[2023-03-19 05:32:20,809] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:32:20,809] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:32:20,809] [INFO] DQC Reference Directory: /var/lib/cwl/stg7045a676-b671-4f00-8690-a9ff273cc504/dqc_reference
[2023-03-19 05:32:22,386] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:32:22,387] [INFO] Task started: Prodigal
[2023-03-19 05:32:22,387] [INFO] Running command: cat /var/lib/cwl/stg4f16cec9-92bd-47ce-b81e-351054e4d9c2/OceanDNA-b16516.fa | prodigal -d OceanDNA-b16516/cds.fna -a OceanDNA-b16516/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:32:34,265] [INFO] Task succeeded: Prodigal
[2023-03-19 05:32:34,266] [INFO] Task started: HMMsearch
[2023-03-19 05:32:34,266] [INFO] Running command: hmmsearch --tblout OceanDNA-b16516/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7045a676-b671-4f00-8690-a9ff273cc504/dqc_reference/reference_markers.hmm OceanDNA-b16516/protein.faa > /dev/null
[2023-03-19 05:32:34,419] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:32:34,419] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4f16cec9-92bd-47ce-b81e-351054e4d9c2/OceanDNA-b16516.fa]
[2023-03-19 05:32:34,431] [INFO] Query marker FASTA was written to OceanDNA-b16516/markers.fasta
[2023-03-19 05:32:34,431] [INFO] Task started: Blastn
[2023-03-19 05:32:34,431] [INFO] Running command: blastn -query OceanDNA-b16516/markers.fasta -db /var/lib/cwl/stg7045a676-b671-4f00-8690-a9ff273cc504/dqc_reference/reference_markers.fasta -out OceanDNA-b16516/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:32:34,944] [INFO] Task succeeded: Blastn
[2023-03-19 05:32:34,945] [INFO] Selected 24 target genomes.
[2023-03-19 05:32:34,945] [INFO] Target genome list was writen to OceanDNA-b16516/target_genomes.txt
[2023-03-19 05:32:34,956] [INFO] Task started: fastANI
[2023-03-19 05:32:34,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f16cec9-92bd-47ce-b81e-351054e4d9c2/OceanDNA-b16516.fa --refList OceanDNA-b16516/target_genomes.txt --output OceanDNA-b16516/fastani_result.tsv --threads 1
[2023-03-19 05:32:48,794] [INFO] Task succeeded: fastANI
[2023-03-19 05:32:48,794] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7045a676-b671-4f00-8690-a9ff273cc504/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:32:48,794] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7045a676-b671-4f00-8690-a9ff273cc504/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:32:48,797] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:32:48,797] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 05:32:48,797] [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	77.609	111	374	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 05:32:48,797] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16516/tc_result.tsv
[2023-03-19 05:32:48,798] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:32:48,798] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:32:48,798] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7045a676-b671-4f00-8690-a9ff273cc504/dqc_reference/checkm_data
[2023-03-19 05:32:48,798] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:32:48,802] [INFO] Task started: CheckM
[2023-03-19 05:32:48,802] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16516/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16516/checkm_input OceanDNA-b16516/checkm_result
[2023-03-19 05:33:25,224] [INFO] Task succeeded: CheckM
[2023-03-19 05:33:25,225] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.21%
Contamintation: 8.80%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-19 05:33:25,227] [INFO] ===== Completeness check finished =====
[2023-03-19 05:33:25,227] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:33:25,227] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16516/markers.fasta)
[2023-03-19 05:33:25,227] [INFO] Task started: Blastn
[2023-03-19 05:33:25,227] [INFO] Running command: blastn -query OceanDNA-b16516/markers.fasta -db /var/lib/cwl/stg7045a676-b671-4f00-8690-a9ff273cc504/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16516/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:33:25,951] [INFO] Task succeeded: Blastn
[2023-03-19 05:33:25,952] [INFO] Selected 11 target genomes.
[2023-03-19 05:33:25,952] [INFO] Target genome list was writen to OceanDNA-b16516/target_genomes_gtdb.txt
[2023-03-19 05:33:25,962] [INFO] Task started: fastANI
[2023-03-19 05:33:25,962] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f16cec9-92bd-47ce-b81e-351054e4d9c2/OceanDNA-b16516.fa --refList OceanDNA-b16516/target_genomes_gtdb.txt --output OceanDNA-b16516/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:33:30,526] [INFO] Task succeeded: fastANI
[2023-03-19 05:33:30,533] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 05:33:30,533] [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_014304815.1	s__Synechococcus_C sp001632165	83.4433	328	374	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	97.31	96.03	0.90	0.85	7	-
GCF_014279995.1	s__Synechococcus_C sp001631935	83.4294	340	374	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	96.61	96.58	0.90	0.90	3	-
GCA_003210775.1	s__Synechococcus_C sp003210775	82.7396	233	374	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_003211205.1	s__Synechococcus_C sp003211205	82.7029	264	374	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_003211275.1	s__Synechococcus_C sp003209155	82.7003	221	374	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	97.35	96.97	0.64	0.60	6	-
GCF_900473965.1	s__Synechococcus_C sp900473965	82.6788	333	374	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_014279975.1	s__Synechococcus_C sp014279975	82.3613	325	374	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_002687115.1	s__Synechococcus_C sp002687115	81.939	237	374	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_014279815.1	s__Synechococcus_C sp014279815	78.6343	211	374	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_000737575.1	s__Synechococcus_E sp000737575	77.6629	119	374	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.69	96.21	0.96	0.90	8	-
GCA_007694915.1	s__NIES-981 sp007694915	77.2754	70	374	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	-
--------------------------------------------------------------------------------
[2023-03-19 05:33:30,533] [INFO] GTDB search result was written to OceanDNA-b16516/result_gtdb.tsv
[2023-03-19 05:33:30,533] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:33:30,534] [INFO] DFAST_QC result json was written to OceanDNA-b16516/dqc_result.json
[2023-03-19 05:33:30,534] [INFO] DFAST_QC completed!
[2023-03-19 05:33:30,535] [INFO] Total running time: 0h1m10s