[2023-03-19 02:20:30,852] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:20:30,853] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:20:30,853] [INFO] DQC Reference Directory: /var/lib/cwl/stg8be8107e-23e5-41c9-ac80-2e0baa96640e/dqc_reference
[2023-03-19 02:20:31,954] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:20:31,954] [INFO] Task started: Prodigal
[2023-03-19 02:20:31,954] [INFO] Running command: cat /var/lib/cwl/stgbc6edcdd-b3f9-4286-b191-40e181c7d26c/OceanDNA-b16703.fa | prodigal -d OceanDNA-b16703/cds.fna -a OceanDNA-b16703/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:20:42,546] [INFO] Task succeeded: Prodigal
[2023-03-19 02:20:42,547] [INFO] Task started: HMMsearch
[2023-03-19 02:20:42,547] [INFO] Running command: hmmsearch --tblout OceanDNA-b16703/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8be8107e-23e5-41c9-ac80-2e0baa96640e/dqc_reference/reference_markers.hmm OceanDNA-b16703/protein.faa > /dev/null
[2023-03-19 02:20:42,698] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:20:42,698] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgbc6edcdd-b3f9-4286-b191-40e181c7d26c/OceanDNA-b16703.fa]
[2023-03-19 02:20:42,716] [INFO] Query marker FASTA was written to OceanDNA-b16703/markers.fasta
[2023-03-19 02:20:42,716] [INFO] Task started: Blastn
[2023-03-19 02:20:42,716] [INFO] Running command: blastn -query OceanDNA-b16703/markers.fasta -db /var/lib/cwl/stg8be8107e-23e5-41c9-ac80-2e0baa96640e/dqc_reference/reference_markers.fasta -out OceanDNA-b16703/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:20:43,235] [INFO] Task succeeded: Blastn
[2023-03-19 02:20:43,238] [INFO] Selected 18 target genomes.
[2023-03-19 02:20:43,238] [INFO] Target genome list was writen to OceanDNA-b16703/target_genomes.txt
[2023-03-19 02:20:43,250] [INFO] Task started: fastANI
[2023-03-19 02:20:43,250] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc6edcdd-b3f9-4286-b191-40e181c7d26c/OceanDNA-b16703.fa --refList OceanDNA-b16703/target_genomes.txt --output OceanDNA-b16703/fastani_result.tsv --threads 1
[2023-03-19 02:20:54,702] [INFO] Task succeeded: fastANI
[2023-03-19 02:20:54,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8be8107e-23e5-41c9-ac80-2e0baa96640e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:20:54,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8be8107e-23e5-41c9-ac80-2e0baa96640e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:20:54,705] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:20:54,705] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:20:54,706] [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	78.7364	123	212	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:20:54,707] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16703/tc_result.tsv
[2023-03-19 02:20:54,709] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:20:54,709] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:20:54,709] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8be8107e-23e5-41c9-ac80-2e0baa96640e/dqc_reference/checkm_data
[2023-03-19 02:20:54,710] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:20:54,727] [INFO] Task started: CheckM
[2023-03-19 02:20:54,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16703/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16703/checkm_input OceanDNA-b16703/checkm_result
[2023-03-19 02:21:27,394] [INFO] Task succeeded: CheckM
[2023-03-19 02:21:27,394] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 6.25%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-19 02:21:27,398] [INFO] ===== Completeness check finished =====
[2023-03-19 02:21:27,398] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:21:27,398] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16703/markers.fasta)
[2023-03-19 02:21:27,400] [INFO] Task started: Blastn
[2023-03-19 02:21:27,400] [INFO] Running command: blastn -query OceanDNA-b16703/markers.fasta -db /var/lib/cwl/stg8be8107e-23e5-41c9-ac80-2e0baa96640e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16703/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:21:28,178] [INFO] Task succeeded: Blastn
[2023-03-19 02:21:28,180] [INFO] Selected 14 target genomes.
[2023-03-19 02:21:28,180] [INFO] Target genome list was writen to OceanDNA-b16703/target_genomes_gtdb.txt
[2023-03-19 02:21:28,190] [INFO] Task started: fastANI
[2023-03-19 02:21:28,191] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc6edcdd-b3f9-4286-b191-40e181c7d26c/OceanDNA-b16703.fa --refList OceanDNA-b16703/target_genomes_gtdb.txt --output OceanDNA-b16703/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:21:32,919] [INFO] Task succeeded: fastANI
[2023-03-19 02:21:32,927] [INFO] Found 14 fastANI hits (3 hits with ANI > circumscription radius)
[2023-03-19 02:21:32,928] [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_003211235.1	s__Synechococcus_E sp003211235	96.4857	128	212	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	inconclusive
GCA_003210795.1	s__Synechococcus_E sp003210795	96.1756	162	212	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	inconclusive
GCA_003210735.1	s__Synechococcus_E sp003210735	96.0663	170	212	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	95.42	95.39	0.68	0.68	3	inconclusive
GCF_014280195.1	s__Synechococcus_E sp014280195	78.9584	119	212	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_000195975.1	s__Synechococcus_E sp000195975	78.7364	123	212	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.37	97.74	0.92	0.91	7	-
GCF_014279895.1	s__Synechococcus_E sp002724845	78.6724	114	212	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	-
GCF_000737595.1	s__Synechococcus_E sp000737595	78.4295	107	212	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_014280175.1	s__Synechococcus_E sp004212765	78.4108	128	212	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.21	96.96	0.98	0.97	4	-
GCF_000161795.2	s__Synechococcus_E sp000161795	78.3714	108	212	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_002170825.1	s__Synechococcus_E sp002170825	78.3316	71	212	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.06	98.06	0.77	0.77	2	-
GCA_003211535.1	s__Synechococcus_E sp003211535	78.1709	77	212	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_900474185.1	s__Synechococcus_E sp900474185	78.123	108	212	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	95.68	95.24	0.90	0.90	3	-
GCF_014279755.1	s__Synechococcus_E sp014279755	78.0635	107	212	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_000737535.1	s__Synechococcus_E sp000737535	77.4741	92	212	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	-
--------------------------------------------------------------------------------
[2023-03-19 02:21:32,928] [INFO] GTDB search result was written to OceanDNA-b16703/result_gtdb.tsv
[2023-03-19 02:21:32,929] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:21:32,930] [INFO] DFAST_QC result json was written to OceanDNA-b16703/dqc_result.json
[2023-03-19 02:21:32,930] [INFO] DFAST_QC completed!
[2023-03-19 02:21:32,930] [INFO] Total running time: 0h1m2s