[2023-03-14 10:55:58,909] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,910] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,910] [INFO] DQC Reference Directory: /var/lib/cwl/stg377ead36-1586-4950-b178-f631fc627526/dqc_reference
[2023-03-14 10:56:00,753] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,753] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,753] [INFO] Running command: cat /var/lib/cwl/stg3350b5c2-880d-4dc3-a994-15dc0dde925b/OceanDNA-b19476.fa | prodigal -d OceanDNA-b19476/cds.fna -a OceanDNA-b19476/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:07,465] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:07,465] [INFO] Task started: HMMsearch
[2023-03-14 10:56:07,465] [INFO] Running command: hmmsearch --tblout OceanDNA-b19476/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg377ead36-1586-4950-b178-f631fc627526/dqc_reference/reference_markers.hmm OceanDNA-b19476/protein.faa > /dev/null
[2023-03-14 10:56:07,668] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:07,669] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3350b5c2-880d-4dc3-a994-15dc0dde925b/OceanDNA-b19476.fa]
[2023-03-14 10:56:07,681] [INFO] Query marker FASTA was written to OceanDNA-b19476/markers.fasta
[2023-03-14 10:56:07,681] [INFO] Task started: Blastn
[2023-03-14 10:56:07,681] [INFO] Running command: blastn -query OceanDNA-b19476/markers.fasta -db /var/lib/cwl/stg377ead36-1586-4950-b178-f631fc627526/dqc_reference/reference_markers.fasta -out OceanDNA-b19476/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:08,209] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:08,210] [INFO] Selected 17 target genomes.
[2023-03-14 10:56:08,210] [INFO] Target genome list was writen to OceanDNA-b19476/target_genomes.txt
[2023-03-14 10:56:08,222] [INFO] Task started: fastANI
[2023-03-14 10:56:08,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg3350b5c2-880d-4dc3-a994-15dc0dde925b/OceanDNA-b19476.fa --refList OceanDNA-b19476/target_genomes.txt --output OceanDNA-b19476/fastani_result.tsv --threads 1
[2023-03-14 10:56:15,566] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:15,567] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg377ead36-1586-4950-b178-f631fc627526/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:15,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg377ead36-1586-4950-b178-f631fc627526/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:15,567] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:15,567] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 10:56:15,567] [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
--------------------------------------------------------------------------------
[2023-03-14 10:56:15,567] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19476/tc_result.tsv
[2023-03-14 10:56:15,568] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:15,568] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:15,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg377ead36-1586-4950-b178-f631fc627526/dqc_reference/checkm_data
[2023-03-14 10:56:15,570] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:15,573] [INFO] Task started: CheckM
[2023-03-14 10:56:15,573] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19476/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19476/checkm_input OceanDNA-b19476/checkm_result
[2023-03-14 10:56:38,551] [INFO] Task succeeded: CheckM
[2023-03-14 10:56:38,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:56:38,553] [INFO] ===== Completeness check finished =====
[2023-03-14 10:56:38,553] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:56:38,553] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19476/markers.fasta)
[2023-03-14 10:56:38,554] [INFO] Task started: Blastn
[2023-03-14 10:56:38,554] [INFO] Running command: blastn -query OceanDNA-b19476/markers.fasta -db /var/lib/cwl/stg377ead36-1586-4950-b178-f631fc627526/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19476/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:39,291] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:39,292] [INFO] Selected 15 target genomes.
[2023-03-14 10:56:39,292] [INFO] Target genome list was writen to OceanDNA-b19476/target_genomes_gtdb.txt
[2023-03-14 10:56:39,312] [INFO] Task started: fastANI
[2023-03-14 10:56:39,312] [INFO] Running command: fastANI --query /var/lib/cwl/stg3350b5c2-880d-4dc3-a994-15dc0dde925b/OceanDNA-b19476.fa --refList OceanDNA-b19476/target_genomes_gtdb.txt --output OceanDNA-b19476/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:56:44,619] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:44,623] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 10:56:44,623] [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_004124385.1	s__UBA2126 sp004124385	98.1002	374	382	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__UBA2126	95.0	99.49	99.49	0.93	0.93	2	conclusive
GCA_002713385.1	s__UBA2126 sp002713385	79.4854	133	382	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__UBA2126	95.0	95.44	95.44	0.61	0.61	2	-
GCA_002256485.1	s__UBA2126 sp002256485	79.1295	231	382	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__UBA2126	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002730315.1	s__UBA2126 sp002730315	77.2092	70	382	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__UBA2126	95.0	99.18	99.07	0.56	0.51	3	-
--------------------------------------------------------------------------------
[2023-03-14 10:56:44,624] [INFO] GTDB search result was written to OceanDNA-b19476/result_gtdb.tsv
[2023-03-14 10:56:44,624] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:56:44,624] [INFO] DFAST_QC result json was written to OceanDNA-b19476/dqc_result.json
[2023-03-14 10:56:44,624] [INFO] DFAST_QC completed!
[2023-03-14 10:56:44,624] [INFO] Total running time: 0h0m46s