[2023-03-15 20:49:38,789] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:49:38,789] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:49:38,789] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5f32aba-1c52-4fee-aef3-315727b3ee3f/dqc_reference
[2023-03-15 20:49:39,891] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:49:39,891] [INFO] Task started: Prodigal
[2023-03-15 20:49:39,891] [INFO] Running command: cat /var/lib/cwl/stgbea91be2-b546-412a-8ccb-2a7f70579093/OceanDNA-b22261.fa | prodigal -d OceanDNA-b22261/cds.fna -a OceanDNA-b22261/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:49:55,181] [INFO] Task succeeded: Prodigal
[2023-03-15 20:49:55,181] [INFO] Task started: HMMsearch
[2023-03-15 20:49:55,181] [INFO] Running command: hmmsearch --tblout OceanDNA-b22261/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5f32aba-1c52-4fee-aef3-315727b3ee3f/dqc_reference/reference_markers.hmm OceanDNA-b22261/protein.faa > /dev/null
[2023-03-15 20:49:55,351] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:49:55,352] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbea91be2-b546-412a-8ccb-2a7f70579093/OceanDNA-b22261.fa]
[2023-03-15 20:49:55,367] [INFO] Query marker FASTA was written to OceanDNA-b22261/markers.fasta
[2023-03-15 20:49:55,368] [INFO] Task started: Blastn
[2023-03-15 20:49:55,368] [INFO] Running command: blastn -query OceanDNA-b22261/markers.fasta -db /var/lib/cwl/stgf5f32aba-1c52-4fee-aef3-315727b3ee3f/dqc_reference/reference_markers.fasta -out OceanDNA-b22261/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:49:55,898] [INFO] Task succeeded: Blastn
[2023-03-15 20:49:55,899] [INFO] Selected 20 target genomes.
[2023-03-15 20:49:55,899] [INFO] Target genome list was writen to OceanDNA-b22261/target_genomes.txt
[2023-03-15 20:49:55,909] [INFO] Task started: fastANI
[2023-03-15 20:49:55,909] [INFO] Running command: fastANI --query /var/lib/cwl/stgbea91be2-b546-412a-8ccb-2a7f70579093/OceanDNA-b22261.fa --refList OceanDNA-b22261/target_genomes.txt --output OceanDNA-b22261/fastani_result.tsv --threads 1
[2023-03-15 20:50:12,610] [INFO] Task succeeded: fastANI
[2023-03-15 20:50:12,610] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5f32aba-1c52-4fee-aef3-315727b3ee3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 20:50:12,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5f32aba-1c52-4fee-aef3-315727b3ee3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 20:50:12,614] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 20:50:12,614] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 20:50:12,614] [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
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.8486	56	808	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.8395	58	808	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 20:50:12,614] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22261/tc_result.tsv
[2023-03-15 20:50:12,614] [INFO] ===== Taxonomy check completed =====
[2023-03-15 20:50:12,614] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:50:12,614] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5f32aba-1c52-4fee-aef3-315727b3ee3f/dqc_reference/checkm_data
[2023-03-15 20:50:12,615] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:50:12,619] [INFO] Task started: CheckM
[2023-03-15 20:50:12,619] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22261/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22261/checkm_input OceanDNA-b22261/checkm_result
[2023-03-15 20:51:13,437] [INFO] Task succeeded: CheckM
[2023-03-15 20:51:13,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 20:51:13,439] [INFO] ===== Completeness check finished =====
[2023-03-15 20:51:13,439] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:51:13,439] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22261/markers.fasta)
[2023-03-15 20:51:13,441] [INFO] Task started: Blastn
[2023-03-15 20:51:13,441] [INFO] Running command: blastn -query OceanDNA-b22261/markers.fasta -db /var/lib/cwl/stgf5f32aba-1c52-4fee-aef3-315727b3ee3f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22261/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:51:14,220] [INFO] Task succeeded: Blastn
[2023-03-15 20:51:14,220] [INFO] Selected 15 target genomes.
[2023-03-15 20:51:14,220] [INFO] Target genome list was writen to OceanDNA-b22261/target_genomes_gtdb.txt
[2023-03-15 20:51:14,733] [INFO] Task started: fastANI
[2023-03-15 20:51:14,733] [INFO] Running command: fastANI --query /var/lib/cwl/stgbea91be2-b546-412a-8ccb-2a7f70579093/OceanDNA-b22261.fa --refList OceanDNA-b22261/target_genomes_gtdb.txt --output OceanDNA-b22261/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:51:22,714] [INFO] Task succeeded: fastANI
[2023-03-15 20:51:22,719] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 20:51:22,720] [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_002364485.1	s__UBA854 sp002364485	99.8212	741	808	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA854	95.0	99.87	99.87	0.97	0.97	2	conclusive
GCA_002295885.1	s__UBA854 sp002295885	79.4148	437	808	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA854	95.0	99.78	99.78	0.94	0.94	2	-
GCA_002591705.1	s__UBA854 sp002591705	78.7864	365	808	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA854	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722935.1	s__SP202 sp002722935	77.5512	125	808	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SP202	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014238205.1	s__SP202 sp014238205	76.9408	127	808	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SP202	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702575.1	s__UBA1668 sp002702575	76.5019	77	808	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA1668	95.0	99.83	99.83	0.97	0.97	3	-
GCA_013003065.1	s__JABDLI01 sp013003065	76.3672	99	808	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__JABDLI01	95.0	99.48	99.44	0.94	0.93	3	-
GCA_002684755.1	s__UBA12014 sp002684755	76.2941	75	808	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693845.1	s__SKZB01 sp007693845	76.0009	53	808	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SKZB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 20:51:22,720] [INFO] GTDB search result was written to OceanDNA-b22261/result_gtdb.tsv
[2023-03-15 20:51:22,720] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:51:22,721] [INFO] DFAST_QC result json was written to OceanDNA-b22261/dqc_result.json
[2023-03-15 20:51:22,721] [INFO] DFAST_QC completed!
[2023-03-15 20:51:22,721] [INFO] Total running time: 0h1m44s