[2023-03-19 02:57:44,683] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:57:44,683] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:57:44,684] [INFO] DQC Reference Directory: /var/lib/cwl/stg35cf8767-5bdc-49fc-a32a-6c82ed1c2048/dqc_reference
[2023-03-19 02:57:45,793] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:57:45,793] [INFO] Task started: Prodigal
[2023-03-19 02:57:45,793] [INFO] Running command: cat /var/lib/cwl/stgac3389f7-2da8-42a5-8a83-7b24b8124f28/OceanDNA-b42866.fa | prodigal -d OceanDNA-b42866/cds.fna -a OceanDNA-b42866/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:57:50,184] [INFO] Task succeeded: Prodigal
[2023-03-19 02:57:50,184] [INFO] Task started: HMMsearch
[2023-03-19 02:57:50,184] [INFO] Running command: hmmsearch --tblout OceanDNA-b42866/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35cf8767-5bdc-49fc-a32a-6c82ed1c2048/dqc_reference/reference_markers.hmm OceanDNA-b42866/protein.faa > /dev/null
[2023-03-19 02:57:50,330] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:57:50,331] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgac3389f7-2da8-42a5-8a83-7b24b8124f28/OceanDNA-b42866.fa]
[2023-03-19 02:57:50,342] [INFO] Query marker FASTA was written to OceanDNA-b42866/markers.fasta
[2023-03-19 02:57:50,343] [INFO] Task started: Blastn
[2023-03-19 02:57:50,343] [INFO] Running command: blastn -query OceanDNA-b42866/markers.fasta -db /var/lib/cwl/stg35cf8767-5bdc-49fc-a32a-6c82ed1c2048/dqc_reference/reference_markers.fasta -out OceanDNA-b42866/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:57:50,891] [INFO] Task succeeded: Blastn
[2023-03-19 02:57:50,892] [INFO] Selected 21 target genomes.
[2023-03-19 02:57:50,893] [INFO] Target genome list was writen to OceanDNA-b42866/target_genomes.txt
[2023-03-19 02:57:50,911] [INFO] Task started: fastANI
[2023-03-19 02:57:50,911] [INFO] Running command: fastANI --query /var/lib/cwl/stgac3389f7-2da8-42a5-8a83-7b24b8124f28/OceanDNA-b42866.fa --refList OceanDNA-b42866/target_genomes.txt --output OceanDNA-b42866/fastani_result.tsv --threads 1
[2023-03-19 02:58:01,911] [INFO] Task succeeded: fastANI
[2023-03-19 02:58:01,911] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35cf8767-5bdc-49fc-a32a-6c82ed1c2048/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:58:01,911] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35cf8767-5bdc-49fc-a32a-6c82ed1c2048/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:58:01,912] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:58:01,912] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:58:01,912] [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
--------------------------------------------------------------------------------
[2023-03-19 02:58:01,913] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42866/tc_result.tsv
[2023-03-19 02:58:01,913] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:58:01,913] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:58:01,913] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35cf8767-5bdc-49fc-a32a-6c82ed1c2048/dqc_reference/checkm_data
[2023-03-19 02:58:01,916] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:58:01,920] [INFO] Task started: CheckM
[2023-03-19 02:58:01,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42866/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42866/checkm_input OceanDNA-b42866/checkm_result
[2023-03-19 02:58:19,746] [INFO] Task succeeded: CheckM
[2023-03-19 02:58:19,747] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 02:58:19,750] [INFO] ===== Completeness check finished =====
[2023-03-19 02:58:19,750] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:58:19,751] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42866/markers.fasta)
[2023-03-19 02:58:19,752] [INFO] Task started: Blastn
[2023-03-19 02:58:19,752] [INFO] Running command: blastn -query OceanDNA-b42866/markers.fasta -db /var/lib/cwl/stg35cf8767-5bdc-49fc-a32a-6c82ed1c2048/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42866/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:58:20,572] [INFO] Task succeeded: Blastn
[2023-03-19 02:58:20,573] [INFO] Selected 23 target genomes.
[2023-03-19 02:58:20,573] [INFO] Target genome list was writen to OceanDNA-b42866/target_genomes_gtdb.txt
[2023-03-19 02:58:20,629] [INFO] Task started: fastANI
[2023-03-19 02:58:20,629] [INFO] Running command: fastANI --query /var/lib/cwl/stgac3389f7-2da8-42a5-8a83-7b24b8124f28/OceanDNA-b42866.fa --refList OceanDNA-b42866/target_genomes_gtdb.txt --output OceanDNA-b42866/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:58:27,432] [INFO] Task succeeded: fastANI
[2023-03-19 02:58:27,434] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:58:27,434] [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_012959965.1	s__DUCF01 sp012959965	81.1711	165	232	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__DUCF01	95.0	99.73	99.73	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-19 02:58:27,435] [INFO] GTDB search result was written to OceanDNA-b42866/result_gtdb.tsv
[2023-03-19 02:58:27,436] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:58:27,437] [INFO] DFAST_QC result json was written to OceanDNA-b42866/dqc_result.json
[2023-03-19 02:58:27,437] [INFO] DFAST_QC completed!
[2023-03-19 02:58:27,437] [INFO] Total running time: 0h0m43s