-b32501/markers.fasta -db /var/lib/cwl/stgac179bcd-cd71-4cc0-b381-236a9cff63af/dqc_reference/reference_markers.fasta -out OceanDNA-b32501/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:21:55,428] [INFO] Task succeeded: Blastn
[2023-03-15 10:21:55,429] [INFO] Selected 16 target genomes.
[2023-03-15 10:21:55,429] [INFO] Target genome list was writen to OceanDNA-b32501/target_genomes.txt
[2023-03-15 10:21:55,445] [INFO] Task started: fastANI
[2023-03-15 10:21:55,445] [INFO] Running command: fastANI --query /var/lib/cwl/stg390a736d-f3a0-4f50-918a-5cfe5f62efb8/OceanDNA-b32501.fa --refList OceanDNA-b32501/target_genomes.txt --output OceanDNA-b32501/fastani_result.tsv --threads 1
[2023-03-15 10:22:02,009] [INFO] Task succeeded: fastANI
[2023-03-15 10:22:02,009] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac179bcd-cd71-4cc0-b381-236a9cff63af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:22:02,009] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac179bcd-cd71-4cc0-b381-236a9cff63af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:22:02,009] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:22:02,009] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:22:02,010] [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 10:22:02,010] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32501/tc_result.tsv
[2023-03-15 10:22:02,010] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:22:02,010] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:22:02,010] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac179bcd-cd71-4cc0-b381-236a9cff63af/dqc_reference/checkm_data
[2023-03-15 10:22:02,013] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:22:02,015] [INFO] Task started: CheckM
[2023-03-15 10:22:02,016] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32501/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32501/checkm_input OceanDNA-b32501/checkm_result
[2023-03-15 10:22:24,287] [INFO] Task succeeded: CheckM
[2023-03-15 10:22:24,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:22:24,292] [INFO] ===== Completeness check finished =====
[2023-03-15 10:22:24,292] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:22:24,292] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32501/markers.fasta)
[2023-03-15 10:22:24,293] [INFO] Task started: Blastn
[2023-03-15 10:22:24,293] [INFO] Running command: blastn -query OceanDNA-b32501/markers.fasta -db /var/lib/cwl/stgac179bcd-cd71-4cc0-b381-236a9cff63af/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32501/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:22:25,115] [INFO] Task succeeded: Blastn
[2023-03-15 10:22:25,116] [INFO] Selected 23 target genomes.
[2023-03-15 10:22:25,116] [INFO] Target genome list was writen to OceanDNA-b32501/target_genomes_gtdb.txt
[2023-03-15 10:22:25,716] [INFO] Task started: fastANI
[2023-03-15 10:22:25,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg390a736d-f3a0-4f50-918a-5cfe5f62efb8/OceanDNA-b32501.fa --refList OceanDNA-b32501/target_genomes_gtdb.txt --output OceanDNA-b32501/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:22:30,716] [INFO] Task succeeded: fastANI
[2023-03-15 10:22:30,719] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:22:30,719] [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_002691145.1	s__GCA-2691145 sp002691145	99.8064	401	423	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2691145	95.0	99.68	99.51	0.96	0.92	4	conclusive
GCA_902526175.1	s__CACBWF01 sp902526175	76.4683	53	423	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__CACBWF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:22:30,719] [INFO] GTDB search result was written to OceanDNA-b32501/result_gtdb.tsv
[2023-03-15 10:22:30,719] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:22:30,720] [INFO] DFAST_QC result json was written to OceanDNA-b32501/dqc_result.json
[2023-03-15 10:22:30,720] [INFO] DFAST_QC completed!
[2023-03-15 10:22:30,720] [INFO] Total running time: 0h0m44s