[2023-06-28 22:05:24,613] [INFO] DFAST_QC pipeline started.
[2023-06-28 22:05:24,617] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 22:05:24,617] [INFO] DQC Reference Directory: /var/lib/cwl/stg20d028a8-f9a4-40c1-94d6-8491f0ae0a8b/dqc_reference
[2023-06-28 22:05:27,211] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 22:05:27,212] [INFO] Task started: Prodigal
[2023-06-28 22:05:27,213] [INFO] Running command: gunzip -c /var/lib/cwl/stg85fc2743-192f-4dd8-871a-e0a42851cd03/GCA_020883175.1_ASM2088317v1_genomic.fna.gz | prodigal -d GCA_020883175.1_ASM2088317v1_genomic.fna/cds.fna -a GCA_020883175.1_ASM2088317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 22:05:43,782] [INFO] Task succeeded: Prodigal
[2023-06-28 22:05:43,783] [INFO] Task started: HMMsearch
[2023-06-28 22:05:43,783] [INFO] Running command: hmmsearch --tblout GCA_020883175.1_ASM2088317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20d028a8-f9a4-40c1-94d6-8491f0ae0a8b/dqc_reference/reference_markers.hmm GCA_020883175.1_ASM2088317v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 22:05:44,119] [INFO] Task succeeded: HMMsearch
[2023-06-28 22:05:44,121] [INFO] Found 6/6 markers.
[2023-06-28 22:05:44,177] [INFO] Query marker FASTA was written to GCA_020883175.1_ASM2088317v1_genomic.fna/markers.fasta
[2023-06-28 22:05:44,178] [INFO] Task started: Blastn
[2023-06-28 22:05:44,178] [INFO] Running command: blastn -query GCA_020883175.1_ASM2088317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20d028a8-f9a4-40c1-94d6-8491f0ae0a8b/dqc_reference/reference_markers.fasta -out GCA_020883175.1_ASM2088317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:05:44,754] [INFO] Task succeeded: Blastn
[2023-06-28 22:05:44,759] [INFO] Selected 23 target genomes.
[2023-06-28 22:05:44,760] [INFO] Target genome list was writen to GCA_020883175.1_ASM2088317v1_genomic.fna/target_genomes.txt
[2023-06-28 22:05:44,765] [INFO] Task started: fastANI
[2023-06-28 22:05:44,765] [INFO] Running command: fastANI --query /var/lib/cwl/stg85fc2743-192f-4dd8-871a-e0a42851cd03/GCA_020883175.1_ASM2088317v1_genomic.fna.gz --refList GCA_020883175.1_ASM2088317v1_genomic.fna/target_genomes.txt --output GCA_020883175.1_ASM2088317v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 22:06:06,173] [INFO] Task succeeded: fastANI
[2023-06-28 22:06:06,173] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20d028a8-f9a4-40c1-94d6-8491f0ae0a8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 22:06:06,174] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20d028a8-f9a4-40c1-94d6-8491f0ae0a8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 22:06:06,186] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 22:06:06,186] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 22:06:06,186] [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 antarcticum	strain=A004/B2	GCA_023333585.1	2942763	2942763	type	True	76.2367	243	2394	95	below_threshold
Argonema galeatum	strain=A003/A1	GCA_023333595.1	2942762	2942762	type	True	76.1775	242	2394	95	below_threshold
Planktothrix tepida	strain=PCC9214	GCA_904830955.1	1678309	1678309	type	True	75.9447	102	2394	95	below_threshold
Planktothrix agardhii	strain=NIES-204	GCA_003609755.1	1160	1160	type	True	75.8942	107	2394	95	below_threshold
Brasilonema bromeliae	strain=SPC951	GCA_012912135.1	383615	383615	type	True	75.8668	78	2394	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	75.6289	117	2394	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	75.6285	89	2394	95	below_threshold
Aliterella atlantica	strain=CENA595	GCA_000952155.1	1827278	1827278	type	True	75.6056	84	2394	95	below_threshold
Limnospira indica	strain=PCC 8005	GCA_000973065.1	147322	147322	type	True	75.561	82	2394	95	below_threshold
Scytonema hofmannii	strain=PCC 7110	GCA_000346485.2	34078	34078	type	True	75.4393	125	2394	95	below_threshold
Limnospira indica	strain=PCC 8005	GCA_000176895.2	147322	147322	type	True	75.4008	80	2394	95	below_threshold
Baaleninema simplex	strain=PCC 7105	GCA_000332355.1	2862350	2862350	type	True	75.2752	89	2394	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 22:06:06,188] [INFO] DFAST Taxonomy check result was written to GCA_020883175.1_ASM2088317v1_genomic.fna/tc_result.tsv
[2023-06-28 22:06:06,189] [INFO] ===== Taxonomy check completed =====
[2023-06-28 22:06:06,189] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 22:06:06,189] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20d028a8-f9a4-40c1-94d6-8491f0ae0a8b/dqc_reference/checkm_data
[2023-06-28 22:06:06,190] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 22:06:06,254] [INFO] Task started: CheckM
[2023-06-28 22:06:06,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020883175.1_ASM2088317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020883175.1_ASM2088317v1_genomic.fna/checkm_input GCA_020883175.1_ASM2088317v1_genomic.fna/checkm_result
[2023-06-28 22:06:57,585] [INFO] Task succeeded: CheckM
[2023-06-28 22:06:57,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 22:06:57,611] [INFO] ===== Completeness check finished =====
[2023-06-28 22:06:57,612] [INFO] ===== Start GTDB Search =====
[2023-06-28 22:06:57,612] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020883175.1_ASM2088317v1_genomic.fna/markers.fasta)
[2023-06-28 22:06:57,613] [INFO] Task started: Blastn
[2023-06-28 22:06:57,613] [INFO] Running command: blastn -query GCA_020883175.1_ASM2088317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20d028a8-f9a4-40c1-94d6-8491f0ae0a8b/dqc_reference/reference_markers_gtdb.fasta -out GCA_020883175.1_ASM2088317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:06:58,356] [INFO] Task succeeded: Blastn
[2023-06-28 22:06:58,361] [INFO] Selected 13 target genomes.
[2023-06-28 22:06:58,361] [INFO] Target genome list was writen to GCA_020883175.1_ASM2088317v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 22:06:58,370] [INFO] Task started: fastANI
[2023-06-28 22:06:58,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg85fc2743-192f-4dd8-871a-e0a42851cd03/GCA_020883175.1_ASM2088317v1_genomic.fna.gz --refList GCA_020883175.1_ASM2088317v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020883175.1_ASM2088317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 22:07:38,419] [INFO] Task succeeded: fastANI
[2023-06-28 22:07:38,435] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 22:07:38,435] [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_013299185.1	s__Microcoleus sp013299185	99.918	2367	2394	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004292955.1	s__Microcoleus sp004292955	94.6178	1960	2394	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	98.97	98.79	0.93	0.91	14	-
GCA_004293365.1	s__Microcoleus sp004293365	91.9033	1873	2394	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	88.5192	1833	2394	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	87.1088	1588	2394	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	87.0368	1469	2394	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	98.42	98.42	0.87	0.87	2	-
GCF_013179805.1	s__Microcoleus asticus	86.7782	1620	2394	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207285.1	s__Microcoleus sp015207285	86.5655	1543	2394	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	86.5513	1669	2394	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	86.4214	1774	2394	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	86.1888	1656	2394	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	83.6783	1163	2394	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	83.2065	1207	2394	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 22:07:38,437] [INFO] GTDB search result was written to GCA_020883175.1_ASM2088317v1_genomic.fna/result_gtdb.tsv
[2023-06-28 22:07:38,438] [INFO] ===== GTDB Search completed =====
[2023-06-28 22:07:38,442] [INFO] DFAST_QC result json was written to GCA_020883175.1_ASM2088317v1_genomic.fna/dqc_result.json
[2023-06-28 22:07:38,442] [INFO] DFAST_QC completed!
[2023-06-28 22:07:38,442] [INFO] Total running time: 0h2m14s