[2023-03-17 23:08:31,964] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:08:31,965] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:08:31,965] [INFO] DQC Reference Directory: /var/lib/cwl/stga196a76b-753b-4e61-b874-8b8cd8f5f30a/dqc_reference
[2023-03-17 23:08:33,155] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:08:33,155] [INFO] Task started: Prodigal
[2023-03-17 23:08:33,155] [INFO] Running command: cat /var/lib/cwl/stg590d8d78-1fe9-4842-81da-fb7f0b73122d/OceanDNA-b26056.fa | prodigal -d OceanDNA-b26056/cds.fna -a OceanDNA-b26056/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:08:37,341] [INFO] Task succeeded: Prodigal
[2023-03-17 23:08:37,342] [INFO] Task started: HMMsearch
[2023-03-17 23:08:37,342] [INFO] Running command: hmmsearch --tblout OceanDNA-b26056/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga196a76b-753b-4e61-b874-8b8cd8f5f30a/dqc_reference/reference_markers.hmm OceanDNA-b26056/protein.faa > /dev/null
[2023-03-17 23:08:37,515] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:08:37,516] [INFO] Found 6/6 markers.
[2023-03-17 23:08:37,537] [INFO] Query marker FASTA was written to OceanDNA-b26056/markers.fasta
[2023-03-17 23:08:37,537] [INFO] Task started: Blastn
[2023-03-17 23:08:37,537] [INFO] Running command: blastn -query OceanDNA-b26056/markers.fasta -db /var/lib/cwl/stga196a76b-753b-4e61-b874-8b8cd8f5f30a/dqc_reference/reference_markers.fasta -out OceanDNA-b26056/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:08:38,110] [INFO] Task succeeded: Blastn
[2023-03-17 23:08:38,115] [INFO] Selected 24 target genomes.
[2023-03-17 23:08:38,116] [INFO] Target genome list was writen to OceanDNA-b26056/target_genomes.txt
[2023-03-17 23:08:38,162] [INFO] Task started: fastANI
[2023-03-17 23:08:38,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg590d8d78-1fe9-4842-81da-fb7f0b73122d/OceanDNA-b26056.fa --refList OceanDNA-b26056/target_genomes.txt --output OceanDNA-b26056/fastani_result.tsv --threads 1
[2023-03-17 23:08:50,293] [INFO] Task succeeded: fastANI
[2023-03-17 23:08:50,293] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga196a76b-753b-4e61-b874-8b8cd8f5f30a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:08:50,294] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga196a76b-753b-4e61-b874-8b8cd8f5f30a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:08:50,294] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:08:50,294] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:08:50,294] [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
--------------------------------------------------------------------------------
[2023-03-17 23:08:50,295] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26056/tc_result.tsv
[2023-03-17 23:08:50,295] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:08:50,295] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:08:50,296] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga196a76b-753b-4e61-b874-8b8cd8f5f30a/dqc_reference/checkm_data
[2023-03-17 23:08:50,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:08:50,374] [INFO] Task started: CheckM
[2023-03-17 23:08:50,375] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26056/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26056/checkm_input OceanDNA-b26056/checkm_result
[2023-03-17 23:09:08,048] [INFO] Task succeeded: CheckM
[2023-03-17 23:09:08,048] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.48%
Contamintation: 5.21%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-17 23:09:08,062] [INFO] ===== Completeness check finished =====
[2023-03-17 23:09:08,062] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:09:08,062] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26056/markers.fasta)
[2023-03-17 23:09:08,063] [INFO] Task started: Blastn
[2023-03-17 23:09:08,063] [INFO] Running command: blastn -query OceanDNA-b26056/markers.fasta -db /var/lib/cwl/stga196a76b-753b-4e61-b874-8b8cd8f5f30a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26056/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:09:09,146] [INFO] Task succeeded: Blastn
[2023-03-17 23:09:09,150] [INFO] Selected 12 target genomes.
[2023-03-17 23:09:09,150] [INFO] Target genome list was writen to OceanDNA-b26056/target_genomes_gtdb.txt
[2023-03-17 23:09:09,162] [INFO] Task started: fastANI
[2023-03-17 23:09:09,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg590d8d78-1fe9-4842-81da-fb7f0b73122d/OceanDNA-b26056.fa --refList OceanDNA-b26056/target_genomes_gtdb.txt --output OceanDNA-b26056/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:09:12,368] [INFO] Task succeeded: fastANI
[2023-03-17 23:09:12,375] [INFO] Found 12 fastANI hits (4 hits with ANI > circumscription radius)
[2023-03-17 23:09:12,375] [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_003278095.1	s__AAA536-G10 sp003278095	95.7438	165	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	97.84	95.67	0.90	0.81	3	inconclusive
GCA_003283875.1	s__AAA536-G10 sp003283875	95.3306	110	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	95.33	95.28	0.67	0.61	3	inconclusive
GCA_003282435.1	s__AAA536-G10 sp003282435	95.1986	102	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_003282145.1	s__AAA536-G10 sp003282145	95.1173	156	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	100.00	100.00	1.00	1.00	2	inconclusive
GCA_902528415.1	s__AAA536-G10 sp902528415	94.8984	123	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	95.26	95.26	0.64	0.64	2	-
GCA_902517275.1	s__AAA536-G10 sp902517275	94.7453	106	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000384615.1	s__AAA536-G10 sp000384615	92.2843	152	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902514865.1	s__AAA536-G10 sp902514865	92.0707	94	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003282885.1	s__AAA536-G10 sp003282885	90.57	127	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	98.48	96.96	0.85	0.72	3	-
GCA_902622875.1	s__AAA536-G10 sp902622875	89.9405	141	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000421325.1	s__AAA536-G10 sp000421325	86.5438	146	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902618025.1	s__AAA536-G10 sp902618025	77.8856	57	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:09:12,377] [INFO] GTDB search result was written to OceanDNA-b26056/result_gtdb.tsv
[2023-03-17 23:09:12,379] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:09:12,381] [INFO] DFAST_QC result json was written to OceanDNA-b26056/dqc_result.json
[2023-03-17 23:09:12,381] [INFO] DFAST_QC completed!
[2023-03-17 23:09:12,382] [INFO] Total running time: 0h0m40s