[2024-01-24 13:28:28,792] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:28,795] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:28,795] [INFO] DQC Reference Directory: /var/lib/cwl/stgda164b45-ee07-4996-94ab-f48d496bb982/dqc_reference
[2024-01-24 13:28:30,034] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:30,035] [INFO] Task started: Prodigal
[2024-01-24 13:28:30,035] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e3b20cf-b546-4507-9bc4-b3af21fba159/GCF_000317535.1_ASM31753v1_genomic.fna.gz | prodigal -d GCF_000317535.1_ASM31753v1_genomic.fna/cds.fna -a GCF_000317535.1_ASM31753v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:46,370] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:46,370] [INFO] Task started: HMMsearch
[2024-01-24 13:28:46,370] [INFO] Running command: hmmsearch --tblout GCF_000317535.1_ASM31753v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda164b45-ee07-4996-94ab-f48d496bb982/dqc_reference/reference_markers.hmm GCF_000317535.1_ASM31753v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:46,757] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:46,758] [INFO] Found 6/6 markers.
[2024-01-24 13:28:46,816] [INFO] Query marker FASTA was written to GCF_000317535.1_ASM31753v1_genomic.fna/markers.fasta
[2024-01-24 13:28:46,816] [INFO] Task started: Blastn
[2024-01-24 13:28:46,816] [INFO] Running command: blastn -query GCF_000317535.1_ASM31753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda164b45-ee07-4996-94ab-f48d496bb982/dqc_reference/reference_markers.fasta -out GCF_000317535.1_ASM31753v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:47,376] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:47,378] [INFO] Selected 13 target genomes.
[2024-01-24 13:28:47,379] [INFO] Target genome list was writen to GCF_000317535.1_ASM31753v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:47,387] [INFO] Task started: fastANI
[2024-01-24 13:28:47,387] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e3b20cf-b546-4507-9bc4-b3af21fba159/GCF_000317535.1_ASM31753v1_genomic.fna.gz --refList GCF_000317535.1_ASM31753v1_genomic.fna/target_genomes.txt --output GCF_000317535.1_ASM31753v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:03,678] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:03,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda164b45-ee07-4996-94ab-f48d496bb982/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:03,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda164b45-ee07-4996-94ab-f48d496bb982/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:03,703] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:29:03,703] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:29:03,703] [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	80.1073	1170	2534	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	79.9012	1190	2534	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	79.6832	1050	2534	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	79.6094	1071	2534	95	below_threshold
Brasilonema bromeliae	strain=SPC951	GCA_012912135.1	383615	383615	type	True	77.4227	527	2534	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	77.3683	597	2534	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	77.2874	516	2534	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	77.197	584	2534	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	77.1962	591	2534	95	below_threshold
Moorena producens	strain=3L	GCA_000211815.1	1155739	1155739	type	True	75.6255	100	2534	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:03,706] [INFO] DFAST Taxonomy check result was written to GCF_000317535.1_ASM31753v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:03,706] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:03,707] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:03,707] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda164b45-ee07-4996-94ab-f48d496bb982/dqc_reference/checkm_data
[2024-01-24 13:29:03,708] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:03,781] [INFO] Task started: CheckM
[2024-01-24 13:29:03,781] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000317535.1_ASM31753v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000317535.1_ASM31753v1_genomic.fna/checkm_input GCF_000317535.1_ASM31753v1_genomic.fna/checkm_result
[2024-01-24 13:29:56,941] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:56,942] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:56,969] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:56,970] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:56,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000317535.1_ASM31753v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:56,970] [INFO] Task started: Blastn
[2024-01-24 13:29:56,971] [INFO] Running command: blastn -query GCF_000317535.1_ASM31753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda164b45-ee07-4996-94ab-f48d496bb982/dqc_reference/reference_markers_gtdb.fasta -out GCF_000317535.1_ASM31753v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:57,804] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:57,814] [INFO] Selected 18 target genomes.
[2024-01-24 13:29:57,814] [INFO] Target genome list was writen to GCF_000317535.1_ASM31753v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:57,838] [INFO] Task started: fastANI
[2024-01-24 13:29:57,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e3b20cf-b546-4507-9bc4-b3af21fba159/GCF_000317535.1_ASM31753v1_genomic.fna.gz --refList GCF_000317535.1_ASM31753v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000317535.1_ASM31753v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:28,378] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:28,398] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:28,398] [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_000317535.1	s__Cylindrospermum stagnale	100.0	2530	2534	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Cylindrospermum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014697195.1	s__Cylindrospermum sp014697195	89.5276	1619	2534	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Cylindrospermum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003994795.1	s__Cylindrospermum sp003994795	84.47	1706	2534	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Cylindrospermum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010091925.1	s__Nostoc sp010091925	80.3712	1200	2534	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017115025.1	s__Nostoc sp017115025	80.2838	1128	2534	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904695.1	s__Nostoc sp014904695	80.2342	1166	2534	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698735.1	s__Anabaena variabilis_A	80.1684	1113	2534	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Anabaena	95.0	95.36	95.36	0.83	0.82	3	-
GCA_017114985.1	s__Nostoc sp017114985	80.1581	1134	2534	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002949735.1	s__Nostoc sp002949735	80.1226	1141	2534	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	96.73	95.05	0.82	0.76	3	-
GCF_015206995.1	s__Nostoc sp015206995	80.0932	1035	2534	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017115085.1	s__Nostoc sp017115085	80.0207	1117	2534	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014831675.1	s__Nostoc sp014831675	79.9687	1195	2534	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698305.1	s__Anabaena lutea	79.899	1074	2534	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Anabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014696655.1	s__Nostoc sp014696655	79.8836	1091	2534	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002949795.1	s__Nostoc sp002949795	79.8702	1095	2534	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016056275.1	s__Dendronalium phyllosphericum	79.1006	978	2534	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dendronalium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368195.1	s__Aulosira sp002368195	78.7684	1013	2534	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Aulosira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317245.1	s__Fischerella muscicola_A	77.4575	514	2534	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:28,402] [INFO] GTDB search result was written to GCF_000317535.1_ASM31753v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:28,402] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:28,406] [INFO] DFAST_QC result json was written to GCF_000317535.1_ASM31753v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:28,406] [INFO] DFAST_QC completed!
[2024-01-24 13:30:28,406] [INFO] Total running time: 0h1m60s