[2024-01-25 18:43:35,747] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:35,748] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:35,748] [INFO] DQC Reference Directory: /var/lib/cwl/stg6544ff2f-9d9f-44e4-ad5f-396ab099f5ae/dqc_reference
[2024-01-25 18:43:36,879] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:36,880] [INFO] Task started: Prodigal
[2024-01-25 18:43:36,880] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d1fe824-0d21-4eb6-8e1e-572de3d3f644/GCF_003990575.1_ASM399057v1_genomic.fna.gz | prodigal -d GCF_003990575.1_ASM399057v1_genomic.fna/cds.fna -a GCF_003990575.1_ASM399057v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:43:51,548] [INFO] Task succeeded: Prodigal
[2024-01-25 18:43:51,548] [INFO] Task started: HMMsearch
[2024-01-25 18:43:51,548] [INFO] Running command: hmmsearch --tblout GCF_003990575.1_ASM399057v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6544ff2f-9d9f-44e4-ad5f-396ab099f5ae/dqc_reference/reference_markers.hmm GCF_003990575.1_ASM399057v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:43:51,922] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:43:51,923] [INFO] Found 6/6 markers.
[2024-01-25 18:43:51,981] [INFO] Query marker FASTA was written to GCF_003990575.1_ASM399057v1_genomic.fna/markers.fasta
[2024-01-25 18:43:51,981] [INFO] Task started: Blastn
[2024-01-25 18:43:51,981] [INFO] Running command: blastn -query GCF_003990575.1_ASM399057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6544ff2f-9d9f-44e4-ad5f-396ab099f5ae/dqc_reference/reference_markers.fasta -out GCF_003990575.1_ASM399057v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:52,525] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:52,527] [INFO] Selected 14 target genomes.
[2024-01-25 18:43:52,528] [INFO] Target genome list was writen to GCF_003990575.1_ASM399057v1_genomic.fna/target_genomes.txt
[2024-01-25 18:43:52,536] [INFO] Task started: fastANI
[2024-01-25 18:43:52,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d1fe824-0d21-4eb6-8e1e-572de3d3f644/GCF_003990575.1_ASM399057v1_genomic.fna.gz --refList GCF_003990575.1_ASM399057v1_genomic.fna/target_genomes.txt --output GCF_003990575.1_ASM399057v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:44:14,986] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:14,987] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6544ff2f-9d9f-44e4-ad5f-396ab099f5ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:44:14,988] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6544ff2f-9d9f-44e4-ad5f-396ab099f5ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:44:14,996] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:44:14,996] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:44:14,997] [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	100.0	2546	2548	95	conclusive
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	99.9698	2470	2548	95	conclusive
Fischerella muscicola	strain=PCC 7414	GCA_000317205.1	92938	92938	type	True	79.4595	1108	2548	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	79.0693	943	2548	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	77.4328	701	2548	95	below_threshold
Brasilonema bromeliae	strain=SPC951	GCA_012912135.1	383615	383615	type	True	77.3976	549	2548	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	77.3341	652	2548	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	77.2832	626	2548	95	below_threshold
Scytonema hofmannii	strain=PCC 7110	GCA_000346485.2	34078	34078	type	True	77.113	605	2548	95	below_threshold
Calothrix elsteri	strain=CCALA 953	GCA_002289455.1	1247191	1247191	type	True	76.1177	252	2548	95	below_threshold
Cylindrospermopsis raciborskii	strain=Cr2010	GCA_003367075.2	77022	77022	reftype	True	75.8138	111	2548	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:44:14,998] [INFO] DFAST Taxonomy check result was written to GCF_003990575.1_ASM399057v1_genomic.fna/tc_result.tsv
[2024-01-25 18:44:14,999] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:44:14,999] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:44:14,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6544ff2f-9d9f-44e4-ad5f-396ab099f5ae/dqc_reference/checkm_data
[2024-01-25 18:44:15,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:44:15,073] [INFO] Task started: CheckM
[2024-01-25 18:44:15,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003990575.1_ASM399057v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003990575.1_ASM399057v1_genomic.fna/checkm_input GCF_003990575.1_ASM399057v1_genomic.fna/checkm_result
[2024-01-25 18:44:59,683] [INFO] Task succeeded: CheckM
[2024-01-25 18:44:59,684] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:44:59,702] [INFO] ===== Completeness check finished =====
[2024-01-25 18:44:59,702] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:44:59,702] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003990575.1_ASM399057v1_genomic.fna/markers.fasta)
[2024-01-25 18:44:59,702] [INFO] Task started: Blastn
[2024-01-25 18:44:59,703] [INFO] Running command: blastn -query GCF_003990575.1_ASM399057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6544ff2f-9d9f-44e4-ad5f-396ab099f5ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_003990575.1_ASM399057v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:00,513] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:00,520] [INFO] Selected 10 target genomes.
[2024-01-25 18:45:00,521] [INFO] Target genome list was writen to GCF_003990575.1_ASM399057v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:45:00,532] [INFO] Task started: fastANI
[2024-01-25 18:45:00,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d1fe824-0d21-4eb6-8e1e-572de3d3f644/GCF_003990575.1_ASM399057v1_genomic.fna.gz --refList GCF_003990575.1_ASM399057v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003990575.1_ASM399057v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:45:17,712] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:17,719] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:45:17,719] [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_000317285.1	s__Chlorogloeopsis fritschii	99.9698	2470	2548	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Chlorogloeopsis	95.0	99.29	97.93	0.97	0.93	4	conclusive
GCF_000517105.1	s__Fischerella sp000517105	80.464	1328	2548	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	97.28	97.28	0.93	0.93	2	-
GCA_000332255.1	s__Chlorogloeopsis sp000332255	79.8697	1018	2548	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Chlorogloeopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317205.1	s__Fischerella muscicola	79.474	1106	2548	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	99.84	99.68	0.97	0.95	3	-
GCF_000317225.1	s__Fischerella thermalis	79.0772	941	2548	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	98.97	96.56	0.93	0.78	35	-
GCF_002368315.1	s__Fischerella sp002368315	78.9586	994	2548	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000447295.1	s__Fischerella sp000447295	78.9413	971	2548	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	97.38	97.38	0.86	0.86	2	-
GCF_000317245.1	s__Fischerella muscicola_A	78.8255	1002	2548	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004323185.1	s__Fischerella prolifica	78.7771	976	2548	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	97.11	96.24	0.86	0.82	3	-
GCF_010091925.1	s__Nostoc sp010091925	77.7157	780	2548	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:45:17,721] [INFO] GTDB search result was written to GCF_003990575.1_ASM399057v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:45:17,721] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:45:17,724] [INFO] DFAST_QC result json was written to GCF_003990575.1_ASM399057v1_genomic.fna/dqc_result.json
[2024-01-25 18:45:17,724] [INFO] DFAST_QC completed!
[2024-01-25 18:45:17,724] [INFO] Total running time: 0h1m42s