[2023-03-19 03:10:00,782] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:10:00,782] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:10:00,782] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e85351d-6e26-413d-88a3-ae3ef72644db/dqc_reference
[2023-03-19 03:10:01,865] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:10:01,866] [INFO] Task started: Prodigal
[2023-03-19 03:10:01,866] [INFO] Running command: cat /var/lib/cwl/stg5938ec2f-c91e-4829-82b4-3d68c9f281f7/OceanDNA-b600.fa | prodigal -d OceanDNA-b600/cds.fna -a OceanDNA-b600/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:10:10,925] [INFO] Task succeeded: Prodigal
[2023-03-19 03:10:10,926] [INFO] Task started: HMMsearch
[2023-03-19 03:10:10,926] [INFO] Running command: hmmsearch --tblout OceanDNA-b600/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e85351d-6e26-413d-88a3-ae3ef72644db/dqc_reference/reference_markers.hmm OceanDNA-b600/protein.faa > /dev/null
[2023-03-19 03:10:11,082] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:10:11,083] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5938ec2f-c91e-4829-82b4-3d68c9f281f7/OceanDNA-b600.fa]
[2023-03-19 03:10:11,095] [INFO] Query marker FASTA was written to OceanDNA-b600/markers.fasta
[2023-03-19 03:10:11,096] [INFO] Task started: Blastn
[2023-03-19 03:10:11,096] [INFO] Running command: blastn -query OceanDNA-b600/markers.fasta -db /var/lib/cwl/stg9e85351d-6e26-413d-88a3-ae3ef72644db/dqc_reference/reference_markers.fasta -out OceanDNA-b600/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:10:11,609] [INFO] Task succeeded: Blastn
[2023-03-19 03:10:11,610] [INFO] Selected 25 target genomes.
[2023-03-19 03:10:11,610] [INFO] Target genome list was writen to OceanDNA-b600/target_genomes.txt
[2023-03-19 03:10:11,623] [INFO] Task started: fastANI
[2023-03-19 03:10:11,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg5938ec2f-c91e-4829-82b4-3d68c9f281f7/OceanDNA-b600.fa --refList OceanDNA-b600/target_genomes.txt --output OceanDNA-b600/fastani_result.tsv --threads 1
[2023-03-19 03:10:25,953] [INFO] Task succeeded: fastANI
[2023-03-19 03:10:25,953] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e85351d-6e26-413d-88a3-ae3ef72644db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:10:25,954] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e85351d-6e26-413d-88a3-ae3ef72644db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:10:25,954] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:10:25,954] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:10:25,954] [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
--------------------------------------------------------------------------------
[2023-03-19 03:10:25,954] [INFO] DFAST Taxonomy check result was written to OceanDNA-b600/tc_result.tsv
[2023-03-19 03:10:25,955] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:10:25,955] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:10:25,955] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e85351d-6e26-413d-88a3-ae3ef72644db/dqc_reference/checkm_data
[2023-03-19 03:10:25,957] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:10:25,961] [INFO] Task started: CheckM
[2023-03-19 03:10:25,961] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b600/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b600/checkm_input OceanDNA-b600/checkm_result
[2023-03-19 03:10:53,055] [INFO] Task succeeded: CheckM
[2023-03-19 03:10:53,055] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:10:53,057] [INFO] ===== Completeness check finished =====
[2023-03-19 03:10:53,057] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:10:53,058] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b600/markers.fasta)
[2023-03-19 03:10:53,058] [INFO] Task started: Blastn
[2023-03-19 03:10:53,058] [INFO] Running command: blastn -query OceanDNA-b600/markers.fasta -db /var/lib/cwl/stg9e85351d-6e26-413d-88a3-ae3ef72644db/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b600/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:10:53,771] [INFO] Task succeeded: Blastn
[2023-03-19 03:10:53,772] [INFO] Selected 23 target genomes.
[2023-03-19 03:10:53,772] [INFO] Target genome list was writen to OceanDNA-b600/target_genomes_gtdb.txt
[2023-03-19 03:10:53,792] [INFO] Task started: fastANI
[2023-03-19 03:10:53,792] [INFO] Running command: fastANI --query /var/lib/cwl/stg5938ec2f-c91e-4829-82b4-3d68c9f281f7/OceanDNA-b600.fa --refList OceanDNA-b600/target_genomes_gtdb.txt --output OceanDNA-b600/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:11:01,995] [INFO] Task succeeded: fastANI
[2023-03-19 03:11:01,997] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:11:01,997] [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_012959995.1	s__MedAcidi-G2B sp012959995	95.8122	442	470	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G2B	95.0	96.10	95.68	0.94	0.91	18	conclusive
--------------------------------------------------------------------------------
[2023-03-19 03:11:01,997] [INFO] GTDB search result was written to OceanDNA-b600/result_gtdb.tsv
[2023-03-19 03:11:01,997] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:11:01,998] [INFO] DFAST_QC result json was written to OceanDNA-b600/dqc_result.json
[2023-03-19 03:11:01,998] [INFO] DFAST_QC completed!
[2023-03-19 03:11:01,998] [INFO] Total running time: 0h1m1s