[2023-03-17 03:24:50,918] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:24:50,919] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:24:50,919] [INFO] DQC Reference Directory: /var/lib/cwl/stga14cb485-f2b3-4d38-800d-e77f7f2e3afa/dqc_reference
[2023-03-17 03:24:52,031] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:24:52,032] [INFO] Task started: Prodigal
[2023-03-17 03:24:52,032] [INFO] Running command: cat /var/lib/cwl/stg8224846a-6875-4d0c-b3d8-9dc63c68fd2a/OceanDNA-b33952.fa | prodigal -d OceanDNA-b33952/cds.fna -a OceanDNA-b33952/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:24:56,885] [INFO] Task succeeded: Prodigal
[2023-03-17 03:24:56,885] [INFO] Task started: HMMsearch
[2023-03-17 03:24:56,885] [INFO] Running command: hmmsearch --tblout OceanDNA-b33952/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga14cb485-f2b3-4d38-800d-e77f7f2e3afa/dqc_reference/reference_markers.hmm OceanDNA-b33952/protein.faa > /dev/null
[2023-03-17 03:24:57,036] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:24:57,036] [INFO] Found 6/6 markers.
[2023-03-17 03:24:57,043] [INFO] Query marker FASTA was written to OceanDNA-b33952/markers.fasta
[2023-03-17 03:24:57,044] [INFO] Task started: Blastn
[2023-03-17 03:24:57,045] [INFO] Running command: blastn -query OceanDNA-b33952/markers.fasta -db /var/lib/cwl/stga14cb485-f2b3-4d38-800d-e77f7f2e3afa/dqc_reference/reference_markers.fasta -out OceanDNA-b33952/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:24:57,550] [INFO] Task succeeded: Blastn
[2023-03-17 03:24:57,552] [INFO] Selected 25 target genomes.
[2023-03-17 03:24:57,553] [INFO] Target genome list was writen to OceanDNA-b33952/target_genomes.txt
[2023-03-17 03:24:57,571] [INFO] Task started: fastANI
[2023-03-17 03:24:57,571] [INFO] Running command: fastANI --query /var/lib/cwl/stg8224846a-6875-4d0c-b3d8-9dc63c68fd2a/OceanDNA-b33952.fa --refList OceanDNA-b33952/target_genomes.txt --output OceanDNA-b33952/fastani_result.tsv --threads 1
[2023-03-17 03:25:06,770] [INFO] Task succeeded: fastANI
[2023-03-17 03:25:06,771] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga14cb485-f2b3-4d38-800d-e77f7f2e3afa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:25:06,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga14cb485-f2b3-4d38-800d-e77f7f2e3afa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:25:06,771] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:25:06,771] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 03:25:06,771] [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
--------------------------------------------------------------------------------
[2023-03-17 03:25:06,771] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33952/tc_result.tsv
[2023-03-17 03:25:06,771] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:25:06,772] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:25:06,772] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga14cb485-f2b3-4d38-800d-e77f7f2e3afa/dqc_reference/checkm_data
[2023-03-17 03:25:06,775] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:25:06,777] [INFO] Task started: CheckM
[2023-03-17 03:25:06,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33952/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33952/checkm_input OceanDNA-b33952/checkm_result
[2023-03-17 03:25:24,537] [INFO] Task succeeded: CheckM
[2023-03-17 03:25:24,537] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:25:24,563] [INFO] ===== Completeness check finished =====
[2023-03-17 03:25:24,563] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:25:24,564] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33952/markers.fasta)
[2023-03-17 03:25:24,564] [INFO] Task started: Blastn
[2023-03-17 03:25:24,565] [INFO] Running command: blastn -query OceanDNA-b33952/markers.fasta -db /var/lib/cwl/stga14cb485-f2b3-4d38-800d-e77f7f2e3afa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33952/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:25:25,281] [INFO] Task succeeded: Blastn
[2023-03-17 03:25:25,284] [INFO] Selected 26 target genomes.
[2023-03-17 03:25:25,284] [INFO] Target genome list was writen to OceanDNA-b33952/target_genomes_gtdb.txt
[2023-03-17 03:25:25,360] [INFO] Task started: fastANI
[2023-03-17 03:25:25,360] [INFO] Running command: fastANI --query /var/lib/cwl/stg8224846a-6875-4d0c-b3d8-9dc63c68fd2a/OceanDNA-b33952.fa --refList OceanDNA-b33952/target_genomes_gtdb.txt --output OceanDNA-b33952/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:25:31,910] [INFO] Task succeeded: fastANI
[2023-03-17 03:25:31,912] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:25:31,912] [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_905618945.1	s__BACL14 sp905618945	82.3082	211	327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:25:31,912] [INFO] GTDB search result was written to OceanDNA-b33952/result_gtdb.tsv
[2023-03-17 03:25:31,912] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:25:31,913] [INFO] DFAST_QC result json was written to OceanDNA-b33952/dqc_result.json
[2023-03-17 03:25:31,913] [INFO] DFAST_QC completed!
[2023-03-17 03:25:31,913] [INFO] Total running time: 0h0m41s