[2023-03-14 14:44:33,094] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:44:33,095] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:44:33,095] [INFO] DQC Reference Directory: /var/lib/cwl/stgc446fe57-c4f1-456e-90ce-8fdf9b0208dd/dqc_reference
[2023-03-14 14:44:34,593] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:44:34,593] [INFO] Task started: Prodigal
[2023-03-14 14:44:34,593] [INFO] Running command: cat /var/lib/cwl/stg7f3f43b0-d644-4af1-a225-fe3d1a74c375/OceanDNA-b33100.fa | prodigal -d OceanDNA-b33100/cds.fna -a OceanDNA-b33100/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:44:57,574] [INFO] Task succeeded: Prodigal
[2023-03-14 14:44:57,575] [INFO] Task started: HMMsearch
[2023-03-14 14:44:57,575] [INFO] Running command: hmmsearch --tblout OceanDNA-b33100/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc446fe57-c4f1-456e-90ce-8fdf9b0208dd/dqc_reference/reference_markers.hmm OceanDNA-b33100/protein.faa > /dev/null
[2023-03-14 14:44:57,895] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:44:57,895] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7f3f43b0-d644-4af1-a225-fe3d1a74c375/OceanDNA-b33100.fa]
[2023-03-14 14:44:57,923] [INFO] Query marker FASTA was written to OceanDNA-b33100/markers.fasta
[2023-03-14 14:44:57,924] [INFO] Task started: Blastn
[2023-03-14 14:44:57,924] [INFO] Running command: blastn -query OceanDNA-b33100/markers.fasta -db /var/lib/cwl/stgc446fe57-c4f1-456e-90ce-8fdf9b0208dd/dqc_reference/reference_markers.fasta -out OceanDNA-b33100/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:44:58,515] [INFO] Task succeeded: Blastn
[2023-03-14 14:44:58,517] [INFO] Selected 32 target genomes.
[2023-03-14 14:44:58,517] [INFO] Target genome list was writen to OceanDNA-b33100/target_genomes.txt
[2023-03-14 14:44:58,566] [INFO] Task started: fastANI
[2023-03-14 14:44:58,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f3f43b0-d644-4af1-a225-fe3d1a74c375/OceanDNA-b33100.fa --refList OceanDNA-b33100/target_genomes.txt --output OceanDNA-b33100/fastani_result.tsv --threads 1
[2023-03-14 14:45:26,905] [INFO] Task succeeded: fastANI
[2023-03-14 14:45:26,905] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc446fe57-c4f1-456e-90ce-8fdf9b0208dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:45:26,905] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc446fe57-c4f1-456e-90ce-8fdf9b0208dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:45:26,906] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:45:26,906] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 14:45:26,906] [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 14:45:26,906] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33100/tc_result.tsv
[2023-03-14 14:45:26,907] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:45:26,907] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:45:26,908] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc446fe57-c4f1-456e-90ce-8fdf9b0208dd/dqc_reference/checkm_data
[2023-03-14 14:45:26,910] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:45:26,917] [INFO] Task started: CheckM
[2023-03-14 14:45:26,917] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33100/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33100/checkm_input OceanDNA-b33100/checkm_result
[2023-03-14 14:46:13,589] [INFO] Task succeeded: CheckM
[2023-03-14 14:46:13,590] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.94%
Contamintation: 0.84%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 14:46:13,593] [INFO] ===== Completeness check finished =====
[2023-03-14 14:46:13,593] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:46:13,594] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33100/markers.fasta)
[2023-03-14 14:46:13,595] [INFO] Task started: Blastn
[2023-03-14 14:46:13,595] [INFO] Running command: blastn -query OceanDNA-b33100/markers.fasta -db /var/lib/cwl/stgc446fe57-c4f1-456e-90ce-8fdf9b0208dd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33100/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:46:14,366] [INFO] Task succeeded: Blastn
[2023-03-14 14:46:14,368] [INFO] Selected 28 target genomes.
[2023-03-14 14:46:14,368] [INFO] Target genome list was writen to OceanDNA-b33100/target_genomes_gtdb.txt
[2023-03-14 14:46:14,540] [INFO] Task started: fastANI
[2023-03-14 14:46:14,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f3f43b0-d644-4af1-a225-fe3d1a74c375/OceanDNA-b33100.fa --refList OceanDNA-b33100/target_genomes_gtdb.txt --output OceanDNA-b33100/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:46:32,004] [INFO] Task succeeded: fastANI
[2023-03-14 14:46:32,006] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:46:32,007] [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_002434595.1	s__UBA6544 sp002434595	89.8138	478	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__UBA6544	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018665505.1	s__UBA6544 sp018665505	76.3559	144	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__UBA6544	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:46:32,007] [INFO] GTDB search result was written to OceanDNA-b33100/result_gtdb.tsv
[2023-03-14 14:46:32,007] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:46:32,008] [INFO] DFAST_QC result json was written to OceanDNA-b33100/dqc_result.json
[2023-03-14 14:46:32,008] [INFO] DFAST_QC completed!
[2023-03-14 14:46:32,008] [INFO] Total running time: 0h1m59s