[2023-03-18 05:35:37,306] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:35:37,308] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:35:37,308] [INFO] DQC Reference Directory: /var/lib/cwl/stg567625c3-41b6-43eb-8f90-44f45a7038b4/dqc_reference
[2023-03-18 05:35:38,961] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:35:38,962] [INFO] Task started: Prodigal
[2023-03-18 05:35:38,962] [INFO] Running command: cat /var/lib/cwl/stg1590829c-7ba6-4931-802a-0e0e88e02c65/OceanDNA-b16095.fa | prodigal -d OceanDNA-b16095/cds.fna -a OceanDNA-b16095/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:35:59,639] [INFO] Task succeeded: Prodigal
[2023-03-18 05:35:59,639] [INFO] Task started: HMMsearch
[2023-03-18 05:35:59,639] [INFO] Running command: hmmsearch --tblout OceanDNA-b16095/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg567625c3-41b6-43eb-8f90-44f45a7038b4/dqc_reference/reference_markers.hmm OceanDNA-b16095/protein.faa > /dev/null
[2023-03-18 05:35:59,897] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:35:59,898] [INFO] Found 6/6 markers.
[2023-03-18 05:35:59,935] [INFO] Query marker FASTA was written to OceanDNA-b16095/markers.fasta
[2023-03-18 05:35:59,936] [INFO] Task started: Blastn
[2023-03-18 05:35:59,937] [INFO] Running command: blastn -query OceanDNA-b16095/markers.fasta -db /var/lib/cwl/stg567625c3-41b6-43eb-8f90-44f45a7038b4/dqc_reference/reference_markers.fasta -out OceanDNA-b16095/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:36:00,484] [INFO] Task succeeded: Blastn
[2023-03-18 05:36:00,488] [INFO] Selected 14 target genomes.
[2023-03-18 05:36:00,488] [INFO] Target genome list was writen to OceanDNA-b16095/target_genomes.txt
[2023-03-18 05:36:00,496] [INFO] Task started: fastANI
[2023-03-18 05:36:00,496] [INFO] Running command: fastANI --query /var/lib/cwl/stg1590829c-7ba6-4931-802a-0e0e88e02c65/OceanDNA-b16095.fa --refList OceanDNA-b16095/target_genomes.txt --output OceanDNA-b16095/fastani_result.tsv --threads 1
[2023-03-18 05:36:17,002] [INFO] Task succeeded: fastANI
[2023-03-18 05:36:17,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg567625c3-41b6-43eb-8f90-44f45a7038b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:36:17,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg567625c3-41b6-43eb-8f90-44f45a7038b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:36:17,012] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:36:17,012] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 05:36:17,012] [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
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	78.9858	668	1276	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	78.6931	678	1276	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	78.4856	554	1276	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	78.4427	553	1276	95	below_threshold
Brasilonema bromeliae	strain=SPC951	GCA_012912135.1	383615	383615	type	True	77.213	328	1276	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	77.077	378	1276	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	77.0219	360	1276	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	76.9996	363	1276	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	76.9341	368	1276	95	below_threshold
Aetokthonos hydrillicola	strain=CCALA 1050	GCA_017591665.1	1550245	1550245	type	True	76.8222	268	1276	95	below_threshold
Fischerella muscicola	strain=PCC 7414	GCA_000317205.1	92938	92938	type	True	76.8093	377	1276	95	below_threshold
Cylindrospermopsis raciborskii	strain=Cr2010	GCA_003367075.2	77022	77022	reftype	True	76.6046	133	1276	95	below_threshold
Calothrix elsteri	strain=CCALA 953	GCA_002289455.1	1247191	1247191	type	True	76.21	185	1276	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 05:36:17,015] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16095/tc_result.tsv
[2023-03-18 05:36:17,023] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:36:17,023] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:36:17,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg567625c3-41b6-43eb-8f90-44f45a7038b4/dqc_reference/checkm_data
[2023-03-18 05:36:17,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:36:17,032] [INFO] Task started: CheckM
[2023-03-18 05:36:17,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16095/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16095/checkm_input OceanDNA-b16095/checkm_result
[2023-03-18 05:37:09,853] [INFO] Task succeeded: CheckM
[2023-03-18 05:37:09,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 05:37:09,953] [INFO] ===== Completeness check finished =====
[2023-03-18 05:37:09,953] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:37:09,953] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16095/markers.fasta)
[2023-03-18 05:37:09,954] [INFO] Task started: Blastn
[2023-03-18 05:37:09,954] [INFO] Running command: blastn -query OceanDNA-b16095/markers.fasta -db /var/lib/cwl/stg567625c3-41b6-43eb-8f90-44f45a7038b4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16095/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:37:10,720] [INFO] Task succeeded: Blastn
[2023-03-18 05:37:10,752] [INFO] Selected 8 target genomes.
[2023-03-18 05:37:10,753] [INFO] Target genome list was writen to OceanDNA-b16095/target_genomes_gtdb.txt
[2023-03-18 05:37:10,775] [INFO] Task started: fastANI
[2023-03-18 05:37:10,776] [INFO] Running command: fastANI --query /var/lib/cwl/stg1590829c-7ba6-4931-802a-0e0e88e02c65/OceanDNA-b16095.fa --refList OceanDNA-b16095/target_genomes_gtdb.txt --output OceanDNA-b16095/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:37:22,786] [INFO] Task succeeded: fastANI
[2023-03-18 05:37:22,792] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 05:37:22,792] [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_000340565.2	s__Nodularia spumigena	99.4724	1243	1276	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nodularia	95.0	98.78	96.92	0.95	0.92	4	conclusive
GCF_015207755.1	s__Nodularia sp015207755	89.4162	1060	1276	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nodularia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002218065.1	s__Nodularia sp002218065	89.0204	1037	1276	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nodularia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692755.1	s__Nodularia sp007692755	88.9012	971	1276	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nodularia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003556955.1	s__Nodularia sp003556955	87.3799	620	1276	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nodularia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124525.1	s__Nodularia sp016124525	83.5171	877	1276	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nodularia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903911355.1	s__Nodularia sp903911355	83.0805	809	1276	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nodularia	95.0	99.95	99.90	0.98	0.97	7	-
GCF_015245355.1	s__Nodularia elenkinii	82.4866	847	1276	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nodularia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:37:22,805] [INFO] GTDB search result was written to OceanDNA-b16095/result_gtdb.tsv
[2023-03-18 05:37:22,828] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:37:22,836] [INFO] DFAST_QC result json was written to OceanDNA-b16095/dqc_result.json
[2023-03-18 05:37:22,836] [INFO] DFAST_QC completed!
[2023-03-18 05:37:22,836] [INFO] Total running time: 0h1m46s