[2023-06-18 11:44:52,649] [INFO] DFAST_QC pipeline started.
[2023-06-18 11:44:52,653] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 11:44:52,653] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ed7a8f0-badb-4cc2-924a-8c301031c2fc/dqc_reference
[2023-06-18 11:44:54,045] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 11:44:54,046] [INFO] Task started: Prodigal
[2023-06-18 11:44:54,046] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b6b2d18-8c40-488b-8aa9-bc7120acffc3/GCA_018295965.1_ASM1829596v1_genomic.fna.gz | prodigal -d GCA_018295965.1_ASM1829596v1_genomic.fna/cds.fna -a GCA_018295965.1_ASM1829596v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 11:45:05,461] [INFO] Task succeeded: Prodigal
[2023-06-18 11:45:05,462] [INFO] Task started: HMMsearch
[2023-06-18 11:45:05,462] [INFO] Running command: hmmsearch --tblout GCA_018295965.1_ASM1829596v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ed7a8f0-badb-4cc2-924a-8c301031c2fc/dqc_reference/reference_markers.hmm GCA_018295965.1_ASM1829596v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 11:45:05,850] [INFO] Task succeeded: HMMsearch
[2023-06-18 11:45:05,851] [INFO] Found 6/6 markers.
[2023-06-18 11:45:05,909] [INFO] Query marker FASTA was written to GCA_018295965.1_ASM1829596v1_genomic.fna/markers.fasta
[2023-06-18 11:45:05,910] [INFO] Task started: Blastn
[2023-06-18 11:45:05,910] [INFO] Running command: blastn -query GCA_018295965.1_ASM1829596v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ed7a8f0-badb-4cc2-924a-8c301031c2fc/dqc_reference/reference_markers.fasta -out GCA_018295965.1_ASM1829596v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:45:06,585] [INFO] Task succeeded: Blastn
[2023-06-18 11:45:06,589] [INFO] Selected 18 target genomes.
[2023-06-18 11:45:06,590] [INFO] Target genome list was writen to GCA_018295965.1_ASM1829596v1_genomic.fna/target_genomes.txt
[2023-06-18 11:45:06,592] [INFO] Task started: fastANI
[2023-06-18 11:45:06,592] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b6b2d18-8c40-488b-8aa9-bc7120acffc3/GCA_018295965.1_ASM1829596v1_genomic.fna.gz --refList GCA_018295965.1_ASM1829596v1_genomic.fna/target_genomes.txt --output GCA_018295965.1_ASM1829596v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 11:45:30,373] [INFO] Task succeeded: fastANI
[2023-06-18 11:45:30,373] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ed7a8f0-badb-4cc2-924a-8c301031c2fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 11:45:30,374] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ed7a8f0-badb-4cc2-924a-8c301031c2fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 11:45:30,390] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 11:45:30,390] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 11:45:30,391] [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
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	80.6793	1027	2041	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	80.6619	1022	2041	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	77.3668	501	2041	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	77.3378	510	2041	95	below_threshold
Cylindrospermopsis raciborskii	strain=Cr2010	GCA_003367075.2	77022	77022	reftype	True	77.2191	275	2041	95	below_threshold
Scytonema hofmannii	strain=PCC 7110	GCA_000346485.2	34078	34078	type	True	76.5106	294	2041	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	76.2775	295	2041	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	76.2768	291	2041	95	below_threshold
Fischerella muscicola	strain=PCC 7414	GCA_000317205.1	92938	92938	type	True	76.2149	306	2041	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	76.1847	323	2041	95	below_threshold
Calothrix elsteri	strain=CCALA 953	GCA_002289455.1	1247191	1247191	type	True	75.9935	234	2041	95	below_threshold
Planktothrix tepida	strain=PCC9214	GCA_904830955.1	1678309	1678309	type	True	75.9257	144	2041	95	below_threshold
Mastigocoleus testarum	strain=BC008	GCA_001456025.1	996925	996925	type	True	75.8836	244	2041	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 11:45:30,393] [INFO] DFAST Taxonomy check result was written to GCA_018295965.1_ASM1829596v1_genomic.fna/tc_result.tsv
[2023-06-18 11:45:30,393] [INFO] ===== Taxonomy check completed =====
[2023-06-18 11:45:30,393] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 11:45:30,393] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ed7a8f0-badb-4cc2-924a-8c301031c2fc/dqc_reference/checkm_data
[2023-06-18 11:45:30,394] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 11:45:30,457] [INFO] Task started: CheckM
[2023-06-18 11:45:30,458] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018295965.1_ASM1829596v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018295965.1_ASM1829596v1_genomic.fna/checkm_input GCA_018295965.1_ASM1829596v1_genomic.fna/checkm_result
[2023-06-18 11:46:09,069] [INFO] Task succeeded: CheckM
[2023-06-18 11:46:09,070] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 11:46:09,096] [INFO] ===== Completeness check finished =====
[2023-06-18 11:46:09,096] [INFO] ===== Start GTDB Search =====
[2023-06-18 11:46:09,097] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018295965.1_ASM1829596v1_genomic.fna/markers.fasta)
[2023-06-18 11:46:09,097] [INFO] Task started: Blastn
[2023-06-18 11:46:09,097] [INFO] Running command: blastn -query GCA_018295965.1_ASM1829596v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ed7a8f0-badb-4cc2-924a-8c301031c2fc/dqc_reference/reference_markers_gtdb.fasta -out GCA_018295965.1_ASM1829596v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:46:09,850] [INFO] Task succeeded: Blastn
[2023-06-18 11:46:09,855] [INFO] Selected 12 target genomes.
[2023-06-18 11:46:09,855] [INFO] Target genome list was writen to GCA_018295965.1_ASM1829596v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 11:46:09,863] [INFO] Task started: fastANI
[2023-06-18 11:46:09,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b6b2d18-8c40-488b-8aa9-bc7120acffc3/GCA_018295965.1_ASM1829596v1_genomic.fna.gz --refList GCA_018295965.1_ASM1829596v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018295965.1_ASM1829596v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 11:46:41,381] [INFO] Task succeeded: fastANI
[2023-06-18 11:46:41,400] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 11:46:41,400] [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_017355425.1	s__Dolichospermum sp017355425	99.9969	2010	2041	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	100.00	100.00	1.00	1.00	4	conclusive
GCF_012516395.1	s__Dolichospermum sp000312705	88.3032	1320	2041	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	96.37	95.92	0.82	0.80	18	-
GCF_009712035.1	s__Dolichospermum sp009712035	87.8592	1258	2041	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001277295.1	s__Dolichospermum sp001277295	87.7227	1377	2041	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	96.95	95.52	0.83	0.75	11	-
GCA_903848645.1	s__Dolichospermum sp903848645	87.4243	1244	2041	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711935.1	s__Dolichospermum sp009711935	87.2399	1273	2041	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368115.1	s__Dolichospermum compactum	87.2209	1297	2041	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698755.1	s__Dolichospermum flosaquae	85.7812	1149	2041	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	98.82	97.73	0.93	0.87	17	-
GCF_009711975.1	s__Dolichospermum sp009711975	85.476	1228	2041	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	98.17	98.17	0.93	0.93	2	-
GCF_000426925.1	s__Dolichospermum circinale	84.3936	1135	2041	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	95.89	95.31	0.82	0.78	3	-
GCF_011769525.1	s__Aulosira sp011769525	77.248	462	2041	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Aulosira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018993265.1	s__Nostoc_B sp018993265	77.0803	494	2041	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 11:46:41,402] [INFO] GTDB search result was written to GCA_018295965.1_ASM1829596v1_genomic.fna/result_gtdb.tsv
[2023-06-18 11:46:41,406] [INFO] ===== GTDB Search completed =====
[2023-06-18 11:46:41,411] [INFO] DFAST_QC result json was written to GCA_018295965.1_ASM1829596v1_genomic.fna/dqc_result.json
[2023-06-18 11:46:41,411] [INFO] DFAST_QC completed!
[2023-06-18 11:46:41,411] [INFO] Total running time: 0h1m49s