[2023-03-14 13:08:46,513] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:08:46,513] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:08:46,513] [INFO] DQC Reference Directory: /var/lib/cwl/stga7f98958-4ad2-445c-9b42-c036c4f63a81/dqc_reference
[2023-03-14 13:08:47,631] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:08:47,631] [INFO] Task started: Prodigal
[2023-03-14 13:08:47,631] [INFO] Running command: cat /var/lib/cwl/stgc7df2c28-19bb-436b-8538-61027fca26a4/OceanDNA-b79.fa | prodigal -d OceanDNA-b79/cds.fna -a OceanDNA-b79/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:09:04,668] [INFO] Task succeeded: Prodigal
[2023-03-14 13:09:04,669] [INFO] Task started: HMMsearch
[2023-03-14 13:09:04,669] [INFO] Running command: hmmsearch --tblout OceanDNA-b79/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7f98958-4ad2-445c-9b42-c036c4f63a81/dqc_reference/reference_markers.hmm OceanDNA-b79/protein.faa > /dev/null
[2023-03-14 13:09:04,849] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:09:04,850] [INFO] Found 6/6 markers.
[2023-03-14 13:09:04,867] [INFO] Query marker FASTA was written to OceanDNA-b79/markers.fasta
[2023-03-14 13:09:04,868] [INFO] Task started: Blastn
[2023-03-14 13:09:04,868] [INFO] Running command: blastn -query OceanDNA-b79/markers.fasta -db /var/lib/cwl/stga7f98958-4ad2-445c-9b42-c036c4f63a81/dqc_reference/reference_markers.fasta -out OceanDNA-b79/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:09:05,391] [INFO] Task succeeded: Blastn
[2023-03-14 13:09:05,393] [INFO] Selected 11 target genomes.
[2023-03-14 13:09:05,393] [INFO] Target genome list was writen to OceanDNA-b79/target_genomes.txt
[2023-03-14 13:09:05,401] [INFO] Task started: fastANI
[2023-03-14 13:09:05,401] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7df2c28-19bb-436b-8538-61027fca26a4/OceanDNA-b79.fa --refList OceanDNA-b79/target_genomes.txt --output OceanDNA-b79/fastani_result.tsv --threads 1
[2023-03-14 13:09:12,428] [INFO] Task succeeded: fastANI
[2023-03-14 13:09:12,428] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7f98958-4ad2-445c-9b42-c036c4f63a81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:09:12,428] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7f98958-4ad2-445c-9b42-c036c4f63a81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:09:12,428] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:09:12,429] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:09:12,429] [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 13:09:12,429] [INFO] DFAST Taxonomy check result was written to OceanDNA-b79/tc_result.tsv
[2023-03-14 13:09:12,429] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:09:12,430] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:09:12,430] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7f98958-4ad2-445c-9b42-c036c4f63a81/dqc_reference/checkm_data
[2023-03-14 13:09:12,433] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:09:12,439] [INFO] Task started: CheckM
[2023-03-14 13:09:12,439] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b79/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b79/checkm_input OceanDNA-b79/checkm_result
[2023-03-14 13:10:14,799] [INFO] Task succeeded: CheckM
[2023-03-14 13:10:14,799] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:10:14,802] [INFO] ===== Completeness check finished =====
[2023-03-14 13:10:14,802] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:10:14,802] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b79/markers.fasta)
[2023-03-14 13:10:14,804] [INFO] Task started: Blastn
[2023-03-14 13:10:14,804] [INFO] Running command: blastn -query OceanDNA-b79/markers.fasta -db /var/lib/cwl/stga7f98958-4ad2-445c-9b42-c036c4f63a81/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b79/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:10:16,335] [INFO] Task succeeded: Blastn
[2023-03-14 13:10:16,335] [INFO] Selected 21 target genomes.
[2023-03-14 13:10:16,335] [INFO] Target genome list was writen to OceanDNA-b79/target_genomes_gtdb.txt
[2023-03-14 13:10:16,364] [INFO] Task started: fastANI
[2023-03-14 13:10:16,365] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7df2c28-19bb-436b-8538-61027fca26a4/OceanDNA-b79.fa --refList OceanDNA-b79/target_genomes_gtdb.txt --output OceanDNA-b79/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:10:27,974] [INFO] Task succeeded: fastANI
[2023-03-14 13:10:27,976] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:10:27,976] [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_002722645.1	s__UBA890 sp002722645	98.2894	703	881	d__Bacteria;p__Acidobacteriota;c__UBA890;o__UBA890;f__UBA890;g__UBA890	95.0	97.90	97.61	0.78	0.75	3	conclusive
GCA_002731215.1	s__UBA890 sp002731215	87.9776	302	881	d__Bacteria;p__Acidobacteriota;c__UBA890;o__UBA890;f__UBA890;g__UBA890	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:10:27,977] [INFO] GTDB search result was written to OceanDNA-b79/result_gtdb.tsv
[2023-03-14 13:10:27,978] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:10:27,979] [INFO] DFAST_QC result json was written to OceanDNA-b79/dqc_result.json
[2023-03-14 13:10:27,979] [INFO] DFAST_QC completed!
[2023-03-14 13:10:27,979] [INFO] Total running time: 0h1m41s