[2023-03-15 23:07:02,635] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:07:02,635] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:07:02,635] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f88cd50-5640-455b-a7f5-5e37b5928b46/dqc_reference
[2023-03-15 23:07:03,966] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:07:03,966] [INFO] Task started: Prodigal
[2023-03-15 23:07:03,966] [INFO] Running command: cat /var/lib/cwl/stg232e1fc5-7bd9-4259-8663-5efc24275212/OceanDNA-b33619.fa | prodigal -d OceanDNA-b33619/cds.fna -a OceanDNA-b33619/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:07:10,296] [INFO] Task succeeded: Prodigal
[2023-03-15 23:07:10,297] [INFO] Task started: HMMsearch
[2023-03-15 23:07:10,297] [INFO] Running command: hmmsearch --tblout OceanDNA-b33619/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f88cd50-5640-455b-a7f5-5e37b5928b46/dqc_reference/reference_markers.hmm OceanDNA-b33619/protein.faa > /dev/null
[2023-03-15 23:07:10,467] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:07:10,467] [INFO] Found 6/6 markers.
[2023-03-15 23:07:10,476] [INFO] Query marker FASTA was written to OceanDNA-b33619/markers.fasta
[2023-03-15 23:07:10,476] [INFO] Task started: Blastn
[2023-03-15 23:07:10,476] [INFO] Running command: blastn -query OceanDNA-b33619/markers.fasta -db /var/lib/cwl/stg6f88cd50-5640-455b-a7f5-5e37b5928b46/dqc_reference/reference_markers.fasta -out OceanDNA-b33619/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:07:10,993] [INFO] Task succeeded: Blastn
[2023-03-15 23:07:10,994] [INFO] Selected 27 target genomes.
[2023-03-15 23:07:10,994] [INFO] Target genome list was writen to OceanDNA-b33619/target_genomes.txt
[2023-03-15 23:07:11,057] [INFO] Task started: fastANI
[2023-03-15 23:07:11,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg232e1fc5-7bd9-4259-8663-5efc24275212/OceanDNA-b33619.fa --refList OceanDNA-b33619/target_genomes.txt --output OceanDNA-b33619/fastani_result.tsv --threads 1
[2023-03-15 23:07:23,008] [INFO] Task succeeded: fastANI
[2023-03-15 23:07:23,008] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f88cd50-5640-455b-a7f5-5e37b5928b46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:07:23,008] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f88cd50-5640-455b-a7f5-5e37b5928b46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:07:23,008] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:07:23,008] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:07:23,008] [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 23:07:23,009] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33619/tc_result.tsv
[2023-03-15 23:07:23,009] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:07:23,009] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:07:23,009] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f88cd50-5640-455b-a7f5-5e37b5928b46/dqc_reference/checkm_data
[2023-03-15 23:07:23,012] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:07:23,014] [INFO] Task started: CheckM
[2023-03-15 23:07:23,014] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33619/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33619/checkm_input OceanDNA-b33619/checkm_result
[2023-03-15 23:07:43,784] [INFO] Task succeeded: CheckM
[2023-03-15 23:07:43,785] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:07:43,845] [INFO] ===== Completeness check finished =====
[2023-03-15 23:07:43,846] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:07:43,846] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33619/markers.fasta)
[2023-03-15 23:07:43,847] [INFO] Task started: Blastn
[2023-03-15 23:07:43,847] [INFO] Running command: blastn -query OceanDNA-b33619/markers.fasta -db /var/lib/cwl/stg6f88cd50-5640-455b-a7f5-5e37b5928b46/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33619/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:07:44,609] [INFO] Task succeeded: Blastn
[2023-03-15 23:07:44,618] [INFO] Selected 12 target genomes.
[2023-03-15 23:07:44,619] [INFO] Target genome list was writen to OceanDNA-b33619/target_genomes_gtdb.txt
[2023-03-15 23:07:44,632] [INFO] Task started: fastANI
[2023-03-15 23:07:44,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg232e1fc5-7bd9-4259-8663-5efc24275212/OceanDNA-b33619.fa --refList OceanDNA-b33619/target_genomes_gtdb.txt --output OceanDNA-b33619/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:07:47,731] [INFO] Task succeeded: fastANI
[2023-03-15 23:07:47,735] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:07:47,735] [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_000156155.1	s__BACL14 sp000156155	91.9784	348	380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001044335.1	s__BACL14 sp001044335	91.9608	341	380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	100.00	100.00	1.00	1.00	3	-
GCA_010023085.1	s__BACL14 sp010023085	87.637	264	380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	99.14	98.98	0.85	0.84	6	-
GCA_017852315.1	s__BACL14 sp017852315	77.952	105	380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	99.43	98.84	0.96	0.95	5	-
--------------------------------------------------------------------------------
[2023-03-15 23:07:47,737] [INFO] GTDB search result was written to OceanDNA-b33619/result_gtdb.tsv
[2023-03-15 23:07:47,741] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:07:47,747] [INFO] DFAST_QC result json was written to OceanDNA-b33619/dqc_result.json
[2023-03-15 23:07:47,747] [INFO] DFAST_QC completed!
[2023-03-15 23:07:47,747] [INFO] Total running time: 0h0m45s