[2023-03-16 11:09:34,720] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:09:34,721] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:09:34,721] [INFO] DQC Reference Directory: /var/lib/cwl/stgf56dedc8-d9a3-40cb-8c3b-5b1850ff31a1/dqc_reference
[2023-03-16 11:09:37,989] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:09:37,989] [INFO] Task started: Prodigal
[2023-03-16 11:09:37,990] [INFO] Running command: cat /var/lib/cwl/stg74e53769-f237-40aa-8fa7-0777fa446f17/OceanDNA-b35889.fa | prodigal -d OceanDNA-b35889/cds.fna -a OceanDNA-b35889/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:09:42,429] [INFO] Task succeeded: Prodigal
[2023-03-16 11:09:42,429] [INFO] Task started: HMMsearch
[2023-03-16 11:09:42,429] [INFO] Running command: hmmsearch --tblout OceanDNA-b35889/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf56dedc8-d9a3-40cb-8c3b-5b1850ff31a1/dqc_reference/reference_markers.hmm OceanDNA-b35889/protein.faa > /dev/null
[2023-03-16 11:09:42,570] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:09:42,571] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg74e53769-f237-40aa-8fa7-0777fa446f17/OceanDNA-b35889.fa]
[2023-03-16 11:09:42,579] [INFO] Query marker FASTA was written to OceanDNA-b35889/markers.fasta
[2023-03-16 11:09:42,580] [INFO] Task started: Blastn
[2023-03-16 11:09:42,580] [INFO] Running command: blastn -query OceanDNA-b35889/markers.fasta -db /var/lib/cwl/stgf56dedc8-d9a3-40cb-8c3b-5b1850ff31a1/dqc_reference/reference_markers.fasta -out OceanDNA-b35889/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:09:46,149] [INFO] Task succeeded: Blastn
[2023-03-16 11:09:46,150] [INFO] Selected 25 target genomes.
[2023-03-16 11:09:46,151] [INFO] Target genome list was writen to OceanDNA-b35889/target_genomes.txt
[2023-03-16 11:09:46,185] [INFO] Task started: fastANI
[2023-03-16 11:09:46,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg74e53769-f237-40aa-8fa7-0777fa446f17/OceanDNA-b35889.fa --refList OceanDNA-b35889/target_genomes.txt --output OceanDNA-b35889/fastani_result.tsv --threads 1
[2023-03-16 11:10:01,522] [INFO] Task succeeded: fastANI
[2023-03-16 11:10:01,523] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf56dedc8-d9a3-40cb-8c3b-5b1850ff31a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:10:01,523] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf56dedc8-d9a3-40cb-8c3b-5b1850ff31a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:10:01,523] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 11:10:01,523] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 11:10:01,523] [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
--------------------------------------------------------------------------------
[2023-03-16 11:10:01,524] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35889/tc_result.tsv
[2023-03-16 11:10:01,524] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:10:01,524] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:10:01,524] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf56dedc8-d9a3-40cb-8c3b-5b1850ff31a1/dqc_reference/checkm_data
[2023-03-16 11:10:01,528] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:10:01,532] [INFO] Task started: CheckM
[2023-03-16 11:10:01,532] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35889/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35889/checkm_input OceanDNA-b35889/checkm_result
[2023-03-16 11:10:19,630] [INFO] Task succeeded: CheckM
[2023-03-16 11:10:19,630] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.63%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 11:10:19,632] [INFO] ===== Completeness check finished =====
[2023-03-16 11:10:19,632] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:10:19,632] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35889/markers.fasta)
[2023-03-16 11:10:19,633] [INFO] Task started: Blastn
[2023-03-16 11:10:19,633] [INFO] Running command: blastn -query OceanDNA-b35889/markers.fasta -db /var/lib/cwl/stgf56dedc8-d9a3-40cb-8c3b-5b1850ff31a1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35889/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:10:20,719] [INFO] Task succeeded: Blastn
[2023-03-16 11:10:20,720] [INFO] Selected 26 target genomes.
[2023-03-16 11:10:20,720] [INFO] Target genome list was writen to OceanDNA-b35889/target_genomes_gtdb.txt
[2023-03-16 11:10:20,783] [INFO] Task started: fastANI
[2023-03-16 11:10:20,784] [INFO] Running command: fastANI --query /var/lib/cwl/stg74e53769-f237-40aa-8fa7-0777fa446f17/OceanDNA-b35889.fa --refList OceanDNA-b35889/target_genomes_gtdb.txt --output OceanDNA-b35889/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:10:34,204] [INFO] Task succeeded: fastANI
[2023-03-16 11:10:34,207] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 11:10:34,207] [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_003599485.1	s__SURF-13 sp003599485	77.5927	58	212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SURF-13;f__SURF-13;g__SURF-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195665.1	s__JACPZD01 sp016195665	77.1493	52	212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SURF-13;f__SURF-13;g__JACPZD01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 11:10:34,208] [INFO] GTDB search result was written to OceanDNA-b35889/result_gtdb.tsv
[2023-03-16 11:10:34,208] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:10:34,209] [INFO] DFAST_QC result json was written to OceanDNA-b35889/dqc_result.json
[2023-03-16 11:10:34,209] [INFO] DFAST_QC completed!
[2023-03-16 11:10:34,209] [INFO] Total running time: 0h0m59s