[2023-03-18 03:09:33,542] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:09:33,543] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:09:33,543] [INFO] DQC Reference Directory: /var/lib/cwl/stg14f0fef9-d850-4276-bd71-81e7d693d9c6/dqc_reference
[2023-03-18 03:09:34,689] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:09:34,689] [INFO] Task started: Prodigal
[2023-03-18 03:09:34,689] [INFO] Running command: cat /var/lib/cwl/stg8a2a3de6-713b-4a4d-a9c7-59b853373b22/OceanDNA-b16437.fa | prodigal -d OceanDNA-b16437/cds.fna -a OceanDNA-b16437/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:09:46,979] [INFO] Task succeeded: Prodigal
[2023-03-18 03:09:46,979] [INFO] Task started: HMMsearch
[2023-03-18 03:09:46,979] [INFO] Running command: hmmsearch --tblout OceanDNA-b16437/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14f0fef9-d850-4276-bd71-81e7d693d9c6/dqc_reference/reference_markers.hmm OceanDNA-b16437/protein.faa > /dev/null
[2023-03-18 03:09:47,178] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:09:47,179] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8a2a3de6-713b-4a4d-a9c7-59b853373b22/OceanDNA-b16437.fa]
[2023-03-18 03:09:47,191] [INFO] Query marker FASTA was written to OceanDNA-b16437/markers.fasta
[2023-03-18 03:09:47,192] [INFO] Task started: Blastn
[2023-03-18 03:09:47,192] [INFO] Running command: blastn -query OceanDNA-b16437/markers.fasta -db /var/lib/cwl/stg14f0fef9-d850-4276-bd71-81e7d693d9c6/dqc_reference/reference_markers.fasta -out OceanDNA-b16437/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:09:47,792] [INFO] Task succeeded: Blastn
[2023-03-18 03:09:47,793] [INFO] Selected 20 target genomes.
[2023-03-18 03:09:47,793] [INFO] Target genome list was writen to OceanDNA-b16437/target_genomes.txt
[2023-03-18 03:09:47,804] [INFO] Task started: fastANI
[2023-03-18 03:09:47,804] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a2a3de6-713b-4a4d-a9c7-59b853373b22/OceanDNA-b16437.fa --refList OceanDNA-b16437/target_genomes.txt --output OceanDNA-b16437/fastani_result.tsv --threads 1
[2023-03-18 03:10:01,082] [INFO] Task succeeded: fastANI
[2023-03-18 03:10:01,083] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14f0fef9-d850-4276-bd71-81e7d693d9c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:10:01,083] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14f0fef9-d850-4276-bd71-81e7d693d9c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:10:01,086] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:10:01,086] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:10:01,086] [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	77.6682	116	328	95	below_threshold
Synechococcus lacustris	strain=Tous	GCA_003011125.1	2116544	2116544	suspected-type	True	77.0221	70	328	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:10:01,087] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16437/tc_result.tsv
[2023-03-18 03:10:01,087] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:10:01,087] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:10:01,087] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14f0fef9-d850-4276-bd71-81e7d693d9c6/dqc_reference/checkm_data
[2023-03-18 03:10:01,088] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:10:01,092] [INFO] Task started: CheckM
[2023-03-18 03:10:01,092] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16437/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16437/checkm_input OceanDNA-b16437/checkm_result
[2023-03-18 03:10:36,566] [INFO] Task succeeded: CheckM
[2023-03-18 03:10:36,567] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:10:36,568] [INFO] ===== Completeness check finished =====
[2023-03-18 03:10:36,569] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:10:36,569] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16437/markers.fasta)
[2023-03-18 03:10:36,569] [INFO] Task started: Blastn
[2023-03-18 03:10:36,569] [INFO] Running command: blastn -query OceanDNA-b16437/markers.fasta -db /var/lib/cwl/stg14f0fef9-d850-4276-bd71-81e7d693d9c6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16437/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:10:37,328] [INFO] Task succeeded: Blastn
[2023-03-18 03:10:37,328] [INFO] Selected 16 target genomes.
[2023-03-18 03:10:37,329] [INFO] Target genome list was writen to OceanDNA-b16437/target_genomes_gtdb.txt
[2023-03-18 03:10:37,424] [INFO] Task started: fastANI
[2023-03-18 03:10:37,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a2a3de6-713b-4a4d-a9c7-59b853373b22/OceanDNA-b16437.fa --refList OceanDNA-b16437/target_genomes_gtdb.txt --output OceanDNA-b16437/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:10:43,546] [INFO] Task succeeded: fastANI
[2023-03-18 03:10:43,556] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:10:43,556] [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_002470305.1	s__RCC307 sp002470305	80.5964	219	328	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__RCC307	95.0	98.70	97.75	0.84	0.76	3	-
GCA_000063525.1	s__RCC307 sp000063525	80.0773	234	328	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__RCC307	95.0	98.48	97.86	0.96	0.93	5	-
GCA_012270465.1	s__RCC307 sp012270465	79.9625	182	328	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__RCC307	95.0	98.23	98.23	0.84	0.84	2	-
GCA_002168155.1	s__RCC307 sp002168155	79.4966	219	328	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__RCC307	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016882415.1	s__Vulcanococcus sp016882415	78.9777	111	328	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016882585.1	s__Vulcanococcus sp016882585	78.9051	121	328	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016882385.1	s__Cyanobium_A sp016882385	78.6871	146	328	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016882525.1	s__NIES-981 sp016882525	78.6808	163	328	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	-
GCA_903943975.1	s__Synechococcus_D lacustris_A	78.5922	192	328	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_D	95.0	99.87	99.37	0.98	0.92	31	-
GCA_018400215.1	s__NIES-981 sp018400215	78.3366	116	328	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	99.01	99.01	0.86	0.86	2	-
GCF_014279895.1	s__Synechococcus_E sp002724845	78.234	131	328	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	96.37	95.03	0.93	0.89	13	-
GCA_014191755.1	s__Cyanobium sp014191755	78.0541	135	328	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_015840715.1	s__Cyanobium sp015840715	77.9231	155	328	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_000161795.2	s__Synechococcus_E sp000161795	77.8569	117	328	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280195.1	s__Synechococcus_E sp014280195	77.6982	111	328	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903935205.1	s__Cyanobium sp903935205	77.6859	141	328	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	99.93	99.91	0.96	0.96	3	-
--------------------------------------------------------------------------------
[2023-03-18 03:10:43,556] [INFO] GTDB search result was written to OceanDNA-b16437/result_gtdb.tsv
[2023-03-18 03:10:43,556] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:10:43,557] [INFO] DFAST_QC result json was written to OceanDNA-b16437/dqc_result.json
[2023-03-18 03:10:43,557] [INFO] DFAST_QC completed!
[2023-03-18 03:10:43,557] [INFO] Total running time: 0h1m10s