[2024-01-25 19:11:50,613] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:50,615] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:50,615] [INFO] DQC Reference Directory: /var/lib/cwl/stgce73c63d-1553-45cf-a78f-764b2e048228/dqc_reference
[2024-01-25 19:11:51,733] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:51,735] [INFO] Task started: Prodigal
[2024-01-25 19:11:51,736] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e99f15c-1610-4ee0-8d0b-3f4bdc83661e/GCF_014831675.1_ASM1483167v1_genomic.fna.gz | prodigal -d GCF_014831675.1_ASM1483167v1_genomic.fna/cds.fna -a GCF_014831675.1_ASM1483167v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:12:06,697] [INFO] Task succeeded: Prodigal
[2024-01-25 19:12:06,697] [INFO] Task started: HMMsearch
[2024-01-25 19:12:06,697] [INFO] Running command: hmmsearch --tblout GCF_014831675.1_ASM1483167v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce73c63d-1553-45cf-a78f-764b2e048228/dqc_reference/reference_markers.hmm GCF_014831675.1_ASM1483167v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:12:07,095] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:12:07,096] [INFO] Found 6/6 markers.
[2024-01-25 19:12:07,163] [INFO] Query marker FASTA was written to GCF_014831675.1_ASM1483167v1_genomic.fna/markers.fasta
[2024-01-25 19:12:07,163] [INFO] Task started: Blastn
[2024-01-25 19:12:07,163] [INFO] Running command: blastn -query GCF_014831675.1_ASM1483167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce73c63d-1553-45cf-a78f-764b2e048228/dqc_reference/reference_markers.fasta -out GCF_014831675.1_ASM1483167v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:07,718] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:07,721] [INFO] Selected 14 target genomes.
[2024-01-25 19:12:07,721] [INFO] Target genome list was writen to GCF_014831675.1_ASM1483167v1_genomic.fna/target_genomes.txt
[2024-01-25 19:12:07,728] [INFO] Task started: fastANI
[2024-01-25 19:12:07,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e99f15c-1610-4ee0-8d0b-3f4bdc83661e/GCF_014831675.1_ASM1483167v1_genomic.fna.gz --refList GCF_014831675.1_ASM1483167v1_genomic.fna/target_genomes.txt --output GCF_014831675.1_ASM1483167v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:12:27,662] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:27,663] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce73c63d-1553-45cf-a78f-764b2e048228/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:12:27,663] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce73c63d-1553-45cf-a78f-764b2e048228/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:12:27,672] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:12:27,672] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:12:27,672] [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	82.7939	1547	2733	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	81.8971	1507	2733	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	78.2047	796	2733	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	78.1184	800	2733	95	below_threshold
Fischerella muscicola	strain=PCC 7414	GCA_000317205.1	92938	92938	type	True	77.967	732	2733	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	77.8959	598	2733	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	77.8393	764	2733	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	77.8195	757	2733	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	77.7864	739	2733	95	below_threshold
Brasilonema bromeliae	strain=SPC951	GCA_012912135.1	383615	383615	type	True	77.6609	623	2733	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	77.5678	716	2733	95	below_threshold
Kovacikia minuta	strain=CCNU0001	GCA_020091585.1	2931930	2931930	type	True	75.5525	87	2733	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:12:27,675] [INFO] DFAST Taxonomy check result was written to GCF_014831675.1_ASM1483167v1_genomic.fna/tc_result.tsv
[2024-01-25 19:12:27,675] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:12:27,675] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:12:27,675] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce73c63d-1553-45cf-a78f-764b2e048228/dqc_reference/checkm_data
[2024-01-25 19:12:27,676] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:12:27,757] [INFO] Task started: CheckM
[2024-01-25 19:12:27,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014831675.1_ASM1483167v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014831675.1_ASM1483167v1_genomic.fna/checkm_input GCF_014831675.1_ASM1483167v1_genomic.fna/checkm_result
[2024-01-25 19:13:14,160] [INFO] Task succeeded: CheckM
[2024-01-25 19:13:14,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 19:13:14,182] [INFO] ===== Completeness check finished =====
[2024-01-25 19:13:14,182] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:13:14,183] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014831675.1_ASM1483167v1_genomic.fna/markers.fasta)
[2024-01-25 19:13:14,183] [INFO] Task started: Blastn
[2024-01-25 19:13:14,183] [INFO] Running command: blastn -query GCF_014831675.1_ASM1483167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce73c63d-1553-45cf-a78f-764b2e048228/dqc_reference/reference_markers_gtdb.fasta -out GCF_014831675.1_ASM1483167v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:13:14,989] [INFO] Task succeeded: Blastn
[2024-01-25 19:13:14,991] [INFO] Selected 13 target genomes.
[2024-01-25 19:13:14,991] [INFO] Target genome list was writen to GCF_014831675.1_ASM1483167v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:13:15,010] [INFO] Task started: fastANI
[2024-01-25 19:13:15,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e99f15c-1610-4ee0-8d0b-3f4bdc83661e/GCF_014831675.1_ASM1483167v1_genomic.fna.gz --refList GCF_014831675.1_ASM1483167v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014831675.1_ASM1483167v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:13:46,530] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:46,539] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:13:46,539] [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_014831675.1	s__Nostoc sp014831675	100.0	2727	2733	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014904695.1	s__Nostoc sp014904695	92.2119	2189	2733	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010091925.1	s__Nostoc sp010091925	92.0492	2076	2733	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015206995.1	s__Nostoc sp015206995	88.694	1600	2733	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698505.1	s__Nostoc foliaceum_A	82.9556	1626	2733	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	98.20	96.44	0.93	0.87	3	-
GCA_017115025.1	s__Nostoc sp017115025	82.793	1373	2733	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017114985.1	s__Nostoc sp017114985	82.4472	1435	2733	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	82.2567	1390	2733	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698065.1	s__Nostoc flagelliforme_B	82.1905	1500	2733	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003326195.1	s__Nostoc punctiforme_A	82.0339	1515	2733	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	97.25	97.17	0.91	0.90	3	-
GCF_014698035.1	s__Nostoc muscorum	81.9391	1519	2733	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	96.16	95.01	0.81	0.79	7	-
GCF_002368035.1	s__Nostoc linckia_B	81.2133	1462	2733	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016056305.1	s__Amazonocrinis nigriterrae	80.1074	1248	2733	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Amazonocrinis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:13:46,540] [INFO] GTDB search result was written to GCF_014831675.1_ASM1483167v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:13:46,541] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:13:46,543] [INFO] DFAST_QC result json was written to GCF_014831675.1_ASM1483167v1_genomic.fna/dqc_result.json
[2024-01-25 19:13:46,544] [INFO] DFAST_QC completed!
[2024-01-25 19:13:46,544] [INFO] Total running time: 0h1m56s