[2023-03-15 16:53:06,406] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:53:06,406] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:53:06,406] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3d395e3-de16-4537-aa3d-b87007a8e9f8/dqc_reference
[2023-03-15 16:53:07,521] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:53:07,522] [INFO] Task started: Prodigal
[2023-03-15 16:53:07,522] [INFO] Running command: cat /var/lib/cwl/stg9ccfdfce-0928-4374-b9fa-238e00878c76/OceanDNA-b22211.fa | prodigal -d OceanDNA-b22211/cds.fna -a OceanDNA-b22211/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:53:13,056] [INFO] Task succeeded: Prodigal
[2023-03-15 16:53:13,056] [INFO] Task started: HMMsearch
[2023-03-15 16:53:13,056] [INFO] Running command: hmmsearch --tblout OceanDNA-b22211/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3d395e3-de16-4537-aa3d-b87007a8e9f8/dqc_reference/reference_markers.hmm OceanDNA-b22211/protein.faa > /dev/null
[2023-03-15 16:53:13,210] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:53:13,211] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9ccfdfce-0928-4374-b9fa-238e00878c76/OceanDNA-b22211.fa]
[2023-03-15 16:53:13,233] [INFO] Query marker FASTA was written to OceanDNA-b22211/markers.fasta
[2023-03-15 16:53:13,235] [INFO] Task started: Blastn
[2023-03-15 16:53:13,235] [INFO] Running command: blastn -query OceanDNA-b22211/markers.fasta -db /var/lib/cwl/stgc3d395e3-de16-4537-aa3d-b87007a8e9f8/dqc_reference/reference_markers.fasta -out OceanDNA-b22211/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:53:13,812] [INFO] Task succeeded: Blastn
[2023-03-15 16:53:13,815] [INFO] Selected 19 target genomes.
[2023-03-15 16:53:13,815] [INFO] Target genome list was writen to OceanDNA-b22211/target_genomes.txt
[2023-03-15 16:53:13,825] [INFO] Task started: fastANI
[2023-03-15 16:53:13,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ccfdfce-0928-4374-b9fa-238e00878c76/OceanDNA-b22211.fa --refList OceanDNA-b22211/target_genomes.txt --output OceanDNA-b22211/fastani_result.tsv --threads 1
[2023-03-15 16:53:26,927] [INFO] Task succeeded: fastANI
[2023-03-15 16:53:26,927] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3d395e3-de16-4537-aa3d-b87007a8e9f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:53:26,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3d395e3-de16-4537-aa3d-b87007a8e9f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:53:26,927] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:53:26,928] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 16:53:26,928] [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
--------------------------------------------------------------------------------
[2023-03-15 16:53:26,932] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22211/tc_result.tsv
[2023-03-15 16:53:26,932] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:53:26,932] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:53:26,932] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3d395e3-de16-4537-aa3d-b87007a8e9f8/dqc_reference/checkm_data
[2023-03-15 16:53:26,983] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:53:26,988] [INFO] Task started: CheckM
[2023-03-15 16:53:26,988] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22211/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22211/checkm_input OceanDNA-b22211/checkm_result
[2023-03-15 16:53:47,800] [INFO] Task succeeded: CheckM
[2023-03-15 16:53:47,800] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.23%
Contamintation: 1.28%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-15 16:53:48,041] [INFO] ===== Completeness check finished =====
[2023-03-15 16:53:48,041] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:53:48,041] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22211/markers.fasta)
[2023-03-15 16:53:48,043] [INFO] Task started: Blastn
[2023-03-15 16:53:48,043] [INFO] Running command: blastn -query OceanDNA-b22211/markers.fasta -db /var/lib/cwl/stgc3d395e3-de16-4537-aa3d-b87007a8e9f8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22211/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:53:49,135] [INFO] Task succeeded: Blastn
[2023-03-15 16:53:49,142] [INFO] Selected 14 target genomes.
[2023-03-15 16:53:49,142] [INFO] Target genome list was writen to OceanDNA-b22211/target_genomes_gtdb.txt
[2023-03-15 16:53:49,252] [INFO] Task started: fastANI
[2023-03-15 16:53:49,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ccfdfce-0928-4374-b9fa-238e00878c76/OceanDNA-b22211.fa --refList OceanDNA-b22211/target_genomes_gtdb.txt --output OceanDNA-b22211/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:53:55,033] [INFO] Task succeeded: fastANI
[2023-03-15 16:53:55,035] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:53:55,035] [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_003520025.1	s__UBA12567 sp003520025	80.3665	120	217	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12567	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018663565.1	s__UBA12567 sp018663565	78.1123	55	217	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12567	95.0	98.65	98.57	0.79	0.77	4	-
--------------------------------------------------------------------------------
[2023-03-15 16:53:55,038] [INFO] GTDB search result was written to OceanDNA-b22211/result_gtdb.tsv
[2023-03-15 16:53:55,044] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:53:55,053] [INFO] DFAST_QC result json was written to OceanDNA-b22211/dqc_result.json
[2023-03-15 16:53:55,053] [INFO] DFAST_QC completed!
[2023-03-15 16:53:55,053] [INFO] Total running time: 0h0m49s