[2023-06-29 02:07:36,804] [INFO] DFAST_QC pipeline started.
[2023-06-29 02:07:36,808] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 02:07:36,809] [INFO] DQC Reference Directory: /var/lib/cwl/stg959da840-3bc0-40de-8392-a1ffdfe51b95/dqc_reference
[2023-06-29 02:07:38,228] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 02:07:38,230] [INFO] Task started: Prodigal
[2023-06-29 02:07:38,230] [INFO] Running command: gunzip -c /var/lib/cwl/stgc7f9b2bf-9965-4dba-b249-3b5f814471ee/GCA_020737945.1_ASM2073794v1_genomic.fna.gz | prodigal -d GCA_020737945.1_ASM2073794v1_genomic.fna/cds.fna -a GCA_020737945.1_ASM2073794v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 02:07:55,717] [INFO] Task succeeded: Prodigal
[2023-06-29 02:07:55,717] [INFO] Task started: HMMsearch
[2023-06-29 02:07:55,717] [INFO] Running command: hmmsearch --tblout GCA_020737945.1_ASM2073794v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg959da840-3bc0-40de-8392-a1ffdfe51b95/dqc_reference/reference_markers.hmm GCA_020737945.1_ASM2073794v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 02:07:56,199] [INFO] Task succeeded: HMMsearch
[2023-06-29 02:07:56,201] [INFO] Found 6/6 markers.
[2023-06-29 02:07:56,272] [INFO] Query marker FASTA was written to GCA_020737945.1_ASM2073794v1_genomic.fna/markers.fasta
[2023-06-29 02:07:56,273] [INFO] Task started: Blastn
[2023-06-29 02:07:56,273] [INFO] Running command: blastn -query GCA_020737945.1_ASM2073794v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg959da840-3bc0-40de-8392-a1ffdfe51b95/dqc_reference/reference_markers.fasta -out GCA_020737945.1_ASM2073794v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:07:56,878] [INFO] Task succeeded: Blastn
[2023-06-29 02:07:56,883] [INFO] Selected 29 target genomes.
[2023-06-29 02:07:56,883] [INFO] Target genome list was writen to GCA_020737945.1_ASM2073794v1_genomic.fna/target_genomes.txt
[2023-06-29 02:07:56,894] [INFO] Task started: fastANI
[2023-06-29 02:07:56,895] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7f9b2bf-9965-4dba-b249-3b5f814471ee/GCA_020737945.1_ASM2073794v1_genomic.fna.gz --refList GCA_020737945.1_ASM2073794v1_genomic.fna/target_genomes.txt --output GCA_020737945.1_ASM2073794v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 02:08:26,327] [INFO] Task succeeded: fastANI
[2023-06-29 02:08:26,328] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg959da840-3bc0-40de-8392-a1ffdfe51b95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 02:08:26,328] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg959da840-3bc0-40de-8392-a1ffdfe51b95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 02:08:26,341] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 02:08:26,341] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 02:08:26,341] [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
Argonema galeatum	strain=A003/A1	GCA_023333595.1	2942762	2942762	type	True	76.4693	266	2388	95	below_threshold
Argonema antarcticum	strain=A004/B2	GCA_023333585.1	2942763	2942763	type	True	76.3553	257	2388	95	below_threshold
Aliterella atlantica	strain=CENA595	GCA_000952155.1	1827278	1827278	type	True	76.1134	89	2388	95	below_threshold
Brasilonema bromeliae	strain=SPC951	GCA_012912135.1	383615	383615	type	True	76.0242	83	2388	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	75.8728	100	2388	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	75.7345	110	2388	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	75.7115	108	2388	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	75.445	109	2388	95	below_threshold
Limnospira indica	strain=PCC 8005	GCA_000176895.2	147322	147322	type	True	75.4387	68	2388	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	75.4255	132	2388	95	below_threshold
Limnospira indica	strain=PCC 8005	GCA_000973065.1	147322	147322	type	True	75.4002	76	2388	95	below_threshold
Baaleninema simplex	strain=PCC 7105	GCA_000332355.1	2862350	2862350	type	True	75.3996	80	2388	95	below_threshold
Scytonema hofmannii	strain=PCC 7110	GCA_000346485.2	34078	34078	type	True	75.2997	130	2388	95	below_threshold
Gloeocapsopsis dulcis	strain=AAB1	GCA_002964865.1	2859516	2859516	type	True	75.293	56	2388	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 02:08:26,344] [INFO] DFAST Taxonomy check result was written to GCA_020737945.1_ASM2073794v1_genomic.fna/tc_result.tsv
[2023-06-29 02:08:26,345] [INFO] ===== Taxonomy check completed =====
[2023-06-29 02:08:26,345] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 02:08:26,345] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg959da840-3bc0-40de-8392-a1ffdfe51b95/dqc_reference/checkm_data
[2023-06-29 02:08:26,348] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 02:08:26,418] [INFO] Task started: CheckM
[2023-06-29 02:08:26,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020737945.1_ASM2073794v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020737945.1_ASM2073794v1_genomic.fna/checkm_input GCA_020737945.1_ASM2073794v1_genomic.fna/checkm_result
[2023-06-29 02:09:17,557] [INFO] Task succeeded: CheckM
[2023-06-29 02:09:17,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 02:09:17,589] [INFO] ===== Completeness check finished =====
[2023-06-29 02:09:17,590] [INFO] ===== Start GTDB Search =====
[2023-06-29 02:09:17,590] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020737945.1_ASM2073794v1_genomic.fna/markers.fasta)
[2023-06-29 02:09:17,590] [INFO] Task started: Blastn
[2023-06-29 02:09:17,591] [INFO] Running command: blastn -query GCA_020737945.1_ASM2073794v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg959da840-3bc0-40de-8392-a1ffdfe51b95/dqc_reference/reference_markers_gtdb.fasta -out GCA_020737945.1_ASM2073794v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:09:18,377] [INFO] Task succeeded: Blastn
[2023-06-29 02:09:18,382] [INFO] Selected 14 target genomes.
[2023-06-29 02:09:18,382] [INFO] Target genome list was writen to GCA_020737945.1_ASM2073794v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 02:09:18,383] [INFO] Task started: fastANI
[2023-06-29 02:09:18,383] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7f9b2bf-9965-4dba-b249-3b5f814471ee/GCA_020737945.1_ASM2073794v1_genomic.fna.gz --refList GCA_020737945.1_ASM2073794v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020737945.1_ASM2073794v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 02:10:00,428] [INFO] Task succeeded: fastANI
[2023-06-29 02:10:00,446] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 02:10:00,446] [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_004292955.1	s__Microcoleus sp004292955	98.7963	2146	2388	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	98.97	98.79	0.93	0.91	14	conclusive
GCA_013299185.1	s__Microcoleus sp013299185	94.6021	1992	2388	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293365.1	s__Microcoleus sp004293365	92.8115	1888	2388	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	99.86	99.75	0.98	0.97	5	-
GCA_013299165.1	s__Microcoleus sp013299165	88.8239	1832	2388	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207455.1	s__Microcoleus sp015207455	87.3774	1597	2388	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003003725.1	s__Microcoleus sp003003725	87.3117	1482	2388	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	98.42	98.42	0.87	0.87	2	-
GCF_015207285.1	s__Microcoleus sp015207285	86.9867	1546	2388	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	86.8793	1654	2388	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	86.8573	1635	2388	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214075.1	s__Microcoleus vaginatus	86.5709	1642	2388	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317475.1	s__Microcoleus sp000317475	86.5286	1758	2388	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	83.8228	1158	2388	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002412335.2	s__Microcoleus bourrellyi	83.4723	1205	2388	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	80.9838	1360	2388	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	98.56	98.27	0.85	0.83	4	-
--------------------------------------------------------------------------------
[2023-06-29 02:10:00,448] [INFO] GTDB search result was written to GCA_020737945.1_ASM2073794v1_genomic.fna/result_gtdb.tsv
[2023-06-29 02:10:00,449] [INFO] ===== GTDB Search completed =====
[2023-06-29 02:10:00,457] [INFO] DFAST_QC result json was written to GCA_020737945.1_ASM2073794v1_genomic.fna/dqc_result.json
[2023-06-29 02:10:00,458] [INFO] DFAST_QC completed!
[2023-06-29 02:10:00,458] [INFO] Total running time: 0h2m24s