[2023-03-14 14:23:08,425] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:23:08,426] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:23:08,426] [INFO] DQC Reference Directory: /var/lib/cwl/stg73503226-4367-4e4d-a931-0bd583096311/dqc_reference
[2023-03-14 14:23:14,423] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:23:14,424] [INFO] Task started: Prodigal
[2023-03-14 14:23:14,424] [INFO] Running command: cat /var/lib/cwl/stg203c9b8d-250a-4b56-acc4-36ec2663eb30/OceanDNA-b20404.fa | prodigal -d OceanDNA-b20404/cds.fna -a OceanDNA-b20404/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:23:20,662] [INFO] Task succeeded: Prodigal
[2023-03-14 14:23:20,662] [INFO] Task started: HMMsearch
[2023-03-14 14:23:20,662] [INFO] Running command: hmmsearch --tblout OceanDNA-b20404/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73503226-4367-4e4d-a931-0bd583096311/dqc_reference/reference_markers.hmm OceanDNA-b20404/protein.faa > /dev/null
[2023-03-14 14:23:20,882] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:23:20,883] [INFO] Found 6/6 markers.
[2023-03-14 14:23:20,898] [INFO] Query marker FASTA was written to OceanDNA-b20404/markers.fasta
[2023-03-14 14:23:20,899] [INFO] Task started: Blastn
[2023-03-14 14:23:20,899] [INFO] Running command: blastn -query OceanDNA-b20404/markers.fasta -db /var/lib/cwl/stg73503226-4367-4e4d-a931-0bd583096311/dqc_reference/reference_markers.fasta -out OceanDNA-b20404/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:23:21,600] [INFO] Task succeeded: Blastn
[2023-03-14 14:23:21,601] [INFO] Selected 18 target genomes.
[2023-03-14 14:23:21,601] [INFO] Target genome list was writen to OceanDNA-b20404/target_genomes.txt
[2023-03-14 14:23:21,609] [INFO] Task started: fastANI
[2023-03-14 14:23:21,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg203c9b8d-250a-4b56-acc4-36ec2663eb30/OceanDNA-b20404.fa --refList OceanDNA-b20404/target_genomes.txt --output OceanDNA-b20404/fastani_result.tsv --threads 1
[2023-03-14 14:23:40,373] [INFO] Task succeeded: fastANI
[2023-03-14 14:23:40,373] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73503226-4367-4e4d-a931-0bd583096311/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:23:40,373] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73503226-4367-4e4d-a931-0bd583096311/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:23:40,373] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:23:40,374] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 14:23:40,374] [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 14:23:40,374] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20404/tc_result.tsv
[2023-03-14 14:23:40,374] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:23:40,374] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:23:40,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73503226-4367-4e4d-a931-0bd583096311/dqc_reference/checkm_data
[2023-03-14 14:23:40,423] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:23:40,427] [INFO] Task started: CheckM
[2023-03-14 14:23:40,427] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20404/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20404/checkm_input OceanDNA-b20404/checkm_result
[2023-03-14 14:24:08,311] [INFO] Task succeeded: CheckM
[2023-03-14 14:24:08,311] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.84%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:24:08,313] [INFO] ===== Completeness check finished =====
[2023-03-14 14:24:08,313] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:24:08,313] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20404/markers.fasta)
[2023-03-14 14:24:08,314] [INFO] Task started: Blastn
[2023-03-14 14:24:08,315] [INFO] Running command: blastn -query OceanDNA-b20404/markers.fasta -db /var/lib/cwl/stg73503226-4367-4e4d-a931-0bd583096311/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20404/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:24:09,146] [INFO] Task succeeded: Blastn
[2023-03-14 14:24:09,147] [INFO] Selected 13 target genomes.
[2023-03-14 14:24:09,147] [INFO] Target genome list was writen to OceanDNA-b20404/target_genomes_gtdb.txt
[2023-03-14 14:24:09,238] [INFO] Task started: fastANI
[2023-03-14 14:24:09,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg203c9b8d-250a-4b56-acc4-36ec2663eb30/OceanDNA-b20404.fa --refList OceanDNA-b20404/target_genomes_gtdb.txt --output OceanDNA-b20404/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:24:13,205] [INFO] Task succeeded: fastANI
[2023-03-14 14:24:13,209] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 14:24:13,209] [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_003535775.1	s__UBA8229 sp003535775	98.6037	253	329	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA8229;g__UBA8229	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012964235.1	s__UBA8229 sp012964235	94.291	253	329	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA8229;g__UBA8229	95.0	99.05	99.05	0.88	0.88	2	-
GCA_002686675.1	s__UBA8229 sp002686675	93.7697	135	329	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA8229;g__UBA8229	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726775.1	s__UBA8229 sp002726775	92.5181	206	329	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA8229;g__UBA8229	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:24:13,209] [INFO] GTDB search result was written to OceanDNA-b20404/result_gtdb.tsv
[2023-03-14 14:24:13,209] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:24:13,210] [INFO] DFAST_QC result json was written to OceanDNA-b20404/dqc_result.json
[2023-03-14 14:24:13,210] [INFO] DFAST_QC completed!
[2023-03-14 14:24:13,210] [INFO] Total running time: 0h1m5s