[2023-03-15 15:51:29,972] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:51:29,975] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:51:29,975] [INFO] DQC Reference Directory: /var/lib/cwl/stg12adcbd4-b710-4a21-8adc-543d31aa672b/dqc_reference
[2023-03-15 15:51:31,681] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:51:31,681] [INFO] Task started: Prodigal
[2023-03-15 15:51:31,682] [INFO] Running command: cat /var/lib/cwl/stgd4ec2bcc-07b0-4635-8b18-de5e0b5acc6b/OceanDNA-b288.fa | prodigal -d OceanDNA-b288/cds.fna -a OceanDNA-b288/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:51:46,697] [INFO] Task succeeded: Prodigal
[2023-03-15 15:51:46,697] [INFO] Task started: HMMsearch
[2023-03-15 15:51:46,697] [INFO] Running command: hmmsearch --tblout OceanDNA-b288/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12adcbd4-b710-4a21-8adc-543d31aa672b/dqc_reference/reference_markers.hmm OceanDNA-b288/protein.faa > /dev/null
[2023-03-15 15:51:46,916] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:51:46,916] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd4ec2bcc-07b0-4635-8b18-de5e0b5acc6b/OceanDNA-b288.fa]
[2023-03-15 15:51:46,939] [INFO] Query marker FASTA was written to OceanDNA-b288/markers.fasta
[2023-03-15 15:51:46,939] [INFO] Task started: Blastn
[2023-03-15 15:51:46,939] [INFO] Running command: blastn -query OceanDNA-b288/markers.fasta -db /var/lib/cwl/stg12adcbd4-b710-4a21-8adc-543d31aa672b/dqc_reference/reference_markers.fasta -out OceanDNA-b288/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:51:47,508] [INFO] Task succeeded: Blastn
[2023-03-15 15:51:47,526] [INFO] Selected 28 target genomes.
[2023-03-15 15:51:47,527] [INFO] Target genome list was writen to OceanDNA-b288/target_genomes.txt
[2023-03-15 15:51:47,541] [INFO] Task started: fastANI
[2023-03-15 15:51:47,541] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4ec2bcc-07b0-4635-8b18-de5e0b5acc6b/OceanDNA-b288.fa --refList OceanDNA-b288/target_genomes.txt --output OceanDNA-b288/fastani_result.tsv --threads 1
[2023-03-15 15:52:07,565] [INFO] Task succeeded: fastANI
[2023-03-15 15:52:07,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12adcbd4-b710-4a21-8adc-543d31aa672b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:52:07,566] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12adcbd4-b710-4a21-8adc-543d31aa672b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:52:07,566] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:52:07,566] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:52:07,566] [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 15:52:07,566] [INFO] DFAST Taxonomy check result was written to OceanDNA-b288/tc_result.tsv
[2023-03-15 15:52:07,567] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:52:07,567] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:52:07,567] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12adcbd4-b710-4a21-8adc-543d31aa672b/dqc_reference/checkm_data
[2023-03-15 15:52:07,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:52:07,575] [INFO] Task started: CheckM
[2023-03-15 15:52:07,575] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b288/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b288/checkm_input OceanDNA-b288/checkm_result
[2023-03-15 15:52:47,427] [INFO] Task succeeded: CheckM
[2023-03-15 15:52:47,427] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.77%
Contamintation: 4.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 15:52:47,430] [INFO] ===== Completeness check finished =====
[2023-03-15 15:52:47,430] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:52:47,430] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b288/markers.fasta)
[2023-03-15 15:52:47,430] [INFO] Task started: Blastn
[2023-03-15 15:52:47,430] [INFO] Running command: blastn -query OceanDNA-b288/markers.fasta -db /var/lib/cwl/stg12adcbd4-b710-4a21-8adc-543d31aa672b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b288/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:52:48,366] [INFO] Task succeeded: Blastn
[2023-03-15 15:52:48,367] [INFO] Selected 20 target genomes.
[2023-03-15 15:52:48,367] [INFO] Target genome list was writen to OceanDNA-b288/target_genomes_gtdb.txt
[2023-03-15 15:52:48,423] [INFO] Task started: fastANI
[2023-03-15 15:52:48,424] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4ec2bcc-07b0-4635-8b18-de5e0b5acc6b/OceanDNA-b288.fa --refList OceanDNA-b288/target_genomes_gtdb.txt --output OceanDNA-b288/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:53:04,708] [INFO] Task succeeded: fastANI
[2023-03-15 15:53:04,716] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:53:04,716] [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_002712885.1	s__UBA8438 sp002712885	91.7842	614	752	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA8438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005778315.1	s__UBA8438 sp005778315	78.1155	253	752	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA8438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015659035.1	s__NP936 sp015659035	77.9726	244	752	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726085.1	s__NP936 sp002726085	77.6407	259	752	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523845.1	s__WTFV01 sp011523845	76.5475	163	752	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002346545.1	s__UBA2994 sp002346545	76.4277	171	752	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA2994	95.0	99.87	99.87	0.91	0.91	2	-
GCA_012271165.1	s__JAAXGX01 sp012271165	75.9614	116	752	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__JAAXGX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009380045.1	s__WHSN01 sp009380045	75.8034	54	752	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__WHSN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789705.1	s__CADEFD01 sp016789705	75.6619	52	752	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__CADEFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767435.1	s__2-02-FULL-65-29 sp001767435	75.6364	65	752	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__2-02-FULL-65-29	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826065.1	s__CADEFD01 sp902826065	75.3957	51	752	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__CADEFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001917905.1	s__Gp6-AA45 sp001917905	75.3367	53	752	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.03	98.94	0.79	0.79	3	-
GCA_003222395.1	s__Gp6-AA45 sp003222395	75.2775	52	752	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.74	99.72	0.98	0.98	4	-
--------------------------------------------------------------------------------
[2023-03-15 15:53:04,717] [INFO] GTDB search result was written to OceanDNA-b288/result_gtdb.tsv
[2023-03-15 15:53:04,717] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:53:04,718] [INFO] DFAST_QC result json was written to OceanDNA-b288/dqc_result.json
[2023-03-15 15:53:04,718] [INFO] DFAST_QC completed!
[2023-03-15 15:53:04,718] [INFO] Total running time: 0h1m35s