[2023-03-15 04:05:08,877] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:05:08,877] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:05:08,878] [INFO] DQC Reference Directory: /var/lib/cwl/stg675638c1-2019-4355-9820-d36e699244bb/dqc_reference
[2023-03-15 04:05:09,969] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:05:09,970] [INFO] Task started: Prodigal
[2023-03-15 04:05:09,970] [INFO] Running command: cat /var/lib/cwl/stg6a6a61e2-a830-46db-a297-291e65726547/OceanDNA-b16591.fa | prodigal -d OceanDNA-b16591/cds.fna -a OceanDNA-b16591/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:05:21,211] [INFO] Task succeeded: Prodigal
[2023-03-15 04:05:21,211] [INFO] Task started: HMMsearch
[2023-03-15 04:05:21,211] [INFO] Running command: hmmsearch --tblout OceanDNA-b16591/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg675638c1-2019-4355-9820-d36e699244bb/dqc_reference/reference_markers.hmm OceanDNA-b16591/protein.faa > /dev/null
[2023-03-15 04:05:21,335] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:05:21,336] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6a6a61e2-a830-46db-a297-291e65726547/OceanDNA-b16591.fa]
[2023-03-15 04:05:21,359] [INFO] Query marker FASTA was written to OceanDNA-b16591/markers.fasta
[2023-03-15 04:05:21,359] [INFO] Task started: Blastn
[2023-03-15 04:05:21,359] [INFO] Running command: blastn -query OceanDNA-b16591/markers.fasta -db /var/lib/cwl/stg675638c1-2019-4355-9820-d36e699244bb/dqc_reference/reference_markers.fasta -out OceanDNA-b16591/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:05:21,797] [INFO] Task succeeded: Blastn
[2023-03-15 04:05:21,799] [INFO] Selected 14 target genomes.
[2023-03-15 04:05:21,800] [INFO] Target genome list was writen to OceanDNA-b16591/target_genomes.txt
[2023-03-15 04:05:21,808] [INFO] Task started: fastANI
[2023-03-15 04:05:21,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a6a61e2-a830-46db-a297-291e65726547/OceanDNA-b16591.fa --refList OceanDNA-b16591/target_genomes.txt --output OceanDNA-b16591/fastani_result.tsv --threads 1
[2023-03-15 04:05:33,837] [INFO] Task succeeded: fastANI
[2023-03-15 04:05:33,837] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg675638c1-2019-4355-9820-d36e699244bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:05:33,837] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg675638c1-2019-4355-9820-d36e699244bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:05:33,841] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:05:33,841] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 04:05:33,841] [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
Parasynechococcus marenigrum	strain=WH 8102	GCA_000195975.1	2881428	2881428	type	True	77.3432	112	332	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:05:33,843] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16591/tc_result.tsv
[2023-03-15 04:05:33,847] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:05:33,847] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:05:33,847] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg675638c1-2019-4355-9820-d36e699244bb/dqc_reference/checkm_data
[2023-03-15 04:05:33,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:05:33,941] [INFO] Task started: CheckM
[2023-03-15 04:05:33,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16591/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16591/checkm_input OceanDNA-b16591/checkm_result
[2023-03-15 04:06:07,755] [INFO] Task succeeded: CheckM
[2023-03-15 04:06:07,756] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.27%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 04:06:07,840] [INFO] ===== Completeness check finished =====
[2023-03-15 04:06:07,840] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:06:07,841] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16591/markers.fasta)
[2023-03-15 04:06:07,841] [INFO] Task started: Blastn
[2023-03-15 04:06:07,841] [INFO] Running command: blastn -query OceanDNA-b16591/markers.fasta -db /var/lib/cwl/stg675638c1-2019-4355-9820-d36e699244bb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16591/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:06:08,295] [INFO] Task succeeded: Blastn
[2023-03-15 04:06:08,299] [INFO] Selected 13 target genomes.
[2023-03-15 04:06:08,299] [INFO] Target genome list was writen to OceanDNA-b16591/target_genomes_gtdb.txt
[2023-03-15 04:06:08,334] [INFO] Task started: fastANI
[2023-03-15 04:06:08,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a6a61e2-a830-46db-a297-291e65726547/OceanDNA-b16591.fa --refList OceanDNA-b16591/target_genomes_gtdb.txt --output OceanDNA-b16591/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:06:13,977] [INFO] Task succeeded: fastANI
[2023-03-15 04:06:13,985] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 04:06:13,985] [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
GCF_000153825.1	s__Synechococcus_C sp000153825	95.9712	329	332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018623675.1	s__Synechococcus_C sp018623675	79.6803	146	332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900473935.1	s__Synechococcus_C sp002171995	78.8002	189	332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	98.95	98.80	0.86	0.67	4	-
GCF_900474295.1	s__Synechococcus_C sp900474295	78.7553	190	332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004209775.1	s__Synechococcus_C sp004209775	78.5159	162	332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	99.99	99.99	1.00	1.00	2	-
GCA_011523155.1	s__Synechococcus_C sp011523155	78.399	108	332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014279595.1	s__Synechococcus_C sp000153065	78.1992	166	332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	99.83	99.83	0.99	0.99	2	-
GCA_018399015.1	s__NIES-981 sp018399015	77.9162	99	332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153285.1	s__Synechococcus_C sp000153285	77.6097	97	332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903862155.1	s__UBA5018 sp903862155	77.4169	98	332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__UBA5018	95.0	99.05	99.00	0.85	0.80	5	-
GCF_014280035.1	s__Synechococcus_C sp002693285	77.3727	116	332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	98.95	98.86	0.95	0.94	3	-
GCA_016882315.1	s__Cyanobium sp016882315	77.2349	94	332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001040845.1	s__Synechococcus_C sp001040845	76.9746	76	332	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 04:06:13,987] [INFO] GTDB search result was written to OceanDNA-b16591/result_gtdb.tsv
[2023-03-15 04:06:13,989] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:06:13,992] [INFO] DFAST_QC result json was written to OceanDNA-b16591/dqc_result.json
[2023-03-15 04:06:13,992] [INFO] DFAST_QC completed!
[2023-03-15 04:06:13,992] [INFO] Total running time: 0h1m5s