[2023-03-17 14:35:27,733] [INFO] DFAST_QC pipeline started.
[2023-03-17 14:35:27,733] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 14:35:27,733] [INFO] DQC Reference Directory: /var/lib/cwl/stg73229543-d76c-4e95-b400-8289397c4229/dqc_reference
[2023-03-17 14:35:29,536] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 14:35:29,537] [INFO] Task started: Prodigal
[2023-03-17 14:35:29,537] [INFO] Running command: cat /var/lib/cwl/stgf7f8242c-2c1d-4d18-acf7-56866c6dd2c9/OceanDNA-b17602.fa | prodigal -d OceanDNA-b17602/cds.fna -a OceanDNA-b17602/protein.faa -g 11 -q > /dev/null
[2023-03-17 14:36:10,940] [INFO] Task succeeded: Prodigal
[2023-03-17 14:36:10,940] [INFO] Task started: HMMsearch
[2023-03-17 14:36:10,940] [INFO] Running command: hmmsearch --tblout OceanDNA-b17602/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73229543-d76c-4e95-b400-8289397c4229/dqc_reference/reference_markers.hmm OceanDNA-b17602/protein.faa > /dev/null
[2023-03-17 14:36:11,196] [INFO] Task succeeded: HMMsearch
[2023-03-17 14:36:11,197] [INFO] Found 6/6 markers.
[2023-03-17 14:36:11,253] [INFO] Query marker FASTA was written to OceanDNA-b17602/markers.fasta
[2023-03-17 14:36:11,254] [INFO] Task started: Blastn
[2023-03-17 14:36:11,254] [INFO] Running command: blastn -query OceanDNA-b17602/markers.fasta -db /var/lib/cwl/stg73229543-d76c-4e95-b400-8289397c4229/dqc_reference/reference_markers.fasta -out OceanDNA-b17602/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 14:36:11,786] [INFO] Task succeeded: Blastn
[2023-03-17 14:36:11,787] [INFO] Selected 14 target genomes.
[2023-03-17 14:36:11,787] [INFO] Target genome list was writen to OceanDNA-b17602/target_genomes.txt
[2023-03-17 14:36:11,796] [INFO] Task started: fastANI
[2023-03-17 14:36:11,797] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7f8242c-2c1d-4d18-acf7-56866c6dd2c9/OceanDNA-b17602.fa --refList OceanDNA-b17602/target_genomes.txt --output OceanDNA-b17602/fastani_result.tsv --threads 1
[2023-03-17 14:36:20,556] [INFO] Task succeeded: fastANI
[2023-03-17 14:36:20,557] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73229543-d76c-4e95-b400-8289397c4229/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 14:36:20,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73229543-d76c-4e95-b400-8289397c4229/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 14:36:20,557] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 14:36:20,557] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 14:36:20,557] [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
--------------------------------------------------------------------------------
[2023-03-17 14:36:20,558] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17602/tc_result.tsv
[2023-03-17 14:36:20,558] [INFO] ===== Taxonomy check completed =====
[2023-03-17 14:36:20,558] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 14:36:20,558] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73229543-d76c-4e95-b400-8289397c4229/dqc_reference/checkm_data
[2023-03-17 14:36:20,561] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 14:36:20,568] [INFO] Task started: CheckM
[2023-03-17 14:36:20,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17602/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17602/checkm_input OceanDNA-b17602/checkm_result
[2023-03-17 14:37:35,253] [INFO] Task succeeded: CheckM
[2023-03-17 14:37:35,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.60%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 14:37:35,257] [INFO] ===== Completeness check finished =====
[2023-03-17 14:37:35,257] [INFO] ===== Start GTDB Search =====
[2023-03-17 14:37:35,257] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17602/markers.fasta)
[2023-03-17 14:37:35,259] [INFO] Task started: Blastn
[2023-03-17 14:37:35,259] [INFO] Running command: blastn -query OceanDNA-b17602/markers.fasta -db /var/lib/cwl/stg73229543-d76c-4e95-b400-8289397c4229/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17602/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 14:37:36,247] [INFO] Task succeeded: Blastn
[2023-03-17 14:37:36,248] [INFO] Selected 22 target genomes.
[2023-03-17 14:37:36,248] [INFO] Target genome list was writen to OceanDNA-b17602/target_genomes_gtdb.txt
[2023-03-17 14:37:36,318] [INFO] Task started: fastANI
[2023-03-17 14:37:36,318] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7f8242c-2c1d-4d18-acf7-56866c6dd2c9/OceanDNA-b17602.fa --refList OceanDNA-b17602/target_genomes_gtdb.txt --output OceanDNA-b17602/fastani_result_gtdb.tsv --threads 1
[2023-03-17 14:37:57,771] [INFO] Task succeeded: fastANI
[2023-03-17 14:37:57,775] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 14:37:57,775] [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_002433075.1	s__UBA6620 sp002433075	98.738	1570	1623	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA2968;f__UBA2968;g__UBA6620	95.0	99.96	99.96	0.96	0.95	3	conclusive
GCA_002714465.1	s__UBA2968 sp002714465	76.0347	91	1623	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA2968;f__UBA2968;g__UBA2968	95.0	99.49	99.49	0.96	0.96	2	-
GCA_002727195.1	s__UBA2968 sp002727195	76.0109	157	1623	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA2968;f__UBA2968;g__UBA2968	95.0	98.72	97.66	0.95	0.94	3	-
--------------------------------------------------------------------------------
[2023-03-17 14:37:57,775] [INFO] GTDB search result was written to OceanDNA-b17602/result_gtdb.tsv
[2023-03-17 14:37:57,776] [INFO] ===== GTDB Search completed =====
[2023-03-17 14:37:57,776] [INFO] DFAST_QC result json was written to OceanDNA-b17602/dqc_result.json
[2023-03-17 14:37:57,776] [INFO] DFAST_QC completed!
[2023-03-17 14:37:57,776] [INFO] Total running time: 0h2m30s