[2023-03-14 10:55:58,927] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,932] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,932] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6ceb878-4ee6-42ac-8120-1c72542a90d7/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/stgd5776940-54e6-4529-9b58-73b49eceea60/OceanDNA-b45336.fa | prodigal -d OceanDNA-b45336/cds.fna -a OceanDNA-b45336/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:08,821] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:08,821] [INFO] Task started: HMMsearch
[2023-03-14 10:56:08,821] [INFO] Running command: hmmsearch --tblout OceanDNA-b45336/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6ceb878-4ee6-42ac-8120-1c72542a90d7/dqc_reference/reference_markers.hmm OceanDNA-b45336/protein.faa > /dev/null
[2023-03-14 10:56:09,023] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:09,024] [INFO] Found 6/6 markers.
[2023-03-14 10:56:09,035] [INFO] Query marker FASTA was written to OceanDNA-b45336/markers.fasta
[2023-03-14 10:56:09,045] [INFO] Task started: Blastn
[2023-03-14 10:56:09,045] [INFO] Running command: blastn -query OceanDNA-b45336/markers.fasta -db /var/lib/cwl/stgd6ceb878-4ee6-42ac-8120-1c72542a90d7/dqc_reference/reference_markers.fasta -out OceanDNA-b45336/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:09,687] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:09,688] [INFO] Selected 17 target genomes.
[2023-03-14 10:56:09,688] [INFO] Target genome list was writen to OceanDNA-b45336/target_genomes.txt
[2023-03-14 10:56:09,699] [INFO] Task started: fastANI
[2023-03-14 10:56:09,699] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5776940-54e6-4529-9b58-73b49eceea60/OceanDNA-b45336.fa --refList OceanDNA-b45336/target_genomes.txt --output OceanDNA-b45336/fastani_result.tsv --threads 1
[2023-03-14 10:56:20,105] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:20,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6ceb878-4ee6-42ac-8120-1c72542a90d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:20,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6ceb878-4ee6-42ac-8120-1c72542a90d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:20,106] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:20,106] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 10:56:20,106] [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 10:56:20,106] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45336/tc_result.tsv
[2023-03-14 10:56:20,106] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:20,106] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:20,106] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6ceb878-4ee6-42ac-8120-1c72542a90d7/dqc_reference/checkm_data
[2023-03-14 10:56:20,109] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:20,112] [INFO] Task started: CheckM
[2023-03-14 10:56:20,112] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45336/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45336/checkm_input OceanDNA-b45336/checkm_result
[2023-03-14 10:56:45,600] [INFO] Task succeeded: CheckM
[2023-03-14 10:56:45,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.84%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-14 10:56:45,602] [INFO] ===== Completeness check finished =====
[2023-03-14 10:56:45,602] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:56:45,602] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45336/markers.fasta)
[2023-03-14 10:56:45,603] [INFO] Task started: Blastn
[2023-03-14 10:56:45,603] [INFO] Running command: blastn -query OceanDNA-b45336/markers.fasta -db /var/lib/cwl/stgd6ceb878-4ee6-42ac-8120-1c72542a90d7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45336/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:46,550] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:46,551] [INFO] Selected 20 target genomes.
[2023-03-14 10:56:46,551] [INFO] Target genome list was writen to OceanDNA-b45336/target_genomes_gtdb.txt
[2023-03-14 10:56:46,572] [INFO] Task started: fastANI
[2023-03-14 10:56:46,572] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5776940-54e6-4529-9b58-73b49eceea60/OceanDNA-b45336.fa --refList OceanDNA-b45336/target_genomes_gtdb.txt --output OceanDNA-b45336/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:56:54,983] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:54,986] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 10:56:54,987] [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_002338345.1	s__UBA1859 sp002338345	98.8852	236	448	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__UBA1859	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003532555.1	s__UBA1859 sp003532555	84.9603	223	448	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__UBA1859	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691095.1	s__UBA1859 sp002691095	81.0503	154	448	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__Kiritimatiellales;f__Pontiellaceae;g__UBA1859	95.0	98.96	98.96	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2023-03-14 10:56:54,987] [INFO] GTDB search result was written to OceanDNA-b45336/result_gtdb.tsv
[2023-03-14 10:56:54,987] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:56:54,987] [INFO] DFAST_QC result json was written to OceanDNA-b45336/dqc_result.json
[2023-03-14 10:56:54,988] [INFO] DFAST_QC completed!
[2023-03-14 10:56:54,988] [INFO] Total running time: 0h0m56s