[2023-03-18 23:48:46,637] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:48:46,637] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:48:46,637] [INFO] DQC Reference Directory: /var/lib/cwl/stga8a8d9d8-21f2-486b-818b-952d9858ce99/dqc_reference
[2023-03-18 23:48:47,743] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:48:47,744] [INFO] Task started: Prodigal
[2023-03-18 23:48:47,744] [INFO] Running command: cat /var/lib/cwl/stg2eeafbeb-fc70-437d-946f-ba314ea5d2c5/OceanDNA-b29832.fa | prodigal -d OceanDNA-b29832/cds.fna -a OceanDNA-b29832/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:48:54,969] [INFO] Task succeeded: Prodigal
[2023-03-18 23:48:54,969] [INFO] Task started: HMMsearch
[2023-03-18 23:48:54,969] [INFO] Running command: hmmsearch --tblout OceanDNA-b29832/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8a8d9d8-21f2-486b-818b-952d9858ce99/dqc_reference/reference_markers.hmm OceanDNA-b29832/protein.faa > /dev/null
[2023-03-18 23:48:55,142] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:48:55,143] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2eeafbeb-fc70-437d-946f-ba314ea5d2c5/OceanDNA-b29832.fa]
[2023-03-18 23:48:55,157] [INFO] Query marker FASTA was written to OceanDNA-b29832/markers.fasta
[2023-03-18 23:48:55,158] [INFO] Task started: Blastn
[2023-03-18 23:48:55,158] [INFO] Running command: blastn -query OceanDNA-b29832/markers.fasta -db /var/lib/cwl/stga8a8d9d8-21f2-486b-818b-952d9858ce99/dqc_reference/reference_markers.fasta -out OceanDNA-b29832/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:48:55,742] [INFO] Task succeeded: Blastn
[2023-03-18 23:48:55,743] [INFO] Selected 23 target genomes.
[2023-03-18 23:48:55,743] [INFO] Target genome list was writen to OceanDNA-b29832/target_genomes.txt
[2023-03-18 23:48:55,754] [INFO] Task started: fastANI
[2023-03-18 23:48:55,754] [INFO] Running command: fastANI --query /var/lib/cwl/stg2eeafbeb-fc70-437d-946f-ba314ea5d2c5/OceanDNA-b29832.fa --refList OceanDNA-b29832/target_genomes.txt --output OceanDNA-b29832/fastani_result.tsv --threads 1
[2023-03-18 23:49:06,803] [INFO] Task succeeded: fastANI
[2023-03-18 23:49:06,804] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8a8d9d8-21f2-486b-818b-952d9858ce99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:49:06,804] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8a8d9d8-21f2-486b-818b-952d9858ce99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:49:06,804] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:49:06,804] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:49:06,804] [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
--------------------------------------------------------------------------------
[2023-03-18 23:49:06,804] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29832/tc_result.tsv
[2023-03-18 23:49:06,805] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:49:06,805] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:49:06,805] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8a8d9d8-21f2-486b-818b-952d9858ce99/dqc_reference/checkm_data
[2023-03-18 23:49:06,808] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:49:06,839] [INFO] Task started: CheckM
[2023-03-18 23:49:06,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29832/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29832/checkm_input OceanDNA-b29832/checkm_result
[2023-03-18 23:49:30,659] [INFO] Task succeeded: CheckM
[2023-03-18 23:49:30,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.48%
Contamintation: 0.98%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:49:30,661] [INFO] ===== Completeness check finished =====
[2023-03-18 23:49:30,661] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:49:30,662] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29832/markers.fasta)
[2023-03-18 23:49:30,663] [INFO] Task started: Blastn
[2023-03-18 23:49:30,663] [INFO] Running command: blastn -query OceanDNA-b29832/markers.fasta -db /var/lib/cwl/stga8a8d9d8-21f2-486b-818b-952d9858ce99/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29832/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:49:31,481] [INFO] Task succeeded: Blastn
[2023-03-18 23:49:31,482] [INFO] Selected 24 target genomes.
[2023-03-18 23:49:31,482] [INFO] Target genome list was writen to OceanDNA-b29832/target_genomes_gtdb.txt
[2023-03-18 23:49:31,537] [INFO] Task started: fastANI
[2023-03-18 23:49:31,537] [INFO] Running command: fastANI --query /var/lib/cwl/stg2eeafbeb-fc70-437d-946f-ba314ea5d2c5/OceanDNA-b29832.fa --refList OceanDNA-b29832/target_genomes_gtdb.txt --output OceanDNA-b29832/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:49:41,088] [INFO] Task succeeded: fastANI
[2023-03-18 23:49:41,091] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:49:41,091] [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_905182425.1	s__Planktomarina sp905182425	93.5466	306	340	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000981705.1	s__Planktomarina sp000981705	77.1395	54	340	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	98.80	98.80	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-18 23:49:41,092] [INFO] GTDB search result was written to OceanDNA-b29832/result_gtdb.tsv
[2023-03-18 23:49:41,092] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:49:41,092] [INFO] DFAST_QC result json was written to OceanDNA-b29832/dqc_result.json
[2023-03-18 23:49:41,092] [INFO] DFAST_QC completed!
[2023-03-18 23:49:41,092] [INFO] Total running time: 0h0m54s