[2023-03-15 15:55:16,217] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:55:16,217] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:55:16,217] [INFO] DQC Reference Directory: /var/lib/cwl/stg239f2d92-8d9a-422a-aaca-2064b7bbe677/dqc_reference
[2023-03-15 15:55:17,912] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:55:17,912] [INFO] Task started: Prodigal
[2023-03-15 15:55:17,912] [INFO] Running command: cat /var/lib/cwl/stge2697df2-e8ad-4702-93ce-646c90ba3065/OceanDNA-b37154.fa | prodigal -d OceanDNA-b37154/cds.fna -a OceanDNA-b37154/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:55:26,251] [INFO] Task succeeded: Prodigal
[2023-03-15 15:55:26,252] [INFO] Task started: HMMsearch
[2023-03-15 15:55:26,252] [INFO] Running command: hmmsearch --tblout OceanDNA-b37154/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg239f2d92-8d9a-422a-aaca-2064b7bbe677/dqc_reference/reference_markers.hmm OceanDNA-b37154/protein.faa > /dev/null
[2023-03-15 15:55:26,440] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:55:26,440] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge2697df2-e8ad-4702-93ce-646c90ba3065/OceanDNA-b37154.fa]
[2023-03-15 15:55:26,452] [INFO] Query marker FASTA was written to OceanDNA-b37154/markers.fasta
[2023-03-15 15:55:26,453] [INFO] Task started: Blastn
[2023-03-15 15:55:26,453] [INFO] Running command: blastn -query OceanDNA-b37154/markers.fasta -db /var/lib/cwl/stg239f2d92-8d9a-422a-aaca-2064b7bbe677/dqc_reference/reference_markers.fasta -out OceanDNA-b37154/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:55:27,031] [INFO] Task succeeded: Blastn
[2023-03-15 15:55:27,032] [INFO] Selected 26 target genomes.
[2023-03-15 15:55:27,033] [INFO] Target genome list was writen to OceanDNA-b37154/target_genomes.txt
[2023-03-15 15:55:27,066] [INFO] Task started: fastANI
[2023-03-15 15:55:27,066] [INFO] Running command: fastANI --query /var/lib/cwl/stge2697df2-e8ad-4702-93ce-646c90ba3065/OceanDNA-b37154.fa --refList OceanDNA-b37154/target_genomes.txt --output OceanDNA-b37154/fastani_result.tsv --threads 1
[2023-03-15 15:55:40,847] [INFO] Task succeeded: fastANI
[2023-03-15 15:55:40,847] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg239f2d92-8d9a-422a-aaca-2064b7bbe677/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:55:40,847] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg239f2d92-8d9a-422a-aaca-2064b7bbe677/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:55:40,848] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:55:40,848] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:55:40,848] [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
--------------------------------------------------------------------------------
[2023-03-15 15:55:40,848] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37154/tc_result.tsv
[2023-03-15 15:55:40,848] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:55:40,848] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:55:40,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg239f2d92-8d9a-422a-aaca-2064b7bbe677/dqc_reference/checkm_data
[2023-03-15 15:55:40,851] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:55:40,854] [INFO] Task started: CheckM
[2023-03-15 15:55:40,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37154/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37154/checkm_input OceanDNA-b37154/checkm_result
[2023-03-15 15:56:06,360] [INFO] Task succeeded: CheckM
[2023-03-15 15:56:06,361] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.35%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 15:56:06,362] [INFO] ===== Completeness check finished =====
[2023-03-15 15:56:06,362] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:56:06,363] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37154/markers.fasta)
[2023-03-15 15:56:06,364] [INFO] Task started: Blastn
[2023-03-15 15:56:06,364] [INFO] Running command: blastn -query OceanDNA-b37154/markers.fasta -db /var/lib/cwl/stg239f2d92-8d9a-422a-aaca-2064b7bbe677/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37154/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:56:07,304] [INFO] Task succeeded: Blastn
[2023-03-15 15:56:07,304] [INFO] Selected 14 target genomes.
[2023-03-15 15:56:07,305] [INFO] Target genome list was writen to OceanDNA-b37154/target_genomes_gtdb.txt
[2023-03-15 15:56:07,312] [INFO] Task started: fastANI
[2023-03-15 15:56:07,313] [INFO] Running command: fastANI --query /var/lib/cwl/stge2697df2-e8ad-4702-93ce-646c90ba3065/OceanDNA-b37154.fa --refList OceanDNA-b37154/target_genomes_gtdb.txt --output OceanDNA-b37154/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:56:13,461] [INFO] Task succeeded: fastANI
[2023-03-15 15:56:13,466] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 15:56:13,466] [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_002725095.1	s__UBA4421 sp002725095	99.3483	353	451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	99.07	99.07	0.73	0.73	2	conclusive
GCA_002348825.1	s__UBA4421 sp002348825	82.1823	352	451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	99.36	99.22	0.85	0.84	3	-
GCA_002704325.1	s__UBA4421 sp002704325	78.5881	162	451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684495.1	s__UBA4421 sp002684495	78.4086	247	451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690405.1	s__UBA4421 sp002690405	78.2355	218	451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	98.88	98.84	0.89	0.88	4	-
GCA_902565895.1	s__UBA4421 sp902565895	76.7961	67	451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	96.81	96.81	0.58	0.58	2	-
GCA_002170355.2	s__UBA4421 sp002170355	76.7766	54	451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 15:56:13,466] [INFO] GTDB search result was written to OceanDNA-b37154/result_gtdb.tsv
[2023-03-15 15:56:13,466] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:56:13,467] [INFO] DFAST_QC result json was written to OceanDNA-b37154/dqc_result.json
[2023-03-15 15:56:13,467] [INFO] DFAST_QC completed!
[2023-03-15 15:56:13,467] [INFO] Total running time: 0h0m57s