[2023-03-15 06:50:51,570] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:50:51,576] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:50:51,576] [INFO] DQC Reference Directory: /var/lib/cwl/stgbfdc37d7-db2f-4ac2-9d5e-1a0aab021151/dqc_reference
[2023-03-15 06:50:53,467] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:50:53,468] [INFO] Task started: Prodigal
[2023-03-15 06:50:53,469] [INFO] Running command: cat /var/lib/cwl/stg1d4bb765-d073-486e-b680-03709e06f6ec/OceanDNA-b44048.fa | prodigal -d OceanDNA-b44048/cds.fna -a OceanDNA-b44048/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:50:57,904] [INFO] Task succeeded: Prodigal
[2023-03-15 06:50:57,904] [INFO] Task started: HMMsearch
[2023-03-15 06:50:57,904] [INFO] Running command: hmmsearch --tblout OceanDNA-b44048/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbfdc37d7-db2f-4ac2-9d5e-1a0aab021151/dqc_reference/reference_markers.hmm OceanDNA-b44048/protein.faa > /dev/null
[2023-03-15 06:50:58,105] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:50:58,106] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1d4bb765-d073-486e-b680-03709e06f6ec/OceanDNA-b44048.fa]
[2023-03-15 06:50:58,138] [INFO] Query marker FASTA was written to OceanDNA-b44048/markers.fasta
[2023-03-15 06:50:58,138] [INFO] Task started: Blastn
[2023-03-15 06:50:58,138] [INFO] Running command: blastn -query OceanDNA-b44048/markers.fasta -db /var/lib/cwl/stgbfdc37d7-db2f-4ac2-9d5e-1a0aab021151/dqc_reference/reference_markers.fasta -out OceanDNA-b44048/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:50:59,630] [INFO] Task succeeded: Blastn
[2023-03-15 06:50:59,639] [INFO] Selected 30 target genomes.
[2023-03-15 06:50:59,639] [INFO] Target genome list was writen to OceanDNA-b44048/target_genomes.txt
[2023-03-15 06:50:59,776] [INFO] Task started: fastANI
[2023-03-15 06:50:59,776] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d4bb765-d073-486e-b680-03709e06f6ec/OceanDNA-b44048.fa --refList OceanDNA-b44048/target_genomes.txt --output OceanDNA-b44048/fastani_result.tsv --threads 1
[2023-03-15 06:51:16,405] [INFO] Task succeeded: fastANI
[2023-03-15 06:51:16,405] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbfdc37d7-db2f-4ac2-9d5e-1a0aab021151/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:51:16,406] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbfdc37d7-db2f-4ac2-9d5e-1a0aab021151/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:51:16,406] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:51:16,406] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 06:51:16,406] [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 06:51:16,409] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44048/tc_result.tsv
[2023-03-15 06:51:16,416] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:51:16,416] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:51:16,416] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbfdc37d7-db2f-4ac2-9d5e-1a0aab021151/dqc_reference/checkm_data
[2023-03-15 06:51:16,419] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:51:16,471] [INFO] Task started: CheckM
[2023-03-15 06:51:16,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44048/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44048/checkm_input OceanDNA-b44048/checkm_result
[2023-03-15 06:51:34,510] [INFO] Task succeeded: CheckM
[2023-03-15 06:51:34,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.53%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 06:51:34,927] [INFO] ===== Completeness check finished =====
[2023-03-15 06:51:34,928] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:51:34,928] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44048/markers.fasta)
[2023-03-15 06:51:34,929] [INFO] Task started: Blastn
[2023-03-15 06:51:34,929] [INFO] Running command: blastn -query OceanDNA-b44048/markers.fasta -db /var/lib/cwl/stgbfdc37d7-db2f-4ac2-9d5e-1a0aab021151/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44048/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:51:35,796] [INFO] Task succeeded: Blastn
[2023-03-15 06:51:35,810] [INFO] Selected 22 target genomes.
[2023-03-15 06:51:35,810] [INFO] Target genome list was writen to OceanDNA-b44048/target_genomes_gtdb.txt
[2023-03-15 06:51:36,125] [INFO] Task started: fastANI
[2023-03-15 06:51:36,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d4bb765-d073-486e-b680-03709e06f6ec/OceanDNA-b44048.fa --refList OceanDNA-b44048/target_genomes_gtdb.txt --output OceanDNA-b44048/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:51:46,214] [INFO] Task succeeded: fastANI
[2023-03-15 06:51:46,217] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 06:51:46,217] [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_013112535.1	s__UBA7359 sp013112535	78.3638	97	181	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA7359	95.0	100.00	100.00	1.00	1.00	2	-
GCA_012960105.1	s__UBA7359 sp012960105	77.4901	61	181	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__UBA7359	95.0	99.96	99.96	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-15 06:51:46,228] [INFO] GTDB search result was written to OceanDNA-b44048/result_gtdb.tsv
[2023-03-15 06:51:46,261] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:51:46,279] [INFO] DFAST_QC result json was written to OceanDNA-b44048/dqc_result.json
[2023-03-15 06:51:46,279] [INFO] DFAST_QC completed!
[2023-03-15 06:51:46,279] [INFO] Total running time: 0h0m55s