[2023-03-15 11:22:20,467] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:22:20,467] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:22:20,467] [INFO] DQC Reference Directory: /var/lib/cwl/stg0233698f-5214-4668-a19e-d8e80ad3891c/dqc_reference
[2023-03-15 11:22:21,950] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:22:21,951] [INFO] Task started: Prodigal
[2023-03-15 11:22:21,951] [INFO] Running command: cat /var/lib/cwl/stg8d19c7b9-e598-42e4-a247-a44d844fc4fb/OceanDNA-b22189.fa | prodigal -d OceanDNA-b22189/cds.fna -a OceanDNA-b22189/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:22:33,083] [INFO] Task succeeded: Prodigal
[2023-03-15 11:22:33,083] [INFO] Task started: HMMsearch
[2023-03-15 11:22:33,083] [INFO] Running command: hmmsearch --tblout OceanDNA-b22189/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0233698f-5214-4668-a19e-d8e80ad3891c/dqc_reference/reference_markers.hmm OceanDNA-b22189/protein.faa > /dev/null
[2023-03-15 11:22:33,266] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:22:33,267] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8d19c7b9-e598-42e4-a247-a44d844fc4fb/OceanDNA-b22189.fa]
[2023-03-15 11:22:33,285] [INFO] Query marker FASTA was written to OceanDNA-b22189/markers.fasta
[2023-03-15 11:22:33,286] [INFO] Task started: Blastn
[2023-03-15 11:22:33,286] [INFO] Running command: blastn -query OceanDNA-b22189/markers.fasta -db /var/lib/cwl/stg0233698f-5214-4668-a19e-d8e80ad3891c/dqc_reference/reference_markers.fasta -out OceanDNA-b22189/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:22:33,863] [INFO] Task succeeded: Blastn
[2023-03-15 11:22:33,864] [INFO] Selected 27 target genomes.
[2023-03-15 11:22:33,864] [INFO] Target genome list was writen to OceanDNA-b22189/target_genomes.txt
[2023-03-15 11:22:33,879] [INFO] Task started: fastANI
[2023-03-15 11:22:33,880] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d19c7b9-e598-42e4-a247-a44d844fc4fb/OceanDNA-b22189.fa --refList OceanDNA-b22189/target_genomes.txt --output OceanDNA-b22189/fastani_result.tsv --threads 1
[2023-03-15 11:22:51,153] [INFO] Task succeeded: fastANI
[2023-03-15 11:22:51,153] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0233698f-5214-4668-a19e-d8e80ad3891c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:22:51,153] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0233698f-5214-4668-a19e-d8e80ad3891c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:22:51,154] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:22:51,154] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:22:51,154] [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 11:22:51,154] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22189/tc_result.tsv
[2023-03-15 11:22:51,154] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:22:51,154] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:22:51,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0233698f-5214-4668-a19e-d8e80ad3891c/dqc_reference/checkm_data
[2023-03-15 11:22:51,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:22:51,229] [INFO] Task started: CheckM
[2023-03-15 11:22:51,230] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22189/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22189/checkm_input OceanDNA-b22189/checkm_result
[2023-03-15 11:23:23,658] [INFO] Task succeeded: CheckM
[2023-03-15 11:23:23,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.98%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 11:23:23,661] [INFO] ===== Completeness check finished =====
[2023-03-15 11:23:23,661] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:23:23,661] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22189/markers.fasta)
[2023-03-15 11:23:23,663] [INFO] Task started: Blastn
[2023-03-15 11:23:23,663] [INFO] Running command: blastn -query OceanDNA-b22189/markers.fasta -db /var/lib/cwl/stg0233698f-5214-4668-a19e-d8e80ad3891c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22189/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:23:24,505] [INFO] Task succeeded: Blastn
[2023-03-15 11:23:24,506] [INFO] Selected 13 target genomes.
[2023-03-15 11:23:24,506] [INFO] Target genome list was writen to OceanDNA-b22189/target_genomes_gtdb.txt
[2023-03-15 11:23:24,535] [INFO] Task started: fastANI
[2023-03-15 11:23:24,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d19c7b9-e598-42e4-a247-a44d844fc4fb/OceanDNA-b22189.fa --refList OceanDNA-b22189/target_genomes_gtdb.txt --output OceanDNA-b22189/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:23:30,998] [INFO] Task succeeded: fastANI
[2023-03-15 11:23:31,006] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:23:31,006] [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_003712165.1	s__GCA-2732755 sp003712165	79.1144	266	521	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__GCA-2732755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009827205.1	s__GCA-2732755 sp009827205	78.856	204	521	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__GCA-2732755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002732755.1	s__GCA-2732755 sp002732755	77.8888	163	521	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__GCA-2732755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011053195.1	s__GCA-2732755 sp011053195	77.5898	144	521	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__GCA-2732755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013285505.1	s__PNC22 sp013285505	77.2529	94	521	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364005.1	s__UBA1924 sp002364005	76.9161	70	521	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	99.92	99.89	0.95	0.91	4	-
GCA_007694925.1	s__SLFH01 sp007694925	76.8789	73	521	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__SLFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693785.1	s__RECY01 sp007693785	76.8715	86	521	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709445.1	s__PNC22 sp016709445	76.7412	67	521	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007124345.1	s__SLFH01 sp007124345	76.5564	65	521	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__SLFH01	95.0	98.92	98.92	0.84	0.84	2	-
GCA_016873295.1	s__VGXM01 sp016873295	76.5246	73	521	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__VGXM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693965.1	s__RECQ01 sp007693965	76.3494	59	521	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242645.1	s__JAFEBO01 sp018242645	75.995	51	521	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JAFEBO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:23:31,006] [INFO] GTDB search result was written to OceanDNA-b22189/result_gtdb.tsv
[2023-03-15 11:23:31,006] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:23:31,007] [INFO] DFAST_QC result json was written to OceanDNA-b22189/dqc_result.json
[2023-03-15 11:23:31,007] [INFO] DFAST_QC completed!
[2023-03-15 11:23:31,007] [INFO] Total running time: 0h1m11s