[2023-03-17 05:32:05,515] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:32:05,515] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:32:05,515] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c4def62-1d9d-49df-8ad5-86d8ccda2cea/dqc_reference
[2023-03-17 05:32:06,638] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:32:06,638] [INFO] Task started: Prodigal
[2023-03-17 05:32:06,638] [INFO] Running command: cat /var/lib/cwl/stgf67d57ea-3042-4951-a1fe-d2a2bc9846d6/OceanDNA-b24615.fa | prodigal -d OceanDNA-b24615/cds.fna -a OceanDNA-b24615/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:32:12,381] [INFO] Task succeeded: Prodigal
[2023-03-17 05:32:12,382] [INFO] Task started: HMMsearch
[2023-03-17 05:32:12,382] [INFO] Running command: hmmsearch --tblout OceanDNA-b24615/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c4def62-1d9d-49df-8ad5-86d8ccda2cea/dqc_reference/reference_markers.hmm OceanDNA-b24615/protein.faa > /dev/null
[2023-03-17 05:32:12,518] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:32:12,519] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf67d57ea-3042-4951-a1fe-d2a2bc9846d6/OceanDNA-b24615.fa]
[2023-03-17 05:32:12,528] [INFO] Query marker FASTA was written to OceanDNA-b24615/markers.fasta
[2023-03-17 05:32:12,529] [INFO] Task started: Blastn
[2023-03-17 05:32:12,529] [INFO] Running command: blastn -query OceanDNA-b24615/markers.fasta -db /var/lib/cwl/stg8c4def62-1d9d-49df-8ad5-86d8ccda2cea/dqc_reference/reference_markers.fasta -out OceanDNA-b24615/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:32:12,972] [INFO] Task succeeded: Blastn
[2023-03-17 05:32:12,973] [INFO] Selected 18 target genomes.
[2023-03-17 05:32:12,974] [INFO] Target genome list was writen to OceanDNA-b24615/target_genomes.txt
[2023-03-17 05:32:12,998] [INFO] Task started: fastANI
[2023-03-17 05:32:12,998] [INFO] Running command: fastANI --query /var/lib/cwl/stgf67d57ea-3042-4951-a1fe-d2a2bc9846d6/OceanDNA-b24615.fa --refList OceanDNA-b24615/target_genomes.txt --output OceanDNA-b24615/fastani_result.tsv --threads 1
[2023-03-17 05:32:20,432] [INFO] Task succeeded: fastANI
[2023-03-17 05:32:20,433] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c4def62-1d9d-49df-8ad5-86d8ccda2cea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:32:20,433] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c4def62-1d9d-49df-8ad5-86d8ccda2cea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:32:20,433] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:32:20,433] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:32:20,433] [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 05:32:20,434] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24615/tc_result.tsv
[2023-03-17 05:32:20,434] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:32:20,434] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:32:20,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c4def62-1d9d-49df-8ad5-86d8ccda2cea/dqc_reference/checkm_data
[2023-03-17 05:32:20,444] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:32:20,448] [INFO] Task started: CheckM
[2023-03-17 05:32:20,448] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24615/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24615/checkm_input OceanDNA-b24615/checkm_result
[2023-03-17 05:32:40,521] [INFO] Task succeeded: CheckM
[2023-03-17 05:32:40,522] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:32:40,523] [INFO] ===== Completeness check finished =====
[2023-03-17 05:32:40,524] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:32:40,524] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24615/markers.fasta)
[2023-03-17 05:32:40,524] [INFO] Task started: Blastn
[2023-03-17 05:32:40,525] [INFO] Running command: blastn -query OceanDNA-b24615/markers.fasta -db /var/lib/cwl/stg8c4def62-1d9d-49df-8ad5-86d8ccda2cea/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24615/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:32:40,960] [INFO] Task succeeded: Blastn
[2023-03-17 05:32:40,961] [INFO] Selected 10 target genomes.
[2023-03-17 05:32:40,961] [INFO] Target genome list was writen to OceanDNA-b24615/target_genomes_gtdb.txt
[2023-03-17 05:32:40,973] [INFO] Task started: fastANI
[2023-03-17 05:32:40,974] [INFO] Running command: fastANI --query /var/lib/cwl/stgf67d57ea-3042-4951-a1fe-d2a2bc9846d6/OceanDNA-b24615.fa --refList OceanDNA-b24615/target_genomes_gtdb.txt --output OceanDNA-b24615/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:32:44,190] [INFO] Task succeeded: fastANI
[2023-03-17 05:32:44,193] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:32:44,194] [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_002708415.1	s__GCA-2708415 sp002708415	99.8774	317	342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__Micavibrionaceae;g__GCA-2708415	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013215815.1	s__GCA-2708415 sp013215815	77.699	125	342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__Micavibrionaceae;g__GCA-2708415	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009995595.1	s__GCA-2708415 sp009995595	77.0742	88	342	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__Micavibrionaceae;g__GCA-2708415	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 05:32:44,194] [INFO] GTDB search result was written to OceanDNA-b24615/result_gtdb.tsv
[2023-03-17 05:32:44,194] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:32:44,195] [INFO] DFAST_QC result json was written to OceanDNA-b24615/dqc_result.json
[2023-03-17 05:32:44,195] [INFO] DFAST_QC completed!
[2023-03-17 05:32:44,195] [INFO] Total running time: 0h0m39s