[2023-03-17 11:38:03,708] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:38:03,709] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:38:03,709] [INFO] DQC Reference Directory: /var/lib/cwl/stg5629545b-522f-4213-a94d-5dc995ed6997/dqc_reference
[2023-03-17 11:38:04,797] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:38:04,797] [INFO] Task started: Prodigal
[2023-03-17 11:38:04,797] [INFO] Running command: cat /var/lib/cwl/stg0cb8e539-6b37-4c30-aa00-7fabc7bf25bd/OceanDNA-b41814.fa | prodigal -d OceanDNA-b41814/cds.fna -a OceanDNA-b41814/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:38:07,299] [INFO] Task succeeded: Prodigal
[2023-03-17 11:38:07,299] [INFO] Task started: HMMsearch
[2023-03-17 11:38:07,299] [INFO] Running command: hmmsearch --tblout OceanDNA-b41814/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5629545b-522f-4213-a94d-5dc995ed6997/dqc_reference/reference_markers.hmm OceanDNA-b41814/protein.faa > /dev/null
[2023-03-17 11:38:07,614] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:38:07,615] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0cb8e539-6b37-4c30-aa00-7fabc7bf25bd/OceanDNA-b41814.fa]
[2023-03-17 11:38:07,628] [INFO] Query marker FASTA was written to OceanDNA-b41814/markers.fasta
[2023-03-17 11:38:07,629] [INFO] Task started: Blastn
[2023-03-17 11:38:07,629] [INFO] Running command: blastn -query OceanDNA-b41814/markers.fasta -db /var/lib/cwl/stg5629545b-522f-4213-a94d-5dc995ed6997/dqc_reference/reference_markers.fasta -out OceanDNA-b41814/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:38:08,157] [INFO] Task succeeded: Blastn
[2023-03-17 11:38:08,159] [INFO] Selected 21 target genomes.
[2023-03-17 11:38:08,159] [INFO] Target genome list was writen to OceanDNA-b41814/target_genomes.txt
[2023-03-17 11:38:08,171] [INFO] Task started: fastANI
[2023-03-17 11:38:08,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cb8e539-6b37-4c30-aa00-7fabc7bf25bd/OceanDNA-b41814.fa --refList OceanDNA-b41814/target_genomes.txt --output OceanDNA-b41814/fastani_result.tsv --threads 1
[2023-03-17 11:38:18,771] [INFO] Task succeeded: fastANI
[2023-03-17 11:38:18,772] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5629545b-522f-4213-a94d-5dc995ed6997/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:38:18,772] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5629545b-522f-4213-a94d-5dc995ed6997/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:38:18,772] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:38:18,772] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:38:18,772] [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 11:38:18,773] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41814/tc_result.tsv
[2023-03-17 11:38:18,775] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:38:18,776] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:38:18,776] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5629545b-522f-4213-a94d-5dc995ed6997/dqc_reference/checkm_data
[2023-03-17 11:38:18,779] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:38:18,782] [INFO] Task started: CheckM
[2023-03-17 11:38:18,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41814/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41814/checkm_input OceanDNA-b41814/checkm_result
[2023-03-17 11:38:32,078] [INFO] Task succeeded: CheckM
[2023-03-17 11:38:32,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.85%
Contamintation: 0.84%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 11:38:32,107] [INFO] ===== Completeness check finished =====
[2023-03-17 11:38:32,107] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:38:32,108] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41814/markers.fasta)
[2023-03-17 11:38:32,108] [INFO] Task started: Blastn
[2023-03-17 11:38:32,108] [INFO] Running command: blastn -query OceanDNA-b41814/markers.fasta -db /var/lib/cwl/stg5629545b-522f-4213-a94d-5dc995ed6997/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41814/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:38:32,780] [INFO] Task succeeded: Blastn
[2023-03-17 11:38:32,782] [INFO] Selected 8 target genomes.
[2023-03-17 11:38:32,782] [INFO] Target genome list was writen to OceanDNA-b41814/target_genomes_gtdb.txt
[2023-03-17 11:38:32,789] [INFO] Task started: fastANI
[2023-03-17 11:38:32,789] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cb8e539-6b37-4c30-aa00-7fabc7bf25bd/OceanDNA-b41814.fa --refList OceanDNA-b41814/target_genomes_gtdb.txt --output OceanDNA-b41814/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:38:34,256] [INFO] Task succeeded: fastANI
[2023-03-17 11:38:34,260] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:38:34,260] [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_902524805.1	s__AG-339-G14 sp902524805	93.381	123	149	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902523885.1	s__AG-339-G14 sp902523885	81.8459	102	149	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902614235.1	s__AG-339-G14 sp902614235	81.6303	107	149	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	98.30	98.01	0.83	0.80	7	-
GCA_902522825.1	s__AG-339-G14 sp902522825	81.1218	116	149	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902525735.1	s__AG-339-G14 sp902525735	81.0892	109	149	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	98.66	98.66	0.90	0.90	2	-
GCA_902635045.1	s__AG-339-G14 sp902635045	80.3474	109	149	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	98.24	96.50	0.87	0.84	4	-
--------------------------------------------------------------------------------
[2023-03-17 11:38:34,262] [INFO] GTDB search result was written to OceanDNA-b41814/result_gtdb.tsv
[2023-03-17 11:38:34,263] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:38:34,264] [INFO] DFAST_QC result json was written to OceanDNA-b41814/dqc_result.json
[2023-03-17 11:38:34,265] [INFO] DFAST_QC completed!
[2023-03-17 11:38:34,265] [INFO] Total running time: 0h0m31s