[2023-03-16 12:37:45,845] [INFO] DFAST_QC pipeline started.
[2023-03-16 12:37:45,845] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 12:37:45,845] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd8f145f-41d9-4f02-b96c-15fdb9bd0018/dqc_reference
[2023-03-16 12:37:48,617] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 12:37:48,618] [INFO] Task started: Prodigal
[2023-03-16 12:37:48,618] [INFO] Running command: cat /var/lib/cwl/stge0764a15-2550-4b50-86a9-0e1b8bb5ba95/OceanDNA-b16098.fa | prodigal -d OceanDNA-b16098/cds.fna -a OceanDNA-b16098/protein.faa -g 11 -q > /dev/null
[2023-03-16 12:38:08,915] [INFO] Task succeeded: Prodigal
[2023-03-16 12:38:08,915] [INFO] Task started: HMMsearch
[2023-03-16 12:38:08,915] [INFO] Running command: hmmsearch --tblout OceanDNA-b16098/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd8f145f-41d9-4f02-b96c-15fdb9bd0018/dqc_reference/reference_markers.hmm OceanDNA-b16098/protein.faa > /dev/null
[2023-03-16 12:38:09,130] [INFO] Task succeeded: HMMsearch
[2023-03-16 12:38:09,131] [INFO] Found 6/6 markers.
[2023-03-16 12:38:09,157] [INFO] Query marker FASTA was written to OceanDNA-b16098/markers.fasta
[2023-03-16 12:38:09,157] [INFO] Task started: Blastn
[2023-03-16 12:38:09,157] [INFO] Running command: blastn -query OceanDNA-b16098/markers.fasta -db /var/lib/cwl/stgcd8f145f-41d9-4f02-b96c-15fdb9bd0018/dqc_reference/reference_markers.fasta -out OceanDNA-b16098/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:38:09,673] [INFO] Task succeeded: Blastn
[2023-03-16 12:38:09,674] [INFO] Selected 23 target genomes.
[2023-03-16 12:38:09,674] [INFO] Target genome list was writen to OceanDNA-b16098/target_genomes.txt
[2023-03-16 12:38:09,688] [INFO] Task started: fastANI
[2023-03-16 12:38:09,688] [INFO] Running command: fastANI --query /var/lib/cwl/stge0764a15-2550-4b50-86a9-0e1b8bb5ba95/OceanDNA-b16098.fa --refList OceanDNA-b16098/target_genomes.txt --output OceanDNA-b16098/fastani_result.tsv --threads 1
[2023-03-16 12:38:34,510] [INFO] Task succeeded: fastANI
[2023-03-16 12:38:34,510] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd8f145f-41d9-4f02-b96c-15fdb9bd0018/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 12:38:34,510] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd8f145f-41d9-4f02-b96c-15fdb9bd0018/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 12:38:34,521] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 12:38:34,522] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 12:38:34,522] [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
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	76.775	198	1086	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	76.7467	200	1086	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	76.4698	171	1086	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	76.4462	162	1086	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	76.4194	163	1086	95	below_threshold
Brasilonema bromeliae	strain=SPC951	GCA_012912135.1	383615	383615	type	True	76.3633	122	1086	95	below_threshold
Mastigocoleus testarum	strain=BC008	GCA_001456025.1	996925	996925	type	True	76.3514	161	1086	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	76.3469	192	1086	95	below_threshold
Fischerella muscicola	strain=PCC 7414	GCA_000317205.1	92938	92938	type	True	76.3011	198	1086	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	76.1899	186	1086	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	76.1709	124	1086	95	below_threshold
Aetokthonos hydrillicola	strain=CCALA 1050	GCA_017591665.1	1550245	1550245	type	True	75.9866	114	1086	95	below_threshold
Aliterella atlantica	strain=CENA595	GCA_000952155.1	1827278	1827278	type	True	75.6323	70	1086	95	below_threshold
Planktothrix tepida	strain=PCC9214	GCA_904830955.1	1678309	1678309	type	True	75.5479	52	1086	95	below_threshold
Moorena producens	strain=3L	GCA_001942475.1	1155739	1155739	type	True	75.465	54	1086	95	below_threshold
Moorena producens	strain=3L	GCA_000211815.1	1155739	1155739	type	True	75.4224	55	1086	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 12:38:34,522] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16098/tc_result.tsv
[2023-03-16 12:38:34,522] [INFO] ===== Taxonomy check completed =====
[2023-03-16 12:38:34,522] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 12:38:34,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd8f145f-41d9-4f02-b96c-15fdb9bd0018/dqc_reference/checkm_data
[2023-03-16 12:38:34,523] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 12:38:34,529] [INFO] Task started: CheckM
[2023-03-16 12:38:34,529] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16098/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16098/checkm_input OceanDNA-b16098/checkm_result
[2023-03-16 12:39:30,663] [INFO] Task succeeded: CheckM
[2023-03-16 12:39:30,664] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 12:39:30,667] [INFO] ===== Completeness check finished =====
[2023-03-16 12:39:30,667] [INFO] ===== Start GTDB Search =====
[2023-03-16 12:39:30,667] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16098/markers.fasta)
[2023-03-16 12:39:30,669] [INFO] Task started: Blastn
[2023-03-16 12:39:30,669] [INFO] Running command: blastn -query OceanDNA-b16098/markers.fasta -db /var/lib/cwl/stgcd8f145f-41d9-4f02-b96c-15fdb9bd0018/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16098/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:39:31,532] [INFO] Task succeeded: Blastn
[2023-03-16 12:39:31,533] [INFO] Selected 17 target genomes.
[2023-03-16 12:39:31,533] [INFO] Target genome list was writen to OceanDNA-b16098/target_genomes_gtdb.txt
[2023-03-16 12:39:31,719] [INFO] Task started: fastANI
[2023-03-16 12:39:31,719] [INFO] Running command: fastANI --query /var/lib/cwl/stge0764a15-2550-4b50-86a9-0e1b8bb5ba95/OceanDNA-b16098.fa --refList OceanDNA-b16098/target_genomes_gtdb.txt --output OceanDNA-b16098/fastani_result_gtdb.tsv --threads 1
[2023-03-16 12:40:12,879] [INFO] Task succeeded: fastANI
[2023-03-16 12:40:12,889] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 12:40:12,889] [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_000613065.1	s__Richelia intracellularis_B	98.8968	931	1086	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Richelia	95.0	98.82	98.82	0.85	0.85	2	conclusive
GCF_900185595.1	s__Calothrix_A rhizosoleniae	79.5991	630	1086	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000350105.1	s__Richelia intracellularis	78.7684	461	1086	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Richelia	95.0	99.06	96.63	0.97	0.96	5	-
GCF_000317285.1	s__Chlorogloeopsis fritschii	76.7686	198	1086	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Chlorogloeopsis	95.0	99.29	97.93	0.97	0.93	4	-
GCF_001298445.1	s__Nostoc_B piscinale	76.5689	177	1086	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000316645.1	s__Trichormus sp000316645	76.5626	177	1086	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Trichormus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000517105.1	s__Fischerella sp000517105	76.5361	211	1086	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	97.28	97.28	0.93	0.93	2	-
GCF_016056275.1	s__Dendronalium phyllosphericum	76.5133	180	1086	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dendronalium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368275.1	s__Aulosira diplosiphon	76.4708	209	1086	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Aulosira	95.0	99.95	99.93	0.99	0.99	3	-
GCF_001456025.1	s__Mastigocoleus testarum	76.3811	162	1086	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Mastigocoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317225.1	s__Fischerella thermalis	76.3559	191	1086	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	98.97	96.56	0.93	0.78	35	-
GCF_015207705.1	s__Anabaenopsis sp015207705	76.3519	181	1086	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Anabaenopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002608075.1	s__Nostoc linckia	76.3111	187	1086	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	99.35	97.13	0.95	0.84	14	-
GCA_016124525.1	s__Nodularia sp016124525	76.2517	143	1086	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nodularia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001712795.1	s__Nostoc sp001712795	76.2134	170	1086	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317435.1	s__Calothrix sp000317435	76.1207	141	1086	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015272215.1	s__Rivularia sp015272215	76.009	147	1086	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Rivularia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 12:40:12,889] [INFO] GTDB search result was written to OceanDNA-b16098/result_gtdb.tsv
[2023-03-16 12:40:12,889] [INFO] ===== GTDB Search completed =====
[2023-03-16 12:40:12,891] [INFO] DFAST_QC result json was written to OceanDNA-b16098/dqc_result.json
[2023-03-16 12:40:12,891] [INFO] DFAST_QC completed!
[2023-03-16 12:40:12,891] [INFO] Total running time: 0h2m27s