[2023-03-15 11:51:17,350] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:51:17,350] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:51:17,350] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e807e76-c949-490e-a1d7-fdb39e7334a6/dqc_reference
[2023-03-15 11:51:18,950] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:51:18,951] [INFO] Task started: Prodigal
[2023-03-15 11:51:18,951] [INFO] Running command: cat /var/lib/cwl/stgb1c59f70-f073-4eb7-87ac-189f48f6e333/OceanDNA-b22179.fa | prodigal -d OceanDNA-b22179/cds.fna -a OceanDNA-b22179/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:51:29,403] [INFO] Task succeeded: Prodigal
[2023-03-15 11:51:29,403] [INFO] Task started: HMMsearch
[2023-03-15 11:51:29,403] [INFO] Running command: hmmsearch --tblout OceanDNA-b22179/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e807e76-c949-490e-a1d7-fdb39e7334a6/dqc_reference/reference_markers.hmm OceanDNA-b22179/protein.faa > /dev/null
[2023-03-15 11:51:29,585] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:51:29,586] [INFO] Found 6/6 markers.
[2023-03-15 11:51:29,597] [INFO] Query marker FASTA was written to OceanDNA-b22179/markers.fasta
[2023-03-15 11:51:29,598] [INFO] Task started: Blastn
[2023-03-15 11:51:29,598] [INFO] Running command: blastn -query OceanDNA-b22179/markers.fasta -db /var/lib/cwl/stg7e807e76-c949-490e-a1d7-fdb39e7334a6/dqc_reference/reference_markers.fasta -out OceanDNA-b22179/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:51:30,106] [INFO] Task succeeded: Blastn
[2023-03-15 11:51:30,106] [INFO] Selected 13 target genomes.
[2023-03-15 11:51:30,107] [INFO] Target genome list was writen to OceanDNA-b22179/target_genomes.txt
[2023-03-15 11:51:30,116] [INFO] Task started: fastANI
[2023-03-15 11:51:30,116] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1c59f70-f073-4eb7-87ac-189f48f6e333/OceanDNA-b22179.fa --refList OceanDNA-b22179/target_genomes.txt --output OceanDNA-b22179/fastani_result.tsv --threads 1
[2023-03-15 11:51:36,284] [INFO] Task succeeded: fastANI
[2023-03-15 11:51:36,285] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e807e76-c949-490e-a1d7-fdb39e7334a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:51:36,285] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e807e76-c949-490e-a1d7-fdb39e7334a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:51:36,285] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:51:36,285] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:51:36,285] [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 11:51:36,286] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22179/tc_result.tsv
[2023-03-15 11:51:36,286] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:51:36,286] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:51:36,286] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e807e76-c949-490e-a1d7-fdb39e7334a6/dqc_reference/checkm_data
[2023-03-15 11:51:36,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:51:36,292] [INFO] Task started: CheckM
[2023-03-15 11:51:36,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22179/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22179/checkm_input OceanDNA-b22179/checkm_result
[2023-03-15 11:52:06,737] [INFO] Task succeeded: CheckM
[2023-03-15 11:52:06,737] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:52:06,739] [INFO] ===== Completeness check finished =====
[2023-03-15 11:52:06,739] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:52:06,739] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22179/markers.fasta)
[2023-03-15 11:52:06,740] [INFO] Task started: Blastn
[2023-03-15 11:52:06,740] [INFO] Running command: blastn -query OceanDNA-b22179/markers.fasta -db /var/lib/cwl/stg7e807e76-c949-490e-a1d7-fdb39e7334a6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22179/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:52:07,465] [INFO] Task succeeded: Blastn
[2023-03-15 11:52:07,466] [INFO] Selected 13 target genomes.
[2023-03-15 11:52:07,466] [INFO] Target genome list was writen to OceanDNA-b22179/target_genomes_gtdb.txt
[2023-03-15 11:52:07,493] [INFO] Task started: fastANI
[2023-03-15 11:52:07,493] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1c59f70-f073-4eb7-87ac-189f48f6e333/OceanDNA-b22179.fa --refList OceanDNA-b22179/target_genomes_gtdb.txt --output OceanDNA-b22179/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:52:12,033] [INFO] Task succeeded: fastANI
[2023-03-15 11:52:12,038] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:52:12,038] [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_002689385.1	s__GCA-002718515 sp002689385	99.6733	484	560	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018701395.1	s__GCA-002718515 sp018701395	78.2361	192	560	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	99.63	99.41	0.94	0.92	4	-
GCA_014381385.1	s__GCA-002718515 sp014381385	77.9517	117	560	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014238785.1	s__GCA-002718515 sp014238785	77.844	166	560	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012965315.1	s__GCA-002718515 sp012965315	77.6558	177	560	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	99.71	99.67	0.87	0.85	4	-
GCA_014381555.1	s__GCA-002718515 sp014381555	77.3296	103	560	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	99.84	99.84	0.86	0.86	2	-
GCA_018657585.1	s__GCA-002718515 sp018657585	77.023	99	560	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002718515	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:52:12,038] [INFO] GTDB search result was written to OceanDNA-b22179/result_gtdb.tsv
[2023-03-15 11:52:12,038] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:52:12,039] [INFO] DFAST_QC result json was written to OceanDNA-b22179/dqc_result.json
[2023-03-15 11:52:12,039] [INFO] DFAST_QC completed!
[2023-03-15 11:52:12,039] [INFO] Total running time: 0h0m55s