[2023-03-14 10:56:00,250] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:56:00,251] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:56:00,251] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ea93d12-46a5-46d7-a499-8298d7849538/dqc_reference
[2023-03-14 10:56:01,423] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:01,423] [INFO] Task started: Prodigal
[2023-03-14 10:56:01,423] [INFO] Running command: cat /var/lib/cwl/stg9979a0f5-48f6-49d1-b621-39f8b8b51db0/OceanDNA-b21477.fa | prodigal -d OceanDNA-b21477/cds.fna -a OceanDNA-b21477/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:08,876] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:08,876] [INFO] Task started: HMMsearch
[2023-03-14 10:56:08,876] [INFO] Running command: hmmsearch --tblout OceanDNA-b21477/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ea93d12-46a5-46d7-a499-8298d7849538/dqc_reference/reference_markers.hmm OceanDNA-b21477/protein.faa > /dev/null
[2023-03-14 10:56:09,123] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:09,123] [INFO] Found 6/6 markers.
[2023-03-14 10:56:09,131] [INFO] Query marker FASTA was written to OceanDNA-b21477/markers.fasta
[2023-03-14 10:56:09,131] [INFO] Task started: Blastn
[2023-03-14 10:56:09,131] [INFO] Running command: blastn -query OceanDNA-b21477/markers.fasta -db /var/lib/cwl/stg9ea93d12-46a5-46d7-a499-8298d7849538/dqc_reference/reference_markers.fasta -out OceanDNA-b21477/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:09,665] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:09,666] [INFO] Selected 10 target genomes.
[2023-03-14 10:56:09,666] [INFO] Target genome list was writen to OceanDNA-b21477/target_genomes.txt
[2023-03-14 10:56:09,673] [INFO] Task started: fastANI
[2023-03-14 10:56:09,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg9979a0f5-48f6-49d1-b621-39f8b8b51db0/OceanDNA-b21477.fa --refList OceanDNA-b21477/target_genomes.txt --output OceanDNA-b21477/fastani_result.tsv --threads 1
[2023-03-14 10:56:15,414] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:15,414] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ea93d12-46a5-46d7-a499-8298d7849538/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:15,414] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ea93d12-46a5-46d7-a499-8298d7849538/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:15,415] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:15,415] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 10:56:15,415] [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
--------------------------------------------------------------------------------
[2023-03-14 10:56:15,415] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21477/tc_result.tsv
[2023-03-14 10:56:15,415] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:15,415] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:15,415] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ea93d12-46a5-46d7-a499-8298d7849538/dqc_reference/checkm_data
[2023-03-14 10:56:15,418] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:15,420] [INFO] Task started: CheckM
[2023-03-14 10:56:15,420] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21477/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21477/checkm_input OceanDNA-b21477/checkm_result
[2023-03-14 10:56:39,436] [INFO] Task succeeded: CheckM
[2023-03-14 10:56:39,436] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:56:39,437] [INFO] ===== Completeness check finished =====
[2023-03-14 10:56:39,438] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:56:39,438] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21477/markers.fasta)
[2023-03-14 10:56:39,438] [INFO] Task started: Blastn
[2023-03-14 10:56:39,438] [INFO] Running command: blastn -query OceanDNA-b21477/markers.fasta -db /var/lib/cwl/stg9ea93d12-46a5-46d7-a499-8298d7849538/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21477/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:40,186] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:40,187] [INFO] Selected 19 target genomes.
[2023-03-14 10:56:40,187] [INFO] Target genome list was writen to OceanDNA-b21477/target_genomes_gtdb.txt
[2023-03-14 10:56:40,242] [INFO] Task started: fastANI
[2023-03-14 10:56:40,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg9979a0f5-48f6-49d1-b621-39f8b8b51db0/OceanDNA-b21477.fa --refList OceanDNA-b21477/target_genomes_gtdb.txt --output OceanDNA-b21477/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:56:43,795] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:43,799] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 10:56:43,800] [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_018669975.1	s__JABHSK01 sp018669975	99.9816	345	365	d__Bacteria;p__Patescibacteria;c__ABY1;o__UBA1558;f__GWA2-36-10;g__JABHSK01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018664825.1	s__JABJNO01 sp018664825	77.2576	70	365	d__Bacteria;p__Patescibacteria;c__ABY1;o__UBA1558;f__GWA2-36-10;g__JABJNO01	95.0	99.86	99.86	0.95	0.95	2	-
GCA_018656065.1	s__XYD1-37-29 sp018656065	77.1923	56	365	d__Bacteria;p__Patescibacteria;c__ABY1;o__UBA1558;f__GWA2-36-10;g__XYD1-37-29	95.0	99.99	99.99	0.98	0.98	2	-
GCA_018656655.1	s__XYD1-37-29 sp018656655	77.0971	52	365	d__Bacteria;p__Patescibacteria;c__ABY1;o__UBA1558;f__GWA2-36-10;g__XYD1-37-29	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869235.1	s__BM519 sp002869235	76.9869	56	365	d__Bacteria;p__Patescibacteria;c__ABY1;o__UBA1558;f__GWA2-36-10;g__BM519	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 10:56:43,800] [INFO] GTDB search result was written to OceanDNA-b21477/result_gtdb.tsv
[2023-03-14 10:56:43,800] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:56:43,800] [INFO] DFAST_QC result json was written to OceanDNA-b21477/dqc_result.json
[2023-03-14 10:56:43,801] [INFO] DFAST_QC completed!
[2023-03-14 10:56:43,801] [INFO] Total running time: 0h0m44s