[2023-06-05 18:53:28,647] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:53:28,765] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:53:28,766] [INFO] DQC Reference Directory: /var/lib/cwl/stg51d72ab9-2c32-4e71-995d-9ac3dde44b16/dqc_reference
[2023-06-05 18:53:29,968] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:53:29,969] [INFO] Task started: Prodigal
[2023-06-05 18:53:29,969] [INFO] Running command: gunzip -c /var/lib/cwl/stgb77caa8e-efeb-4ede-a45a-3fd84f3f4110/GCA_010672865.1_ASM1067286v1_genomic.fna.gz | prodigal -d GCA_010672865.1_ASM1067286v1_genomic.fna/cds.fna -a GCA_010672865.1_ASM1067286v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:53:39,779] [INFO] Task succeeded: Prodigal
[2023-06-05 18:53:39,779] [INFO] Task started: HMMsearch
[2023-06-05 18:53:39,779] [INFO] Running command: hmmsearch --tblout GCA_010672865.1_ASM1067286v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51d72ab9-2c32-4e71-995d-9ac3dde44b16/dqc_reference/reference_markers.hmm GCA_010672865.1_ASM1067286v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:53:40,060] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:53:40,061] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb77caa8e-efeb-4ede-a45a-3fd84f3f4110/GCA_010672865.1_ASM1067286v1_genomic.fna.gz]
[2023-06-05 18:53:40,103] [INFO] Query marker FASTA was written to GCA_010672865.1_ASM1067286v1_genomic.fna/markers.fasta
[2023-06-05 18:53:40,103] [INFO] Task started: Blastn
[2023-06-05 18:53:40,103] [INFO] Running command: blastn -query GCA_010672865.1_ASM1067286v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51d72ab9-2c32-4e71-995d-9ac3dde44b16/dqc_reference/reference_markers.fasta -out GCA_010672865.1_ASM1067286v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:53:40,614] [INFO] Task succeeded: Blastn
[2023-06-05 18:53:40,617] [INFO] Selected 22 target genomes.
[2023-06-05 18:53:40,617] [INFO] Target genome list was writen to GCA_010672865.1_ASM1067286v1_genomic.fna/target_genomes.txt
[2023-06-05 18:53:40,630] [INFO] Task started: fastANI
[2023-06-05 18:53:40,630] [INFO] Running command: fastANI --query /var/lib/cwl/stgb77caa8e-efeb-4ede-a45a-3fd84f3f4110/GCA_010672865.1_ASM1067286v1_genomic.fna.gz --refList GCA_010672865.1_ASM1067286v1_genomic.fna/target_genomes.txt --output GCA_010672865.1_ASM1067286v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:53:59,460] [INFO] Task succeeded: fastANI
[2023-06-05 18:53:59,461] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51d72ab9-2c32-4e71-995d-9ac3dde44b16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:53:59,462] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51d72ab9-2c32-4e71-995d-9ac3dde44b16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:53:59,469] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:53:59,469] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:53:59,469] [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
Crocosphaera watsonii	strain=WH 8501	GCA_000167195.1	263511	263511	suspected-type	True	75.8238	78	1888	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	75.7682	113	1888	95	below_threshold
Crocosphaera subtropica	strain=ATCC 51142	GCA_000017845.1	2546360	2546360	type	True	75.7676	95	1888	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	75.7086	87	1888	95	below_threshold
Aliterella atlantica	strain=CENA595	GCA_000952155.1	1827278	1827278	type	True	75.5972	86	1888	95	below_threshold
Crocosphaera chwakensis	strain=CCY0110	GCA_000169335.1	2546361	2546361	type	True	75.5782	110	1888	95	below_threshold
Rippkaea orientalis	strain=PCC 8801	GCA_000021805.1	2546366	2546366	type	True	75.5059	89	1888	95	below_threshold
Argonema antarcticum	strain=A004/B2	GCA_023333585.1	2942763	2942763	type	True	75.4994	120	1888	95	below_threshold
Argonema galeatum	strain=A003/A1	GCA_023333595.1	2942762	2942762	type	True	75.3796	111	1888	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:53:59,471] [INFO] DFAST Taxonomy check result was written to GCA_010672865.1_ASM1067286v1_genomic.fna/tc_result.tsv
[2023-06-05 18:53:59,472] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:53:59,472] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:53:59,472] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51d72ab9-2c32-4e71-995d-9ac3dde44b16/dqc_reference/checkm_data
[2023-06-05 18:53:59,473] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:53:59,541] [INFO] Task started: CheckM
[2023-06-05 18:53:59,541] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_010672865.1_ASM1067286v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_010672865.1_ASM1067286v1_genomic.fna/checkm_input GCA_010672865.1_ASM1067286v1_genomic.fna/checkm_result
[2023-06-05 18:54:32,495] [INFO] Task succeeded: CheckM
[2023-06-05 18:54:32,496] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:54:32,516] [INFO] ===== Completeness check finished =====
[2023-06-05 18:54:32,516] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:54:32,517] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_010672865.1_ASM1067286v1_genomic.fna/markers.fasta)
[2023-06-05 18:54:32,517] [INFO] Task started: Blastn
[2023-06-05 18:54:32,517] [INFO] Running command: blastn -query GCA_010672865.1_ASM1067286v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51d72ab9-2c32-4e71-995d-9ac3dde44b16/dqc_reference/reference_markers_gtdb.fasta -out GCA_010672865.1_ASM1067286v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:54:33,205] [INFO] Task succeeded: Blastn
[2023-06-05 18:54:33,209] [INFO] Selected 23 target genomes.
[2023-06-05 18:54:33,209] [INFO] Target genome list was writen to GCA_010672865.1_ASM1067286v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:54:33,263] [INFO] Task started: fastANI
[2023-06-05 18:54:33,263] [INFO] Running command: fastANI --query /var/lib/cwl/stgb77caa8e-efeb-4ede-a45a-3fd84f3f4110/GCA_010672865.1_ASM1067286v1_genomic.fna.gz --refList GCA_010672865.1_ASM1067286v1_genomic.fna/target_genomes_gtdb.txt --output GCA_010672865.1_ASM1067286v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:55:00,139] [INFO] Task succeeded: fastANI
[2023-06-05 18:55:00,152] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:55:00,153] [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
GCA_010672865.1	s__SIO1D9 sp010672865	100.0	1869	1888	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__SIO1D9;g__SIO1D9	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015207735.1	s__Phormidium_B sp015207735	76.2792	142	1888	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Phormidiaceae_A;g__Phormidium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317025.1	s__Hydrococcus sp000317025	75.9927	103	1888	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Hydrococcus	95.3004	99.40	99.40	0.98	0.98	2	-
GCF_000317555.1	s__Chroogloeocystis sp000317555	75.9663	84	1888	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Chroococcidiopsidaceae;g__Chroogloeocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002949795.1	s__Nostoc sp002949795	75.8886	94	1888	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332155.1	s__Kamptonema formosum	75.8863	114	1888	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Kamptonema	95.0	99.87	99.87	0.99	0.99	2	-
GCF_014698145.1	s__FACHB-1406 sp014698145	75.8585	101	1888	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Spirulinaceae;g__FACHB-1406	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001904725.1	s__Phormidium_B ambiguum	75.854	156	1888	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Phormidiaceae_A;g__Phormidium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014695725.1	s__FACHB-68 sp014695725	75.804	69	1888	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae_A;g__FACHB-68	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017845.1	s__Crocosphaera subtropica	75.784	91	1888	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003511885.1	s__UBA11153 sp003511885	75.7314	124	1888	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__UBA11153	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003864295.1	s__Aphanothece_B sacrum	75.7043	83	1888	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Aphanothece_B	95.0	99.99	99.99	0.99	0.99	2	-
GCA_000252485.1	s__Prochloron didemni	75.699	84	1888	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Prochloraceae;g__Prochloron	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003448685.1	s__Rippkaea sp003448685	75.6714	82	1888	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Rippkaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014695915.1	s__FACHB-40 sp014695915	75.6475	123	1888	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__FACHB-T130;g__FACHB-40	95.0	96.30	95.91	0.87	0.85	6	-
GCA_003021505.1	s__QS-4-48-99 sp003021505	75.6173	64	1888	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Rubidibacteraceae;g__QS-4-48-99	95.0	99.10	98.86	0.92	0.88	24	-
GCF_000169335.1	s__Crocosphaera chwakensis	75.5672	105	1888	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296455.1	s__Calothrix sp004296455	75.5341	99	1888	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021805.1	s__Rippkaea orientalis	75.5195	87	1888	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Rippkaea	95.0	98.84	98.84	0.95	0.95	2	-
GCF_016888125.1	s__CCY15215 sp016888125	75.4427	101	1888	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Spirulinaceae;g__CCY15215	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007785.1	s__Chroococcus hegewaldii	75.4258	80	1888	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Chroococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019192545.1	s__Rivularia sp019192545	75.2872	114	1888	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Rivularia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:55:00,154] [INFO] GTDB search result was written to GCA_010672865.1_ASM1067286v1_genomic.fna/result_gtdb.tsv
[2023-06-05 18:55:00,155] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:55:00,158] [INFO] DFAST_QC result json was written to GCA_010672865.1_ASM1067286v1_genomic.fna/dqc_result.json
[2023-06-05 18:55:00,158] [INFO] DFAST_QC completed!
[2023-06-05 18:55:00,158] [INFO] Total running time: 0h1m32s