[2023-03-16 17:50:13,069] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:50:13,069] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:50:13,069] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e0438cd-018a-4038-9898-8c67459de4b8/dqc_reference
[2023-03-16 17:50:14,179] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:50:14,180] [INFO] Task started: Prodigal
[2023-03-16 17:50:14,180] [INFO] Running command: cat /var/lib/cwl/stg65b6128a-9c47-4476-a65b-674cbb0ec0c0/OceanDNA-b18407.fa | prodigal -d OceanDNA-b18407/cds.fna -a OceanDNA-b18407/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:50:21,204] [INFO] Task succeeded: Prodigal
[2023-03-16 17:50:21,205] [INFO] Task started: HMMsearch
[2023-03-16 17:50:21,205] [INFO] Running command: hmmsearch --tblout OceanDNA-b18407/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e0438cd-018a-4038-9898-8c67459de4b8/dqc_reference/reference_markers.hmm OceanDNA-b18407/protein.faa > /dev/null
[2023-03-16 17:50:21,517] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:50:21,517] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg65b6128a-9c47-4476-a65b-674cbb0ec0c0/OceanDNA-b18407.fa]
[2023-03-16 17:50:21,533] [INFO] Query marker FASTA was written to OceanDNA-b18407/markers.fasta
[2023-03-16 17:50:21,536] [INFO] Task started: Blastn
[2023-03-16 17:50:21,536] [INFO] Running command: blastn -query OceanDNA-b18407/markers.fasta -db /var/lib/cwl/stg1e0438cd-018a-4038-9898-8c67459de4b8/dqc_reference/reference_markers.fasta -out OceanDNA-b18407/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:50:22,319] [INFO] Task succeeded: Blastn
[2023-03-16 17:50:22,320] [INFO] Selected 9 target genomes.
[2023-03-16 17:50:22,321] [INFO] Target genome list was writen to OceanDNA-b18407/target_genomes.txt
[2023-03-16 17:50:22,326] [INFO] Task started: fastANI
[2023-03-16 17:50:22,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg65b6128a-9c47-4476-a65b-674cbb0ec0c0/OceanDNA-b18407.fa --refList OceanDNA-b18407/target_genomes.txt --output OceanDNA-b18407/fastani_result.tsv --threads 1
[2023-03-16 17:50:30,442] [INFO] Task succeeded: fastANI
[2023-03-16 17:50:30,442] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e0438cd-018a-4038-9898-8c67459de4b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:50:30,442] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e0438cd-018a-4038-9898-8c67459de4b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:50:30,443] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:50:30,443] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:50:30,443] [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 17:50:30,443] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18407/tc_result.tsv
[2023-03-16 17:50:30,443] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:50:30,443] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:50:30,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e0438cd-018a-4038-9898-8c67459de4b8/dqc_reference/checkm_data
[2023-03-16 17:50:30,454] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:50:30,543] [INFO] Task started: CheckM
[2023-03-16 17:50:30,543] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18407/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18407/checkm_input OceanDNA-b18407/checkm_result
[2023-03-16 17:50:59,286] [INFO] Task succeeded: CheckM
[2023-03-16 17:50:59,287] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.40%
Contamintation: 3.01%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-16 17:50:59,290] [INFO] ===== Completeness check finished =====
[2023-03-16 17:50:59,290] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:50:59,290] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18407/markers.fasta)
[2023-03-16 17:50:59,292] [INFO] Task started: Blastn
[2023-03-16 17:50:59,292] [INFO] Running command: blastn -query OceanDNA-b18407/markers.fasta -db /var/lib/cwl/stg1e0438cd-018a-4038-9898-8c67459de4b8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18407/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:51:00,075] [INFO] Task succeeded: Blastn
[2023-03-16 17:51:00,077] [INFO] Selected 23 target genomes.
[2023-03-16 17:51:00,077] [INFO] Target genome list was writen to OceanDNA-b18407/target_genomes_gtdb.txt
[2023-03-16 17:51:00,126] [INFO] Task started: fastANI
[2023-03-16 17:51:00,126] [INFO] Running command: fastANI --query /var/lib/cwl/stg65b6128a-9c47-4476-a65b-674cbb0ec0c0/OceanDNA-b18407.fa --refList OceanDNA-b18407/target_genomes_gtdb.txt --output OceanDNA-b18407/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:51:11,492] [INFO] Task succeeded: fastANI
[2023-03-16 17:51:11,495] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:51:11,495] [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_002448795.1	s__S15-B10 sp002448795	87.6276	340	375	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__S15-B10;g__S15-B10	95.0	99.97	99.96	0.93	0.86	3	-
GCA_001626655.1	s__S15-B10 sp001626655	79.7693	174	375	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__S15-B10;g__S15-B10	95.0	98.13	97.75	0.76	0.70	4	-
--------------------------------------------------------------------------------
[2023-03-16 17:51:11,495] [INFO] GTDB search result was written to OceanDNA-b18407/result_gtdb.tsv
[2023-03-16 17:51:11,495] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:51:11,495] [INFO] DFAST_QC result json was written to OceanDNA-b18407/dqc_result.json
[2023-03-16 17:51:11,495] [INFO] DFAST_QC completed!
[2023-03-16 17:51:11,496] [INFO] Total running time: 0h0m58s