[2024-01-24 13:46:26,043] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:26,044] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:26,044] [INFO] DQC Reference Directory: /var/lib/cwl/stg45f72abd-a65e-46db-b585-b411e84bd084/dqc_reference
[2024-01-24 13:46:27,737] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:27,739] [INFO] Task started: Prodigal
[2024-01-24 13:46:27,740] [INFO] Running command: gunzip -c /var/lib/cwl/stg949fad74-1877-4e32-9e73-3ff634f5fc81/GCF_013177315.1_ASM1317731v1_genomic.fna.gz | prodigal -d GCF_013177315.1_ASM1317731v1_genomic.fna/cds.fna -a GCF_013177315.1_ASM1317731v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:41,345] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:41,346] [INFO] Task started: HMMsearch
[2024-01-24 13:46:41,346] [INFO] Running command: hmmsearch --tblout GCF_013177315.1_ASM1317731v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45f72abd-a65e-46db-b585-b411e84bd084/dqc_reference/reference_markers.hmm GCF_013177315.1_ASM1317731v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:41,698] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:41,698] [INFO] Found 6/6 markers.
[2024-01-24 13:46:41,736] [INFO] Query marker FASTA was written to GCF_013177315.1_ASM1317731v1_genomic.fna/markers.fasta
[2024-01-24 13:46:41,736] [INFO] Task started: Blastn
[2024-01-24 13:46:41,737] [INFO] Running command: blastn -query GCF_013177315.1_ASM1317731v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45f72abd-a65e-46db-b585-b411e84bd084/dqc_reference/reference_markers.fasta -out GCF_013177315.1_ASM1317731v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:42,282] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:42,284] [INFO] Selected 19 target genomes.
[2024-01-24 13:46:42,285] [INFO] Target genome list was writen to GCF_013177315.1_ASM1317731v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:42,305] [INFO] Task started: fastANI
[2024-01-24 13:46:42,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg949fad74-1877-4e32-9e73-3ff634f5fc81/GCF_013177315.1_ASM1317731v1_genomic.fna.gz --refList GCF_013177315.1_ASM1317731v1_genomic.fna/target_genomes.txt --output GCF_013177315.1_ASM1317731v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:07,565] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:07,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45f72abd-a65e-46db-b585-b411e84bd084/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:07,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45f72abd-a65e-46db-b585-b411e84bd084/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:07,571] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:07,572] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:07,572] [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
Thermoleptolyngbya sichuanensis	strain=PKUAC-SCTA183	GCA_013177315.1	2885951	2885951	type	True	100.0	1840	1841	95	conclusive
Leptothermofonsia sichuanensis	strain=PKUAC-SCTE412	GCA_019891175.1	2917832	2917832	type	True	77.9477	131	1841	95	below_threshold
Kovacikia minuta	strain=CCNU0001	GCA_020091585.1	2931930	2931930	type	True	76.3816	128	1841	95	below_threshold
Prochlorothrix hollandica	strain=PCC 9006	GCA_000332315.1	1223	1223	type	True	76.1016	85	1841	95	below_threshold
Leptolyngbya boryana	strain=PCC 6306	GCA_000353285.1	1184	1184	type	True	76.0104	59	1841	95	below_threshold
Argonema antarcticum	strain=A004/B2	GCA_023333585.1	2942763	2942763	type	True	75.8364	56	1841	95	below_threshold
Argonema galeatum	strain=A003/A1	GCA_023333595.1	2942762	2942762	type	True	75.5823	56	1841	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:07,573] [INFO] DFAST Taxonomy check result was written to GCF_013177315.1_ASM1317731v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:07,573] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:07,573] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:07,574] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45f72abd-a65e-46db-b585-b411e84bd084/dqc_reference/checkm_data
[2024-01-24 13:47:07,574] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:07,627] [INFO] Task started: CheckM
[2024-01-24 13:47:07,627] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013177315.1_ASM1317731v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013177315.1_ASM1317731v1_genomic.fna/checkm_input GCF_013177315.1_ASM1317731v1_genomic.fna/checkm_result
[2024-01-24 13:47:47,409] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:47,410] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:47,426] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:47,426] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:47,427] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013177315.1_ASM1317731v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:47,427] [INFO] Task started: Blastn
[2024-01-24 13:47:47,427] [INFO] Running command: blastn -query GCF_013177315.1_ASM1317731v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45f72abd-a65e-46db-b585-b411e84bd084/dqc_reference/reference_markers_gtdb.fasta -out GCF_013177315.1_ASM1317731v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:48,212] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:48,214] [INFO] Selected 15 target genomes.
[2024-01-24 13:47:48,214] [INFO] Target genome list was writen to GCF_013177315.1_ASM1317731v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:48,233] [INFO] Task started: fastANI
[2024-01-24 13:47:48,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg949fad74-1877-4e32-9e73-3ff634f5fc81/GCF_013177315.1_ASM1317731v1_genomic.fna.gz --refList GCF_013177315.1_ASM1317731v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013177315.1_ASM1317731v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:10,840] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:10,849] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:10,850] [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_013177315.1	s__O-77 sp013177315	100.0	1841	1841	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__O-77	95.0	97.76	95.83	0.96	0.94	3	conclusive
GCF_001548395.1	s__O-77 sp001548395	91.34	1593	1841	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__O-77	95.0	95.35	95.35	0.93	0.93	2	-
GCA_003695655.1	s__O-77 sp003695655	81.6559	916	1841	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__O-77	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015295905.1	s__DVEB01 sp015295905	76.9108	208	1841	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__DVEB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000309385.1	s__Nodosilinea nodulosa	76.623	217	1841	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015272325.1	s__JACYLU01 sp015272325	76.5848	200	1841	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__JACYLU01	95.0	98.57	98.57	0.96	0.96	2	-
GCA_014695325.1	s__Leptolyngbya_A sp014695325	76.2653	189	1841	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__Leptolyngbya_A	95.0	99.45	99.45	0.94	0.94	2	-
GCA_003017855.1	s__Nodosilinea sp003017855	76.1854	200	1841	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	99.92	99.92	0.94	0.94	2	-
GCF_014697545.1	s__FACHB-1407 sp014697545	76.058	186	1841	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__FACHB-1407	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317045.1	s__PCC-7407 sp000317045	76.0133	230	1841	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-7407;f__PCC-7407;g__PCC-7407	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207605.1	s__Oculatella sp015207605	75.9718	157	1841	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__Oculatella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693275.1	s__Limnothrix sp001693275	75.6536	65	1841	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Cyanobacteriaceae;g__Limnothrix	95.0	96.93	96.67	0.92	0.91	11	-
GCA_012031475.1	s__JAAUTJ01 sp012031475	75.6026	163	1841	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__JAAUTJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015272155.1	s__JACYME01 sp015272155	75.5967	140	1841	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__JACYME01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746915.1	s__Desertifilum sp001746915	75.5203	81	1841	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Desertifilaceae;g__Desertifilum	95.0	99.94	99.93	0.99	0.98	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:10,851] [INFO] GTDB search result was written to GCF_013177315.1_ASM1317731v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:10,851] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:10,853] [INFO] DFAST_QC result json was written to GCF_013177315.1_ASM1317731v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:10,854] [INFO] DFAST_QC completed!
[2024-01-24 13:48:10,854] [INFO] Total running time: 0h1m45s