[2023-03-16 17:34:52,384] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:34:52,384] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:34:52,384] [INFO] DQC Reference Directory: /var/lib/cwl/stgabf6e8cc-f88a-4e61-9593-8b12b0886025/dqc_reference
[2023-03-16 17:34:55,527] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:34:55,528] [INFO] Task started: Prodigal
[2023-03-16 17:34:55,528] [INFO] Running command: cat /var/lib/cwl/stg13e26c23-4208-48d2-9c2d-cdfd7e185afd/OceanDNA-b21413.fa | prodigal -d OceanDNA-b21413/cds.fna -a OceanDNA-b21413/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:35:00,753] [INFO] Task succeeded: Prodigal
[2023-03-16 17:35:00,753] [INFO] Task started: HMMsearch
[2023-03-16 17:35:00,753] [INFO] Running command: hmmsearch --tblout OceanDNA-b21413/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabf6e8cc-f88a-4e61-9593-8b12b0886025/dqc_reference/reference_markers.hmm OceanDNA-b21413/protein.faa > /dev/null
[2023-03-16 17:35:00,972] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:35:00,972] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg13e26c23-4208-48d2-9c2d-cdfd7e185afd/OceanDNA-b21413.fa]
[2023-03-16 17:35:00,979] [INFO] Query marker FASTA was written to OceanDNA-b21413/markers.fasta
[2023-03-16 17:35:00,980] [INFO] Task started: Blastn
[2023-03-16 17:35:00,980] [INFO] Running command: blastn -query OceanDNA-b21413/markers.fasta -db /var/lib/cwl/stgabf6e8cc-f88a-4e61-9593-8b12b0886025/dqc_reference/reference_markers.fasta -out OceanDNA-b21413/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:35:02,469] [INFO] Task succeeded: Blastn
[2023-03-16 17:35:02,469] [INFO] Selected 13 target genomes.
[2023-03-16 17:35:02,470] [INFO] Target genome list was writen to OceanDNA-b21413/target_genomes.txt
[2023-03-16 17:35:02,482] [INFO] Task started: fastANI
[2023-03-16 17:35:02,482] [INFO] Running command: fastANI --query /var/lib/cwl/stg13e26c23-4208-48d2-9c2d-cdfd7e185afd/OceanDNA-b21413.fa --refList OceanDNA-b21413/target_genomes.txt --output OceanDNA-b21413/fastani_result.tsv --threads 1
[2023-03-16 17:35:12,933] [INFO] Task succeeded: fastANI
[2023-03-16 17:35:12,934] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabf6e8cc-f88a-4e61-9593-8b12b0886025/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:35:12,934] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabf6e8cc-f88a-4e61-9593-8b12b0886025/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:35:12,934] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:35:12,934] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:35:12,934] [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 17:35:12,935] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21413/tc_result.tsv
[2023-03-16 17:35:12,935] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:35:12,935] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:35:12,935] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabf6e8cc-f88a-4e61-9593-8b12b0886025/dqc_reference/checkm_data
[2023-03-16 17:35:12,938] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:35:12,941] [INFO] Task started: CheckM
[2023-03-16 17:35:12,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21413/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21413/checkm_input OceanDNA-b21413/checkm_result
[2023-03-16 17:35:38,355] [INFO] Task succeeded: CheckM
[2023-03-16 17:35:38,355] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:35:38,357] [INFO] ===== Completeness check finished =====
[2023-03-16 17:35:38,357] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:35:38,357] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21413/markers.fasta)
[2023-03-16 17:35:38,358] [INFO] Task started: Blastn
[2023-03-16 17:35:38,358] [INFO] Running command: blastn -query OceanDNA-b21413/markers.fasta -db /var/lib/cwl/stgabf6e8cc-f88a-4e61-9593-8b12b0886025/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21413/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:35:39,363] [INFO] Task succeeded: Blastn
[2023-03-16 17:35:39,363] [INFO] Selected 14 target genomes.
[2023-03-16 17:35:39,364] [INFO] Target genome list was writen to OceanDNA-b21413/target_genomes_gtdb.txt
[2023-03-16 17:35:39,378] [INFO] Task started: fastANI
[2023-03-16 17:35:39,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg13e26c23-4208-48d2-9c2d-cdfd7e185afd/OceanDNA-b21413.fa --refList OceanDNA-b21413/target_genomes_gtdb.txt --output OceanDNA-b21413/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:35:42,745] [INFO] Task succeeded: fastANI
[2023-03-16 17:35:42,747] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 17:35:42,748] [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_018650085.1	s__JAHJIX01 sp018650085	99.4124	212	230	d__Bacteria;p__Patescibacteria;c__ABY1;o__Magasanikbacterales;f__UBA922;g__JAHJIX01	95.0	99.67	99.67	0.91	0.91	2	conclusive
GCA_018823045.1	s__JAHJIX01 sp018823045	78.0781	65	230	d__Bacteria;p__Patescibacteria;c__ABY1;o__Magasanikbacterales;f__UBA922;g__JAHJIX01	95.0	99.99	99.99	0.94	0.91	3	-
--------------------------------------------------------------------------------
[2023-03-16 17:35:42,748] [INFO] GTDB search result was written to OceanDNA-b21413/result_gtdb.tsv
[2023-03-16 17:35:42,748] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:35:42,748] [INFO] DFAST_QC result json was written to OceanDNA-b21413/dqc_result.json
[2023-03-16 17:35:42,749] [INFO] DFAST_QC completed!
[2023-03-16 17:35:42,749] [INFO] Total running time: 0h0m50s