[2023-03-19 04:29:37,751] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:37,751] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:37,751] [INFO] DQC Reference Directory: /var/lib/cwl/stg66b0b11d-5a6f-4bc7-bb39-b23087cc7b76/dqc_reference
[2023-03-19 04:29:38,862] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:38,863] [INFO] Task started: Prodigal
[2023-03-19 04:29:38,864] [INFO] Running command: cat /var/lib/cwl/stg03f32279-5f52-49eb-abba-5b3d96d100ee/OceanDNA-b26153.fa | prodigal -d OceanDNA-b26153/cds.fna -a OceanDNA-b26153/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:29:41,767] [INFO] Task succeeded: Prodigal
[2023-03-19 04:29:41,768] [INFO] Task started: HMMsearch
[2023-03-19 04:29:41,768] [INFO] Running command: hmmsearch --tblout OceanDNA-b26153/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66b0b11d-5a6f-4bc7-bb39-b23087cc7b76/dqc_reference/reference_markers.hmm OceanDNA-b26153/protein.faa > /dev/null
[2023-03-19 04:29:41,932] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:29:41,933] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg03f32279-5f52-49eb-abba-5b3d96d100ee/OceanDNA-b26153.fa]
[2023-03-19 04:29:41,938] [INFO] Query marker FASTA was written to OceanDNA-b26153/markers.fasta
[2023-03-19 04:29:41,940] [INFO] Task started: Blastn
[2023-03-19 04:29:41,940] [INFO] Running command: blastn -query OceanDNA-b26153/markers.fasta -db /var/lib/cwl/stg66b0b11d-5a6f-4bc7-bb39-b23087cc7b76/dqc_reference/reference_markers.fasta -out OceanDNA-b26153/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:29:42,565] [INFO] Task succeeded: Blastn
[2023-03-19 04:29:42,565] [INFO] Selected 14 target genomes.
[2023-03-19 04:29:42,566] [INFO] Target genome list was writen to OceanDNA-b26153/target_genomes.txt
[2023-03-19 04:29:42,573] [INFO] Task started: fastANI
[2023-03-19 04:29:42,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg03f32279-5f52-49eb-abba-5b3d96d100ee/OceanDNA-b26153.fa --refList OceanDNA-b26153/target_genomes.txt --output OceanDNA-b26153/fastani_result.tsv --threads 1
[2023-03-19 04:29:48,006] [INFO] Task succeeded: fastANI
[2023-03-19 04:29:48,007] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66b0b11d-5a6f-4bc7-bb39-b23087cc7b76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:29:48,007] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66b0b11d-5a6f-4bc7-bb39-b23087cc7b76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:29:48,007] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:29:48,007] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:29:48,007] [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 04:29:48,007] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26153/tc_result.tsv
[2023-03-19 04:29:48,007] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:29:48,007] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:29:48,008] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66b0b11d-5a6f-4bc7-bb39-b23087cc7b76/dqc_reference/checkm_data
[2023-03-19 04:29:48,010] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:29:48,012] [INFO] Task started: CheckM
[2023-03-19 04:29:48,012] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26153/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26153/checkm_input OceanDNA-b26153/checkm_result
[2023-03-19 04:30:02,249] [INFO] Task succeeded: CheckM
[2023-03-19 04:30:02,249] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.65%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:30:02,250] [INFO] ===== Completeness check finished =====
[2023-03-19 04:30:02,250] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:30:02,250] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26153/markers.fasta)
[2023-03-19 04:30:02,251] [INFO] Task started: Blastn
[2023-03-19 04:30:02,251] [INFO] Running command: blastn -query OceanDNA-b26153/markers.fasta -db /var/lib/cwl/stg66b0b11d-5a6f-4bc7-bb39-b23087cc7b76/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26153/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:03,087] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:03,088] [INFO] Selected 12 target genomes.
[2023-03-19 04:30:03,088] [INFO] Target genome list was writen to OceanDNA-b26153/target_genomes_gtdb.txt
[2023-03-19 04:30:03,131] [INFO] Task started: fastANI
[2023-03-19 04:30:03,131] [INFO] Running command: fastANI --query /var/lib/cwl/stg03f32279-5f52-49eb-abba-5b3d96d100ee/OceanDNA-b26153.fa --refList OceanDNA-b26153/target_genomes_gtdb.txt --output OceanDNA-b26153/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:30:06,685] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:06,690] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:30:06,690] [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_902518965.1	s__HIMB100 sp902518965	97.2788	116	151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002700485.1	s__HIMB100 sp002700485	92.6833	124	151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	98.09	96.19	0.88	0.78	3	-
GCA_902523435.1	s__HIMB100 sp902523435	91.359	90	151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002348585.1	s__HIMB100 sp002348585	91.1923	131	151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721775.1	s__HIMB100 sp002721775	83.9663	93	151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000238815.2	s__HIMB100 sp000238815	77.4316	54	151	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:30:06,690] [INFO] GTDB search result was written to OceanDNA-b26153/result_gtdb.tsv
[2023-03-19 04:30:06,690] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:30:06,691] [INFO] DFAST_QC result json was written to OceanDNA-b26153/dqc_result.json
[2023-03-19 04:30:06,691] [INFO] DFAST_QC completed!
[2023-03-19 04:30:06,691] [INFO] Total running time: 0h0m29s