[2023-03-19 03:50:07,820] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:50:07,821] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:50:07,821] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e574951-0faa-4568-a776-fc66c2a6976e/dqc_reference
[2023-03-19 03:50:09,580] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:50:09,581] [INFO] Task started: Prodigal
[2023-03-19 03:50:09,581] [INFO] Running command: cat /var/lib/cwl/stg97e4e6d3-a58b-4b02-be88-58cfbf2cee4d/OceanDNA-b41610.fa | prodigal -d OceanDNA-b41610/cds.fna -a OceanDNA-b41610/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:50:14,532] [INFO] Task succeeded: Prodigal
[2023-03-19 03:50:14,533] [INFO] Task started: HMMsearch
[2023-03-19 03:50:14,533] [INFO] Running command: hmmsearch --tblout OceanDNA-b41610/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e574951-0faa-4568-a776-fc66c2a6976e/dqc_reference/reference_markers.hmm OceanDNA-b41610/protein.faa > /dev/null
[2023-03-19 03:50:14,692] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:50:14,693] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg97e4e6d3-a58b-4b02-be88-58cfbf2cee4d/OceanDNA-b41610.fa]
[2023-03-19 03:50:14,704] [INFO] Query marker FASTA was written to OceanDNA-b41610/markers.fasta
[2023-03-19 03:50:14,704] [INFO] Task started: Blastn
[2023-03-19 03:50:14,704] [INFO] Running command: blastn -query OceanDNA-b41610/markers.fasta -db /var/lib/cwl/stg3e574951-0faa-4568-a776-fc66c2a6976e/dqc_reference/reference_markers.fasta -out OceanDNA-b41610/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:15,859] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:15,860] [INFO] Selected 26 target genomes.
[2023-03-19 03:50:15,860] [INFO] Target genome list was writen to OceanDNA-b41610/target_genomes.txt
[2023-03-19 03:50:15,872] [INFO] Task started: fastANI
[2023-03-19 03:50:15,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg97e4e6d3-a58b-4b02-be88-58cfbf2cee4d/OceanDNA-b41610.fa --refList OceanDNA-b41610/target_genomes.txt --output OceanDNA-b41610/fastani_result.tsv --threads 1
[2023-03-19 03:50:30,081] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:30,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e574951-0faa-4568-a776-fc66c2a6976e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:50:30,082] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e574951-0faa-4568-a776-fc66c2a6976e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:50:30,082] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:50:30,082] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:50:30,082] [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 03:50:30,082] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41610/tc_result.tsv
[2023-03-19 03:50:30,082] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:50:30,082] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:50:30,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e574951-0faa-4568-a776-fc66c2a6976e/dqc_reference/checkm_data
[2023-03-19 03:50:30,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:50:30,088] [INFO] Task started: CheckM
[2023-03-19 03:50:30,088] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41610/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41610/checkm_input OceanDNA-b41610/checkm_result
[2023-03-19 03:50:48,472] [INFO] Task succeeded: CheckM
[2023-03-19 03:50:48,473] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.80%
Contamintation: 3.12%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:50:48,475] [INFO] ===== Completeness check finished =====
[2023-03-19 03:50:48,475] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:50:48,475] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41610/markers.fasta)
[2023-03-19 03:50:48,475] [INFO] Task started: Blastn
[2023-03-19 03:50:48,475] [INFO] Running command: blastn -query OceanDNA-b41610/markers.fasta -db /var/lib/cwl/stg3e574951-0faa-4568-a776-fc66c2a6976e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41610/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:49,213] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:49,214] [INFO] Selected 17 target genomes.
[2023-03-19 03:50:49,214] [INFO] Target genome list was writen to OceanDNA-b41610/target_genomes_gtdb.txt
[2023-03-19 03:50:49,258] [INFO] Task started: fastANI
[2023-03-19 03:50:49,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg97e4e6d3-a58b-4b02-be88-58cfbf2cee4d/OceanDNA-b41610.fa --refList OceanDNA-b41610/target_genomes_gtdb.txt --output OceanDNA-b41610/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:50:57,093] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:57,096] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:50:57,096] [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_002339085.1	s__UBA7434 sp002339085	94.2484	221	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	99.78	99.78	0.84	0.84	2	-
GCA_002726445.1	s__UBA7434 sp002726445	88.3036	165	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	99.17	99.17	0.72	0.72	2	-
GCA_002336035.1	s__UBA7434 sp002336035	78.1889	128	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:50:57,096] [INFO] GTDB search result was written to OceanDNA-b41610/result_gtdb.tsv
[2023-03-19 03:50:57,096] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:50:57,097] [INFO] DFAST_QC result json was written to OceanDNA-b41610/dqc_result.json
[2023-03-19 03:50:57,097] [INFO] DFAST_QC completed!
[2023-03-19 03:50:57,097] [INFO] Total running time: 0h0m49s