[2023-03-14 11:40:05,647] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:40:05,648] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:40:05,648] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b817600-2c47-4649-97d0-63ae625447c0/dqc_reference
[2023-03-14 11:40:06,750] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:40:06,750] [INFO] Task started: Prodigal
[2023-03-14 11:40:06,751] [INFO] Running command: cat /var/lib/cwl/stgf94bd690-7353-4f40-872a-e2540b44e3b7/OceanDNA-b26149.fa | prodigal -d OceanDNA-b26149/cds.fna -a OceanDNA-b26149/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:40:16,657] [INFO] Task succeeded: Prodigal
[2023-03-14 11:40:16,658] [INFO] Task started: HMMsearch
[2023-03-14 11:40:16,658] [INFO] Running command: hmmsearch --tblout OceanDNA-b26149/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b817600-2c47-4649-97d0-63ae625447c0/dqc_reference/reference_markers.hmm OceanDNA-b26149/protein.faa > /dev/null
[2023-03-14 11:40:16,825] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:40:16,826] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf94bd690-7353-4f40-872a-e2540b44e3b7/OceanDNA-b26149.fa]
[2023-03-14 11:40:16,847] [INFO] Query marker FASTA was written to OceanDNA-b26149/markers.fasta
[2023-03-14 11:40:16,848] [INFO] Task started: Blastn
[2023-03-14 11:40:16,848] [INFO] Running command: blastn -query OceanDNA-b26149/markers.fasta -db /var/lib/cwl/stg2b817600-2c47-4649-97d0-63ae625447c0/dqc_reference/reference_markers.fasta -out OceanDNA-b26149/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:40:17,465] [INFO] Task succeeded: Blastn
[2023-03-14 11:40:17,468] [INFO] Selected 29 target genomes.
[2023-03-14 11:40:17,469] [INFO] Target genome list was writen to OceanDNA-b26149/target_genomes.txt
[2023-03-14 11:40:17,486] [INFO] Task started: fastANI
[2023-03-14 11:40:17,486] [INFO] Running command: fastANI --query /var/lib/cwl/stgf94bd690-7353-4f40-872a-e2540b44e3b7/OceanDNA-b26149.fa --refList OceanDNA-b26149/target_genomes.txt --output OceanDNA-b26149/fastani_result.tsv --threads 1
[2023-03-14 11:40:35,968] [INFO] Task succeeded: fastANI
[2023-03-14 11:40:35,968] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b817600-2c47-4649-97d0-63ae625447c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:40:35,968] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b817600-2c47-4649-97d0-63ae625447c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:40:35,969] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:40:35,969] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:40:35,969] [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 11:40:35,970] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26149/tc_result.tsv
[2023-03-14 11:40:35,974] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:40:35,974] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:40:35,974] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b817600-2c47-4649-97d0-63ae625447c0/dqc_reference/checkm_data
[2023-03-14 11:40:35,978] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:40:35,984] [INFO] Task started: CheckM
[2023-03-14 11:40:35,984] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26149/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26149/checkm_input OceanDNA-b26149/checkm_result
[2023-03-14 11:41:04,822] [INFO] Task succeeded: CheckM
[2023-03-14 11:41:04,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:41:04,841] [INFO] ===== Completeness check finished =====
[2023-03-14 11:41:04,841] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:41:04,841] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26149/markers.fasta)
[2023-03-14 11:41:04,842] [INFO] Task started: Blastn
[2023-03-14 11:41:04,842] [INFO] Running command: blastn -query OceanDNA-b26149/markers.fasta -db /var/lib/cwl/stg2b817600-2c47-4649-97d0-63ae625447c0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26149/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:41:05,935] [INFO] Task succeeded: Blastn
[2023-03-14 11:41:05,939] [INFO] Selected 28 target genomes.
[2023-03-14 11:41:05,939] [INFO] Target genome list was writen to OceanDNA-b26149/target_genomes_gtdb.txt
[2023-03-14 11:41:05,959] [INFO] Task started: fastANI
[2023-03-14 11:41:05,959] [INFO] Running command: fastANI --query /var/lib/cwl/stgf94bd690-7353-4f40-872a-e2540b44e3b7/OceanDNA-b26149.fa --refList OceanDNA-b26149/target_genomes_gtdb.txt --output OceanDNA-b26149/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:41:19,415] [INFO] Task succeeded: fastANI
[2023-03-14 11:41:19,420] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:41:19,420] [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_016780695.1	s__JADHLK01 sp016780695	88.695	274	527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__JADHLK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009920665.1	s__UBA8309 sp009920665	76.6579	79	527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011522725.1	s__UBA8309 sp001627655	76.6181	52	527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.91	98.58	0.92	0.89	8	-
GCA_002686685.1	s__UBA8309 sp002686685	76.4704	66	527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	97.96	97.78	0.70	0.66	5	-
GCA_018624035.1	s__UBA8309 sp018624035	76.4143	62	527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000238815.2	s__HIMB100 sp000238815	76.2178	78	527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:41:19,423] [INFO] GTDB search result was written to OceanDNA-b26149/result_gtdb.tsv
[2023-03-14 11:41:19,426] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:41:19,429] [INFO] DFAST_QC result json was written to OceanDNA-b26149/dqc_result.json
[2023-03-14 11:41:19,429] [INFO] DFAST_QC completed!
[2023-03-14 11:41:19,429] [INFO] Total running time: 0h1m14s