[2023-06-30 23:02:52,339] [INFO] DFAST_QC pipeline started.
[2023-06-30 23:02:52,345] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 23:02:52,346] [INFO] DQC Reference Directory: /var/lib/cwl/stg5dac3891-098f-4250-9ecc-44773064be05/dqc_reference
[2023-06-30 23:02:53,835] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 23:02:53,836] [INFO] Task started: Prodigal
[2023-06-30 23:02:53,836] [INFO] Running command: gunzip -c /var/lib/cwl/stgd490369f-8d7f-4a03-8170-70cc3f22556e/GCA_019359075.1_ASM1935907v1_genomic.fna.gz | prodigal -d GCA_019359075.1_ASM1935907v1_genomic.fna/cds.fna -a GCA_019359075.1_ASM1935907v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 23:03:12,708] [INFO] Task succeeded: Prodigal
[2023-06-30 23:03:12,708] [INFO] Task started: HMMsearch
[2023-06-30 23:03:12,708] [INFO] Running command: hmmsearch --tblout GCA_019359075.1_ASM1935907v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5dac3891-098f-4250-9ecc-44773064be05/dqc_reference/reference_markers.hmm GCA_019359075.1_ASM1935907v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 23:03:13,196] [INFO] Task succeeded: HMMsearch
[2023-06-30 23:03:13,198] [INFO] Found 6/6 markers.
[2023-06-30 23:03:13,266] [INFO] Query marker FASTA was written to GCA_019359075.1_ASM1935907v1_genomic.fna/markers.fasta
[2023-06-30 23:03:13,266] [INFO] Task started: Blastn
[2023-06-30 23:03:13,266] [INFO] Running command: blastn -query GCA_019359075.1_ASM1935907v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dac3891-098f-4250-9ecc-44773064be05/dqc_reference/reference_markers.fasta -out GCA_019359075.1_ASM1935907v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 23:03:13,855] [INFO] Task succeeded: Blastn
[2023-06-30 23:03:13,859] [INFO] Selected 13 target genomes.
[2023-06-30 23:03:13,860] [INFO] Target genome list was writen to GCA_019359075.1_ASM1935907v1_genomic.fna/target_genomes.txt
[2023-06-30 23:03:13,868] [INFO] Task started: fastANI
[2023-06-30 23:03:13,869] [INFO] Running command: fastANI --query /var/lib/cwl/stgd490369f-8d7f-4a03-8170-70cc3f22556e/GCA_019359075.1_ASM1935907v1_genomic.fna.gz --refList GCA_019359075.1_ASM1935907v1_genomic.fna/target_genomes.txt --output GCA_019359075.1_ASM1935907v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 23:03:32,987] [INFO] Task succeeded: fastANI
[2023-06-30 23:03:32,987] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5dac3891-098f-4250-9ecc-44773064be05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 23:03:32,988] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5dac3891-098f-4250-9ecc-44773064be05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 23:03:33,002] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 23:03:33,003] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 23:03:33,003] [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
Brasilonema bromeliae	strain=SPC951	GCA_012912135.1	383615	383615	type	True	83.2641	1308	2710	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	82.7686	1615	2710	95	below_threshold
Scytonema hofmannii	strain=PCC 7110	GCA_000346485.2	34078	34078	type	True	78.3533	1006	2710	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	78.1545	965	2710	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	78.0649	856	2710	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	77.9618	761	2710	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	77.8792	731	2710	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	77.877	730	2710	95	below_threshold
Fischerella muscicola	strain=PCC 7414	GCA_000317205.1	92938	92938	type	True	77.5511	679	2710	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	77.5233	582	2710	95	below_threshold
Aetokthonos hydrillicola	strain=CCALA 1050	GCA_017591665.1	1550245	1550245	type	True	77.3009	629	2710	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 23:03:33,005] [INFO] DFAST Taxonomy check result was written to GCA_019359075.1_ASM1935907v1_genomic.fna/tc_result.tsv
[2023-06-30 23:03:33,006] [INFO] ===== Taxonomy check completed =====
[2023-06-30 23:03:33,006] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 23:03:33,006] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5dac3891-098f-4250-9ecc-44773064be05/dqc_reference/checkm_data
[2023-06-30 23:03:33,007] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 23:03:33,080] [INFO] Task started: CheckM
[2023-06-30 23:03:33,081] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019359075.1_ASM1935907v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019359075.1_ASM1935907v1_genomic.fna/checkm_input GCA_019359075.1_ASM1935907v1_genomic.fna/checkm_result
[2023-06-30 23:04:29,793] [INFO] Task succeeded: CheckM
[2023-06-30 23:04:29,794] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 23:04:29,820] [INFO] ===== Completeness check finished =====
[2023-06-30 23:04:29,820] [INFO] ===== Start GTDB Search =====
[2023-06-30 23:04:29,821] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019359075.1_ASM1935907v1_genomic.fna/markers.fasta)
[2023-06-30 23:04:29,821] [INFO] Task started: Blastn
[2023-06-30 23:04:29,821] [INFO] Running command: blastn -query GCA_019359075.1_ASM1935907v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5dac3891-098f-4250-9ecc-44773064be05/dqc_reference/reference_markers_gtdb.fasta -out GCA_019359075.1_ASM1935907v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 23:04:30,599] [INFO] Task succeeded: Blastn
[2023-06-30 23:04:30,604] [INFO] Selected 10 target genomes.
[2023-06-30 23:04:30,605] [INFO] Target genome list was writen to GCA_019359075.1_ASM1935907v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 23:04:30,613] [INFO] Task started: fastANI
[2023-06-30 23:04:30,613] [INFO] Running command: fastANI --query /var/lib/cwl/stgd490369f-8d7f-4a03-8170-70cc3f22556e/GCA_019359075.1_ASM1935907v1_genomic.fna.gz --refList GCA_019359075.1_ASM1935907v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019359075.1_ASM1935907v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 23:04:53,197] [INFO] Task succeeded: fastANI
[2023-06-30 23:04:53,212] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 23:04:53,212] [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_002368435.1	s__Tolypothrix_B sp002368435	93.9065	2163	2710	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Tolypothrix_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368235.1	s__Tolypothrix_B sp002368235	92.9095	2124	2710	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Tolypothrix_B	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000828075.3	s__Tolypothrix_B campylonemoides	92.0348	2060	2710	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Tolypothrix_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315565.1	s__Mastigocladopsis repens	86.2912	1610	2710	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Mastigocladopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163975.1	s__HT-58-2 sp002163975	83.7638	1672	2710	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__HT-58-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012912135.1	s__Brasilonema bromeliae	83.2577	1309	2710	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828085.3	s__Brasilonema tolypothrichoides	82.8892	1622	2710	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006968915.1	s__Brasilonema octagenarum	82.7656	1611	2710	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	99.69	99.40	0.99	0.99	3	-
GCF_017982655.1	s__Brasilonema sp017982655	82.6309	1524	2710	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012912105.1	s__Brasilonema sp012912105	82.5588	1560	2710	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 23:04:53,214] [INFO] GTDB search result was written to GCA_019359075.1_ASM1935907v1_genomic.fna/result_gtdb.tsv
[2023-06-30 23:04:53,215] [INFO] ===== GTDB Search completed =====
[2023-06-30 23:04:53,218] [INFO] DFAST_QC result json was written to GCA_019359075.1_ASM1935907v1_genomic.fna/dqc_result.json
[2023-06-30 23:04:53,218] [INFO] DFAST_QC completed!
[2023-06-30 23:04:53,219] [INFO] Total running time: 0h2m1s