[2023-03-18 07:54:30,541] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:54:30,542] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:54:30,542] [INFO] DQC Reference Directory: /var/lib/cwl/stg84e36032-f4a3-4bb4-ad39-93e6d3f90e8e/dqc_reference
[2023-03-18 07:54:32,271] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:54:32,271] [INFO] Task started: Prodigal
[2023-03-18 07:54:32,271] [INFO] Running command: cat /var/lib/cwl/stg7a71d5ff-8526-42c5-91ba-af28180b6655/OceanDNA-b36872.fa | prodigal -d OceanDNA-b36872/cds.fna -a OceanDNA-b36872/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:54:52,375] [INFO] Task succeeded: Prodigal
[2023-03-18 07:54:52,376] [INFO] Task started: HMMsearch
[2023-03-18 07:54:52,376] [INFO] Running command: hmmsearch --tblout OceanDNA-b36872/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84e36032-f4a3-4bb4-ad39-93e6d3f90e8e/dqc_reference/reference_markers.hmm OceanDNA-b36872/protein.faa > /dev/null
[2023-03-18 07:54:52,587] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:54:52,588] [INFO] Found 6/6 markers.
[2023-03-18 07:54:52,607] [INFO] Query marker FASTA was written to OceanDNA-b36872/markers.fasta
[2023-03-18 07:54:52,608] [INFO] Task started: Blastn
[2023-03-18 07:54:52,608] [INFO] Running command: blastn -query OceanDNA-b36872/markers.fasta -db /var/lib/cwl/stg84e36032-f4a3-4bb4-ad39-93e6d3f90e8e/dqc_reference/reference_markers.fasta -out OceanDNA-b36872/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:54:53,295] [INFO] Task succeeded: Blastn
[2023-03-18 07:54:53,296] [INFO] Selected 27 target genomes.
[2023-03-18 07:54:53,296] [INFO] Target genome list was writen to OceanDNA-b36872/target_genomes.txt
[2023-03-18 07:54:53,313] [INFO] Task started: fastANI
[2023-03-18 07:54:53,313] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a71d5ff-8526-42c5-91ba-af28180b6655/OceanDNA-b36872.fa --refList OceanDNA-b36872/target_genomes.txt --output OceanDNA-b36872/fastani_result.tsv --threads 1
[2023-03-18 07:55:08,668] [INFO] Task succeeded: fastANI
[2023-03-18 07:55:08,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84e36032-f4a3-4bb4-ad39-93e6d3f90e8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:55:08,668] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84e36032-f4a3-4bb4-ad39-93e6d3f90e8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:55:08,672] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:55:08,672] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:55:08,672] [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
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	75.7484	59	1042	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	75.6029	51	1042	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:55:08,672] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36872/tc_result.tsv
[2023-03-18 07:55:08,672] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:55:08,673] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:55:08,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84e36032-f4a3-4bb4-ad39-93e6d3f90e8e/dqc_reference/checkm_data
[2023-03-18 07:55:08,673] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:55:08,678] [INFO] Task started: CheckM
[2023-03-18 07:55:08,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36872/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36872/checkm_input OceanDNA-b36872/checkm_result
[2023-03-18 07:55:58,962] [INFO] Task succeeded: CheckM
[2023-03-18 07:55:58,962] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:55:58,965] [INFO] ===== Completeness check finished =====
[2023-03-18 07:55:58,965] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:55:58,965] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36872/markers.fasta)
[2023-03-18 07:55:58,966] [INFO] Task started: Blastn
[2023-03-18 07:55:58,966] [INFO] Running command: blastn -query OceanDNA-b36872/markers.fasta -db /var/lib/cwl/stg84e36032-f4a3-4bb4-ad39-93e6d3f90e8e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36872/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:56:00,183] [INFO] Task succeeded: Blastn
[2023-03-18 07:56:00,184] [INFO] Selected 23 target genomes.
[2023-03-18 07:56:00,184] [INFO] Target genome list was writen to OceanDNA-b36872/target_genomes_gtdb.txt
[2023-03-18 07:56:00,232] [INFO] Task started: fastANI
[2023-03-18 07:56:00,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a71d5ff-8526-42c5-91ba-af28180b6655/OceanDNA-b36872.fa --refList OceanDNA-b36872/target_genomes_gtdb.txt --output OceanDNA-b36872/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:56:13,012] [INFO] Task succeeded: fastANI
[2023-03-18 07:56:13,017] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:56:13,018] [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_002348385.1	s__UBA2965 sp002348385	99.9292	997	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA2965	95.0	98.25	98.25	0.91	0.91	2	conclusive
GCA_002480525.1	s__UBA7803 sp002480525	76.6184	198	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA7803	95.0	99.35	98.95	0.83	0.81	3	-
GCA_009843635.1	s__UBA2168 sp009843635	76.3371	134	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA2168	95.0	97.76	96.95	0.89	0.86	7	-
GCA_003247835.1	s__SZUA-309 sp003247835	76.3303	130	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__SZUA-309	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337735.1	s__Thioalbus denitrificans	75.7261	60	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004357385.1	s__SMWF01 sp004357385	75.6335	75	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__SMWF01	95.0	99.34	99.34	0.91	0.91	2	-
GCA_007694905.1	s__SLTB01 sp007694905	75.574	61	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__SLTB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:56:13,018] [INFO] GTDB search result was written to OceanDNA-b36872/result_gtdb.tsv
[2023-03-18 07:56:13,018] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:56:13,019] [INFO] DFAST_QC result json was written to OceanDNA-b36872/dqc_result.json
[2023-03-18 07:56:13,019] [INFO] DFAST_QC completed!
[2023-03-18 07:56:13,019] [INFO] Total running time: 0h1m42s