[2023-03-18 21:43:12,558] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:43:12,558] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:43:12,558] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ef53511-4940-405f-9a49-15583ca6deb0/dqc_reference
[2023-03-18 21:43:13,666] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:43:13,666] [INFO] Task started: Prodigal
[2023-03-18 21:43:13,666] [INFO] Running command: cat /var/lib/cwl/stgb6d9e464-6edf-4056-8988-575fb1d7a864/OceanDNA-b26157.fa | prodigal -d OceanDNA-b26157/cds.fna -a OceanDNA-b26157/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:43:22,794] [INFO] Task succeeded: Prodigal
[2023-03-18 21:43:22,794] [INFO] Task started: HMMsearch
[2023-03-18 21:43:22,794] [INFO] Running command: hmmsearch --tblout OceanDNA-b26157/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ef53511-4940-405f-9a49-15583ca6deb0/dqc_reference/reference_markers.hmm OceanDNA-b26157/protein.faa > /dev/null
[2023-03-18 21:43:22,965] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:43:22,966] [INFO] Found 6/6 markers.
[2023-03-18 21:43:22,979] [INFO] Query marker FASTA was written to OceanDNA-b26157/markers.fasta
[2023-03-18 21:43:22,980] [INFO] Task started: Blastn
[2023-03-18 21:43:22,980] [INFO] Running command: blastn -query OceanDNA-b26157/markers.fasta -db /var/lib/cwl/stg7ef53511-4940-405f-9a49-15583ca6deb0/dqc_reference/reference_markers.fasta -out OceanDNA-b26157/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:43:23,545] [INFO] Task succeeded: Blastn
[2023-03-18 21:43:23,546] [INFO] Selected 26 target genomes.
[2023-03-18 21:43:23,546] [INFO] Target genome list was writen to OceanDNA-b26157/target_genomes.txt
[2023-03-18 21:43:23,558] [INFO] Task started: fastANI
[2023-03-18 21:43:23,558] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6d9e464-6edf-4056-8988-575fb1d7a864/OceanDNA-b26157.fa --refList OceanDNA-b26157/target_genomes.txt --output OceanDNA-b26157/fastani_result.tsv --threads 1
[2023-03-18 21:43:34,964] [INFO] Task succeeded: fastANI
[2023-03-18 21:43:34,964] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ef53511-4940-405f-9a49-15583ca6deb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:43:34,964] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ef53511-4940-405f-9a49-15583ca6deb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:43:34,965] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:43:34,965] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:43:34,965] [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
--------------------------------------------------------------------------------
[2023-03-18 21:43:34,965] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26157/tc_result.tsv
[2023-03-18 21:43:34,965] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:43:34,965] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:43:34,965] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ef53511-4940-405f-9a49-15583ca6deb0/dqc_reference/checkm_data
[2023-03-18 21:43:34,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:43:34,971] [INFO] Task started: CheckM
[2023-03-18 21:43:34,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26157/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26157/checkm_input OceanDNA-b26157/checkm_result
[2023-03-18 21:44:02,792] [INFO] Task succeeded: CheckM
[2023-03-18 21:44:02,792] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 1.39%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-18 21:44:02,794] [INFO] ===== Completeness check finished =====
[2023-03-18 21:44:02,794] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:44:02,795] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26157/markers.fasta)
[2023-03-18 21:44:02,796] [INFO] Task started: Blastn
[2023-03-18 21:44:02,796] [INFO] Running command: blastn -query OceanDNA-b26157/markers.fasta -db /var/lib/cwl/stg7ef53511-4940-405f-9a49-15583ca6deb0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26157/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:44:03,735] [INFO] Task succeeded: Blastn
[2023-03-18 21:44:03,736] [INFO] Selected 16 target genomes.
[2023-03-18 21:44:03,736] [INFO] Target genome list was writen to OceanDNA-b26157/target_genomes_gtdb.txt
[2023-03-18 21:44:03,745] [INFO] Task started: fastANI
[2023-03-18 21:44:03,745] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6d9e464-6edf-4056-8988-575fb1d7a864/OceanDNA-b26157.fa --refList OceanDNA-b26157/target_genomes_gtdb.txt --output OceanDNA-b26157/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:44:09,686] [INFO] Task succeeded: fastANI
[2023-03-18 21:44:09,692] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:44:09,692] [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_002700485.1	s__HIMB100 sp002700485	99.1154	406	514	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	98.09	96.19	0.88	0.78	3	conclusive
GCA_902518965.1	s__HIMB100 sp902518965	94.0637	370	514	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902523435.1	s__HIMB100 sp902523435	93.3329	293	514	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520575.1	s__HIMB100 sp902520575	92.9326	205	514	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002348585.1	s__HIMB100 sp002348585	91.8148	345	514	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721775.1	s__HIMB100 sp002721775	85.8724	243	514	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722385.1	s__HIMB100 sp002722385	77.624	70	514	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	98.88	98.88	0.69	0.69	2	-
GCA_000238815.2	s__HIMB100 sp000238815	77.4086	151	514	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:44:09,692] [INFO] GTDB search result was written to OceanDNA-b26157/result_gtdb.tsv
[2023-03-18 21:44:09,692] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:44:09,693] [INFO] DFAST_QC result json was written to OceanDNA-b26157/dqc_result.json
[2023-03-18 21:44:09,693] [INFO] DFAST_QC completed!
[2023-03-18 21:44:09,693] [INFO] Total running time: 0h0m57s