[2024-01-24 13:46:18,119] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:18,127] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:18,127] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa4ab6cb-7783-48ad-baf1-a3e248aaead9/dqc_reference
[2024-01-24 13:46:19,381] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:19,382] [INFO] Task started: Prodigal
[2024-01-24 13:46:19,383] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e35c5e1-6754-47c7-8089-e2b70428aa5e/GCF_000317475.1_ASM31747v1_genomic.fna.gz | prodigal -d GCF_000317475.1_ASM31747v1_genomic.fna/cds.fna -a GCF_000317475.1_ASM31747v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:39,550] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:39,550] [INFO] Task started: HMMsearch
[2024-01-24 13:46:39,550] [INFO] Running command: hmmsearch --tblout GCF_000317475.1_ASM31747v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa4ab6cb-7783-48ad-baf1-a3e248aaead9/dqc_reference/reference_markers.hmm GCF_000317475.1_ASM31747v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:39,997] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:39,999] [INFO] Found 6/6 markers.
[2024-01-24 13:46:40,060] [INFO] Query marker FASTA was written to GCF_000317475.1_ASM31747v1_genomic.fna/markers.fasta
[2024-01-24 13:46:40,061] [INFO] Task started: Blastn
[2024-01-24 13:46:40,061] [INFO] Running command: blastn -query GCF_000317475.1_ASM31747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa4ab6cb-7783-48ad-baf1-a3e248aaead9/dqc_reference/reference_markers.fasta -out GCF_000317475.1_ASM31747v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:40,730] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:40,733] [INFO] Selected 22 target genomes.
[2024-01-24 13:46:40,733] [INFO] Target genome list was writen to GCF_000317475.1_ASM31747v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:40,743] [INFO] Task started: fastANI
[2024-01-24 13:46:40,744] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e35c5e1-6754-47c7-8089-e2b70428aa5e/GCF_000317475.1_ASM31747v1_genomic.fna.gz --refList GCF_000317475.1_ASM31747v1_genomic.fna/target_genomes.txt --output GCF_000317475.1_ASM31747v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:06,474] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:06,474] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa4ab6cb-7783-48ad-baf1-a3e248aaead9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:06,475] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa4ab6cb-7783-48ad-baf1-a3e248aaead9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:06,490] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:47:06,490] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:47:06,490] [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
Gloeocapsopsis dulcis	strain=AAB1	GCA_002964865.1	2859516	2859516	type	True	77.185	73	2755	95	below_threshold
Argonema antarcticum	strain=A004/B2	GCA_023333585.1	2942763	2942763	type	True	77.1218	278	2755	95	below_threshold
Argonema galeatum	strain=A003/A1	GCA_023333595.1	2942762	2942762	type	True	76.9753	265	2755	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	76.949	128	2755	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	76.4583	105	2755	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	76.4181	104	2755	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	76.1756	141	2755	95	below_threshold
Baaleninema simplex	strain=PCC 7105	GCA_000332355.1	2862350	2862350	type	True	76.0648	82	2755	95	below_threshold
Gloeocapsopsis crepidinum	strain=LEGE 06123	GCA_015207655.1	693223	693223	type	True	75.9008	64	2755	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	75.8843	115	2755	95	below_threshold
Oscillatoria acuminata	strain=PCC 6304	GCA_000317105.1	118323	118323	type	True	75.8793	128	2755	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	75.7486	132	2755	95	below_threshold
Fischerella muscicola	strain=PCC 7414	GCA_000317205.1	92938	92938	type	True	75.728	92	2755	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	75.7044	85	2755	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	75.6585	89	2755	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	75.5966	91	2755	95	below_threshold
Moorena producens	strain=3L	GCA_001942475.1	1155739	1155739	type	True	75.5017	82	2755	95	below_threshold
Moorena producens	strain=3L	GCA_000211815.1	1155739	1155739	type	True	75.3277	80	2755	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:06,492] [INFO] DFAST Taxonomy check result was written to GCF_000317475.1_ASM31747v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:06,492] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:06,492] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:06,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa4ab6cb-7783-48ad-baf1-a3e248aaead9/dqc_reference/checkm_data
[2024-01-24 13:47:06,493] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:06,569] [INFO] Task started: CheckM
[2024-01-24 13:47:06,570] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000317475.1_ASM31747v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000317475.1_ASM31747v1_genomic.fna/checkm_input GCF_000317475.1_ASM31747v1_genomic.fna/checkm_result
[2024-01-24 13:48:04,880] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:04,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:04,899] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:04,899] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:04,900] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000317475.1_ASM31747v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:04,900] [INFO] Task started: Blastn
[2024-01-24 13:48:04,900] [INFO] Running command: blastn -query GCF_000317475.1_ASM31747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa4ab6cb-7783-48ad-baf1-a3e248aaead9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000317475.1_ASM31747v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:05,724] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:05,728] [INFO] Selected 9 target genomes.
[2024-01-24 13:48:05,728] [INFO] Target genome list was writen to GCF_000317475.1_ASM31747v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:05,737] [INFO] Task started: fastANI
[2024-01-24 13:48:05,737] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e35c5e1-6754-47c7-8089-e2b70428aa5e/GCF_000317475.1_ASM31747v1_genomic.fna.gz --refList GCF_000317475.1_ASM31747v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000317475.1_ASM31747v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:28,010] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:28,023] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:28,023] [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_000317475.1	s__Microcoleus sp000317475	100.0	2753	2755	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014695175.1	s__Microcoleus sp014695175	93.1336	1714	2755	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	96.46	96.46	0.87	0.87	3	-
GCF_000214075.1	s__Microcoleus vaginatus	92.9008	1906	2755	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013179805.1	s__Microcoleus asticus	92.4565	1870	2755	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014695295.1	s__Microcoleus sp014695295	92.288	1845	2755	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013299165.1	s__Microcoleus sp013299165	86.0948	1765	2755	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003542015.1	s__Microcoleus sp003542015	85.0484	1247	2755	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012034575.1	s__Microcoleus sp012034575	81.6146	1357	2755	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	98.56	98.27	0.85	0.83	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:28,025] [INFO] GTDB search result was written to GCF_000317475.1_ASM31747v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:28,026] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:28,029] [INFO] DFAST_QC result json was written to GCF_000317475.1_ASM31747v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:28,030] [INFO] DFAST_QC completed!
[2024-01-24 13:48:28,030] [INFO] Total running time: 0h2m10s