[2023-03-16 00:09:30,341] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:09:30,343] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:09:30,343] [INFO] DQC Reference Directory: /var/lib/cwl/stg68ddaa9a-8b9f-427a-8879-f10fc1f77eca/dqc_reference
[2023-03-16 00:09:32,555] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:09:32,556] [INFO] Task started: Prodigal
[2023-03-16 00:09:32,556] [INFO] Running command: cat /var/lib/cwl/stgb4e34741-4cc8-43db-98c5-045ad016ad38/OceanDNA-b20902.fa | prodigal -d OceanDNA-b20902/cds.fna -a OceanDNA-b20902/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:10:15,634] [INFO] Task succeeded: Prodigal
[2023-03-16 00:10:15,635] [INFO] Task started: HMMsearch
[2023-03-16 00:10:15,635] [INFO] Running command: hmmsearch --tblout OceanDNA-b20902/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68ddaa9a-8b9f-427a-8879-f10fc1f77eca/dqc_reference/reference_markers.hmm OceanDNA-b20902/protein.faa > /dev/null
[2023-03-16 00:10:15,902] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:10:15,903] [INFO] Found 6/6 markers.
[2023-03-16 00:10:15,941] [INFO] Query marker FASTA was written to OceanDNA-b20902/markers.fasta
[2023-03-16 00:10:15,942] [INFO] Task started: Blastn
[2023-03-16 00:10:15,942] [INFO] Running command: blastn -query OceanDNA-b20902/markers.fasta -db /var/lib/cwl/stg68ddaa9a-8b9f-427a-8879-f10fc1f77eca/dqc_reference/reference_markers.fasta -out OceanDNA-b20902/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:10:16,476] [INFO] Task succeeded: Blastn
[2023-03-16 00:10:16,477] [INFO] Selected 20 target genomes.
[2023-03-16 00:10:16,477] [INFO] Target genome list was writen to OceanDNA-b20902/target_genomes.txt
[2023-03-16 00:10:16,489] [INFO] Task started: fastANI
[2023-03-16 00:10:16,490] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4e34741-4cc8-43db-98c5-045ad016ad38/OceanDNA-b20902.fa --refList OceanDNA-b20902/target_genomes.txt --output OceanDNA-b20902/fastani_result.tsv --threads 1
[2023-03-16 00:10:32,279] [INFO] Task succeeded: fastANI
[2023-03-16 00:10:32,279] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68ddaa9a-8b9f-427a-8879-f10fc1f77eca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:10:32,280] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68ddaa9a-8b9f-427a-8879-f10fc1f77eca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:10:32,283] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:10:32,283] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 00:10:32,283] [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
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	75.1674	92	2208	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 00:10:32,283] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20902/tc_result.tsv
[2023-03-16 00:10:32,284] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:10:32,284] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:10:32,284] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68ddaa9a-8b9f-427a-8879-f10fc1f77eca/dqc_reference/checkm_data
[2023-03-16 00:10:32,284] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:10:32,459] [INFO] Task started: CheckM
[2023-03-16 00:10:32,459] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20902/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20902/checkm_input OceanDNA-b20902/checkm_result
[2023-03-16 00:12:14,029] [INFO] Task succeeded: CheckM
[2023-03-16 00:12:14,030] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:12:14,034] [INFO] ===== Completeness check finished =====
[2023-03-16 00:12:14,035] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:12:14,035] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20902/markers.fasta)
[2023-03-16 00:12:14,036] [INFO] Task started: Blastn
[2023-03-16 00:12:14,036] [INFO] Running command: blastn -query OceanDNA-b20902/markers.fasta -db /var/lib/cwl/stg68ddaa9a-8b9f-427a-8879-f10fc1f77eca/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20902/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:12:14,982] [INFO] Task succeeded: Blastn
[2023-03-16 00:12:14,984] [INFO] Selected 27 target genomes.
[2023-03-16 00:12:14,984] [INFO] Target genome list was writen to OceanDNA-b20902/target_genomes_gtdb.txt
[2023-03-16 00:12:15,005] [INFO] Task started: fastANI
[2023-03-16 00:12:15,005] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4e34741-4cc8-43db-98c5-045ad016ad38/OceanDNA-b20902.fa --refList OceanDNA-b20902/target_genomes_gtdb.txt --output OceanDNA-b20902/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:12:39,768] [INFO] Task succeeded: fastANI
[2023-03-16 00:12:39,774] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:12:39,774] [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_016763395.1	s__NORP324 sp016763395	76.1237	126	2208	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__NORP324	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024805.1	s__Haliangium ochraceum	75.1674	92	2208	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__Haliangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707895.1	s__UBA2376 sp016707895	75.0713	65	2208	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	99.64	99.63	0.96	0.96	3	-
GCA_011526095.1	s__WYBA01 sp011526095	75.0083	59	2208	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__WYBA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717005.1	s__UBA2376 sp016717005	74.9437	71	2208	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018057825.1	s__UBA2376 sp018057825	74.8998	56	2208	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	99.99	99.98	0.98	0.98	3	-
GCA_013812655.1	s__JABFXX01 sp013812655	74.8251	55	2208	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__JABFXX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002344285.1	s__UBA2376 sp002344285	74.8238	57	2208	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794525.1	s__UBA2376 sp016794525	74.7548	87	2208	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 00:12:39,775] [INFO] GTDB search result was written to OceanDNA-b20902/result_gtdb.tsv
[2023-03-16 00:12:39,775] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:12:39,775] [INFO] DFAST_QC result json was written to OceanDNA-b20902/dqc_result.json
[2023-03-16 00:12:39,776] [INFO] DFAST_QC completed!
[2023-03-16 00:12:39,776] [INFO] Total running time: 0h3m9s