[2024-01-24 13:36:28,210] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:28,212] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:28,212] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a7c0818-041e-41bb-b465-88e5f93e16bc/dqc_reference
[2024-01-24 13:36:29,429] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:29,430] [INFO] Task started: Prodigal
[2024-01-24 13:36:29,430] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b31490d-2307-43d3-8070-cd8edbac4050/GCF_002368295.1_ASM236829v1_genomic.fna.gz | prodigal -d GCF_002368295.1_ASM236829v1_genomic.fna/cds.fna -a GCF_002368295.1_ASM236829v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:50,126] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:50,127] [INFO] Task started: HMMsearch
[2024-01-24 13:36:50,127] [INFO] Running command: hmmsearch --tblout GCF_002368295.1_ASM236829v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a7c0818-041e-41bb-b465-88e5f93e16bc/dqc_reference/reference_markers.hmm GCF_002368295.1_ASM236829v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:50,551] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:50,553] [INFO] Found 6/6 markers.
[2024-01-24 13:36:50,625] [INFO] Query marker FASTA was written to GCF_002368295.1_ASM236829v1_genomic.fna/markers.fasta
[2024-01-24 13:36:50,625] [INFO] Task started: Blastn
[2024-01-24 13:36:50,626] [INFO] Running command: blastn -query GCF_002368295.1_ASM236829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a7c0818-041e-41bb-b465-88e5f93e16bc/dqc_reference/reference_markers.fasta -out GCF_002368295.1_ASM236829v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:51,212] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:51,216] [INFO] Selected 12 target genomes.
[2024-01-24 13:36:51,216] [INFO] Target genome list was writen to GCF_002368295.1_ASM236829v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:51,226] [INFO] Task started: fastANI
[2024-01-24 13:36:51,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b31490d-2307-43d3-8070-cd8edbac4050/GCF_002368295.1_ASM236829v1_genomic.fna.gz --refList GCF_002368295.1_ASM236829v1_genomic.fna/target_genomes.txt --output GCF_002368295.1_ASM236829v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:07,348] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:07,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a7c0818-041e-41bb-b465-88e5f93e16bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:07,349] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a7c0818-041e-41bb-b465-88e5f93e16bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:07,357] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:37:07,357] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:37:07,357] [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	79.2484	1097	3115	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	78.8873	1095	3115	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	78.2833	747	3115	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	78.2557	762	3115	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	77.6479	606	3115	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	77.2825	521	3115	95	below_threshold
Brasilonema bromeliae	strain=SPC951	GCA_012912135.1	383615	383615	type	True	77.1269	457	3115	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	77.0033	565	3115	95	below_threshold
Planktothrix tepida	strain=PCC9214	GCA_904830955.1	1678309	1678309	type	True	76.2818	109	3115	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:07,359] [INFO] DFAST Taxonomy check result was written to GCF_002368295.1_ASM236829v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:07,360] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:07,360] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:07,360] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a7c0818-041e-41bb-b465-88e5f93e16bc/dqc_reference/checkm_data
[2024-01-24 13:37:07,361] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:07,450] [INFO] Task started: CheckM
[2024-01-24 13:37:07,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002368295.1_ASM236829v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002368295.1_ASM236829v1_genomic.fna/checkm_input GCF_002368295.1_ASM236829v1_genomic.fna/checkm_result
[2024-01-24 13:38:10,934] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:10,935] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:10,961] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:10,962] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:10,962] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002368295.1_ASM236829v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:10,963] [INFO] Task started: Blastn
[2024-01-24 13:38:10,963] [INFO] Running command: blastn -query GCF_002368295.1_ASM236829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a7c0818-041e-41bb-b465-88e5f93e16bc/dqc_reference/reference_markers_gtdb.fasta -out GCF_002368295.1_ASM236829v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:11,809] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:11,813] [INFO] Selected 8 target genomes.
[2024-01-24 13:38:11,813] [INFO] Target genome list was writen to GCF_002368295.1_ASM236829v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:11,876] [INFO] Task started: fastANI
[2024-01-24 13:38:11,877] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b31490d-2307-43d3-8070-cd8edbac4050/GCF_002368295.1_ASM236829v1_genomic.fna.gz --refList GCF_002368295.1_ASM236829v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002368295.1_ASM236829v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:50,820] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:50,832] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:50,832] [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_002368295.1	s__Aulosira tenue	100.0	3114	3115	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Aulosira	95.0	99.99	99.98	1.00	1.00	3	conclusive
GCF_002368155.1	s__Aulosira carnea	94.4164	2443	3115	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Aulosira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368275.1	s__Aulosira diplosiphon	94.0224	2544	3115	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Aulosira	95.0	99.95	99.93	0.99	0.99	3	-
GCF_011769525.1	s__Aulosira sp011769525	92.0287	2282	3115	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Aulosira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014696615.1	s__Aulosira linckia_A	91.84	2316	3115	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Aulosira	95.0	97.98	97.98	0.87	0.87	2	-
GCF_014696315.1	s__Aulosira membranacea	91.6677	2221	3115	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Aulosira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698305.1	s__Anabaena lutea	78.085	719	3115	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Anabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426925.1	s__Dolichospermum circinale	76.895	369	3115	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	95.89	95.31	0.82	0.78	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:50,833] [INFO] GTDB search result was written to GCF_002368295.1_ASM236829v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:50,834] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:50,836] [INFO] DFAST_QC result json was written to GCF_002368295.1_ASM236829v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:50,837] [INFO] DFAST_QC completed!
[2024-01-24 13:38:50,837] [INFO] Total running time: 0h2m23s