[2023-03-14 14:06:07,223] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:06:07,224] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:06:07,224] [INFO] DQC Reference Directory: /var/lib/cwl/stg06c8cb28-f98d-4e78-9dc7-454a1fe07c5a/dqc_reference
[2023-03-14 14:06:08,362] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:06:08,362] [INFO] Task started: Prodigal
[2023-03-14 14:06:08,362] [INFO] Running command: cat /var/lib/cwl/stgf1eaf663-176c-4611-aabf-0bb5dcbc10b0/OceanDNA-b43720.fa | prodigal -d OceanDNA-b43720/cds.fna -a OceanDNA-b43720/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:06:21,407] [INFO] Task succeeded: Prodigal
[2023-03-14 14:06:21,407] [INFO] Task started: HMMsearch
[2023-03-14 14:06:21,407] [INFO] Running command: hmmsearch --tblout OceanDNA-b43720/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06c8cb28-f98d-4e78-9dc7-454a1fe07c5a/dqc_reference/reference_markers.hmm OceanDNA-b43720/protein.faa > /dev/null
[2023-03-14 14:06:21,601] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:06:21,601] [INFO] Found 6/6 markers.
[2023-03-14 14:06:21,619] [INFO] Query marker FASTA was written to OceanDNA-b43720/markers.fasta
[2023-03-14 14:06:21,620] [INFO] Task started: Blastn
[2023-03-14 14:06:21,620] [INFO] Running command: blastn -query OceanDNA-b43720/markers.fasta -db /var/lib/cwl/stg06c8cb28-f98d-4e78-9dc7-454a1fe07c5a/dqc_reference/reference_markers.fasta -out OceanDNA-b43720/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:06:22,263] [INFO] Task succeeded: Blastn
[2023-03-14 14:06:22,264] [INFO] Selected 21 target genomes.
[2023-03-14 14:06:22,265] [INFO] Target genome list was writen to OceanDNA-b43720/target_genomes.txt
[2023-03-14 14:06:22,283] [INFO] Task started: fastANI
[2023-03-14 14:06:22,283] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1eaf663-176c-4611-aabf-0bb5dcbc10b0/OceanDNA-b43720.fa --refList OceanDNA-b43720/target_genomes.txt --output OceanDNA-b43720/fastani_result.tsv --threads 1
[2023-03-14 14:06:38,016] [INFO] Task succeeded: fastANI
[2023-03-14 14:06:38,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06c8cb28-f98d-4e78-9dc7-454a1fe07c5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:06:38,016] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06c8cb28-f98d-4e78-9dc7-454a1fe07c5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:06:38,017] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:06:38,017] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 14:06:38,017] [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
--------------------------------------------------------------------------------
[2023-03-14 14:06:38,017] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43720/tc_result.tsv
[2023-03-14 14:06:38,017] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:06:38,017] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:06:38,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06c8cb28-f98d-4e78-9dc7-454a1fe07c5a/dqc_reference/checkm_data
[2023-03-14 14:06:38,028] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:06:38,033] [INFO] Task started: CheckM
[2023-03-14 14:06:38,033] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43720/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43720/checkm_input OceanDNA-b43720/checkm_result
[2023-03-14 14:07:31,347] [INFO] Task succeeded: CheckM
[2023-03-14 14:07:31,347] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.01%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-14 14:07:31,350] [INFO] ===== Completeness check finished =====
[2023-03-14 14:07:31,350] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:07:31,350] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43720/markers.fasta)
[2023-03-14 14:07:31,351] [INFO] Task started: Blastn
[2023-03-14 14:07:31,352] [INFO] Running command: blastn -query OceanDNA-b43720/markers.fasta -db /var/lib/cwl/stg06c8cb28-f98d-4e78-9dc7-454a1fe07c5a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43720/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:07:33,224] [INFO] Task succeeded: Blastn
[2023-03-14 14:07:33,225] [INFO] Selected 14 target genomes.
[2023-03-14 14:07:33,225] [INFO] Target genome list was writen to OceanDNA-b43720/target_genomes_gtdb.txt
[2023-03-14 14:07:33,244] [INFO] Task started: fastANI
[2023-03-14 14:07:33,244] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1eaf663-176c-4611-aabf-0bb5dcbc10b0/OceanDNA-b43720.fa --refList OceanDNA-b43720/target_genomes_gtdb.txt --output OceanDNA-b43720/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:07:41,249] [INFO] Task succeeded: fastANI
[2023-03-14 14:07:41,254] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 14:07:41,255] [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_002171735.1	s__UBA868 sp002171735	98.7349	557	692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	98.83	98.60	0.84	0.82	3	conclusive
GCA_018661145.1	s__UBA868 sp018661145	90.1623	471	692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	99.09	98.72	0.78	0.74	4	-
GCA_003529705.1	s__UBA868 sp003529705	82.3015	236	692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002327725.1	s__UBA868 sp002327725	79.9066	364	692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	99.85	99.69	0.88	0.82	5	-
GCA_002346525.1	s__UBA868 sp002346525	78.6647	200	692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845525.1	s__UBA868 sp016845525	78.5756	220	692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713825.1	s__UBA868 sp002713825	77.6263	136	692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726415.1	s__GCA-2726415 sp002726415	76.8833	51	692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__GCA-2726415	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:07:41,255] [INFO] GTDB search result was written to OceanDNA-b43720/result_gtdb.tsv
[2023-03-14 14:07:41,255] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:07:41,256] [INFO] DFAST_QC result json was written to OceanDNA-b43720/dqc_result.json
[2023-03-14 14:07:41,256] [INFO] DFAST_QC completed!
[2023-03-14 14:07:41,256] [INFO] Total running time: 0h1m34s