[2023-06-18 11:25:26,281] [INFO] DFAST_QC pipeline started.
[2023-06-18 11:25:26,286] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 11:25:26,286] [INFO] DQC Reference Directory: /var/lib/cwl/stg26f6e8f7-0390-443a-a078-1f16d87e98b9/dqc_reference
[2023-06-18 11:25:28,277] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 11:25:28,278] [INFO] Task started: Prodigal
[2023-06-18 11:25:28,278] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a6b2ba6-0d1c-498a-a2a7-808fe804d045/GCA_018399015.1_ASM1839901v1_genomic.fna.gz | prodigal -d GCA_018399015.1_ASM1839901v1_genomic.fna/cds.fna -a GCA_018399015.1_ASM1839901v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 11:25:48,065] [INFO] Task succeeded: Prodigal
[2023-06-18 11:25:48,065] [INFO] Task started: HMMsearch
[2023-06-18 11:25:48,065] [INFO] Running command: hmmsearch --tblout GCA_018399015.1_ASM1839901v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26f6e8f7-0390-443a-a078-1f16d87e98b9/dqc_reference/reference_markers.hmm GCA_018399015.1_ASM1839901v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 11:25:48,258] [INFO] Task succeeded: HMMsearch
[2023-06-18 11:25:48,260] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7a6b2ba6-0d1c-498a-a2a7-808fe804d045/GCA_018399015.1_ASM1839901v1_genomic.fna.gz]
[2023-06-18 11:25:48,288] [INFO] Query marker FASTA was written to GCA_018399015.1_ASM1839901v1_genomic.fna/markers.fasta
[2023-06-18 11:25:48,288] [INFO] Task started: Blastn
[2023-06-18 11:25:48,288] [INFO] Running command: blastn -query GCA_018399015.1_ASM1839901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26f6e8f7-0390-443a-a078-1f16d87e98b9/dqc_reference/reference_markers.fasta -out GCA_018399015.1_ASM1839901v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:25:48,895] [INFO] Task succeeded: Blastn
[2023-06-18 11:25:48,899] [INFO] Selected 26 target genomes.
[2023-06-18 11:25:48,900] [INFO] Target genome list was writen to GCA_018399015.1_ASM1839901v1_genomic.fna/target_genomes.txt
[2023-06-18 11:25:48,905] [INFO] Task started: fastANI
[2023-06-18 11:25:48,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a6b2ba6-0d1c-498a-a2a7-808fe804d045/GCA_018399015.1_ASM1839901v1_genomic.fna.gz --refList GCA_018399015.1_ASM1839901v1_genomic.fna/target_genomes.txt --output GCA_018399015.1_ASM1839901v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 11:26:03,854] [INFO] Task succeeded: fastANI
[2023-06-18 11:26:03,855] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26f6e8f7-0390-443a-a078-1f16d87e98b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 11:26:03,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26f6e8f7-0390-443a-a078-1f16d87e98b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 11:26:03,870] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 11:26:03,870] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 11:26:03,870] [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
Parasynechococcus marenigrum	strain=WH 8102	GCA_000195975.1	2881428	2881428	type	True	78.8136	286	1060	95	below_threshold
Gloeobacter violaceus	strain=PCC 7421	GCA_000011385.1	33072	33072	type	True	76.0242	84	1060	95	below_threshold
Guyparkeria hydrothermalis	strain=R3	GCA_023555375.1	923	923	type	True	75.6039	52	1060	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.5344	83	1060	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	75.455	73	1060	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	75.4468	131	1060	95	below_threshold
Mycolicibacterium bacteremicum	strain=DSM 45578	GCA_002086115.1	564198	564198	type	True	75.3228	60	1060	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	75.2901	62	1060	95	below_threshold
Oceanithermus profundus	strain=DSM 14977	GCA_000183745.1	187137	187137	type	True	75.251	62	1060	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	75.2121	88	1060	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	75.1658	87	1060	95	below_threshold
Halomonas alimentaria	strain=DSM 15356	GCA_009902005.1	147248	147248	type	True	75.1557	89	1060	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	75.1527	111	1060	95	below_threshold
Pseudoxanthomonas spadix	strain=DSM 18855	GCA_003703395.1	415229	415229	type	True	75.0894	73	1060	95	below_threshold
Methylorubrum salsuginis	strain=CGMCC 1.6474	GCA_900114375.1	414703	414703	type	True	74.9796	65	1060	95	below_threshold
Nocardia grenadensis	strain=NBRC 108939	GCA_001613445.1	931537	931537	type	True	74.8661	53	1060	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	74.8388	101	1060	95	below_threshold
Deinococcus radiopugnans	strain=ATCC 19172	GCA_006335125.1	57497	57497	type	True	74.775	60	1060	95	below_threshold
Deinococcus radiopugnans	strain=DSM 12027	GCA_014201625.1	57497	57497	type	True	74.738	60	1060	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 11:26:03,872] [INFO] DFAST Taxonomy check result was written to GCA_018399015.1_ASM1839901v1_genomic.fna/tc_result.tsv
[2023-06-18 11:26:03,872] [INFO] ===== Taxonomy check completed =====
[2023-06-18 11:26:03,872] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 11:26:03,872] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26f6e8f7-0390-443a-a078-1f16d87e98b9/dqc_reference/checkm_data
[2023-06-18 11:26:03,873] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 11:26:03,904] [INFO] Task started: CheckM
[2023-06-18 11:26:03,904] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018399015.1_ASM1839901v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018399015.1_ASM1839901v1_genomic.fna/checkm_input GCA_018399015.1_ASM1839901v1_genomic.fna/checkm_result
[2023-06-18 11:27:08,240] [INFO] Task succeeded: CheckM
[2023-06-18 11:27:08,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 11:27:08,259] [INFO] ===== Completeness check finished =====
[2023-06-18 11:27:08,259] [INFO] ===== Start GTDB Search =====
[2023-06-18 11:27:08,260] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018399015.1_ASM1839901v1_genomic.fna/markers.fasta)
[2023-06-18 11:27:08,260] [INFO] Task started: Blastn
[2023-06-18 11:27:08,260] [INFO] Running command: blastn -query GCA_018399015.1_ASM1839901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26f6e8f7-0390-443a-a078-1f16d87e98b9/dqc_reference/reference_markers_gtdb.fasta -out GCA_018399015.1_ASM1839901v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:27:09,098] [INFO] Task succeeded: Blastn
[2023-06-18 11:27:09,101] [INFO] Selected 11 target genomes.
[2023-06-18 11:27:09,101] [INFO] Target genome list was writen to GCA_018399015.1_ASM1839901v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 11:27:09,148] [INFO] Task started: fastANI
[2023-06-18 11:27:09,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a6b2ba6-0d1c-498a-a2a7-808fe804d045/GCA_018399015.1_ASM1839901v1_genomic.fna.gz --refList GCA_018399015.1_ASM1839901v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018399015.1_ASM1839901v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 11:27:16,335] [INFO] Task succeeded: fastANI
[2023-06-18 11:27:16,345] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 11:27:16,346] [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_018399015.1	s__NIES-981 sp018399015	100.0	1060	1060	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018400215.1	s__NIES-981 sp018400215	84.665	366	1060	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	99.01	99.01	0.86	0.86	2	-
GCA_016882525.1	s__NIES-981 sp016882525	84.5865	637	1060	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007694915.1	s__NIES-981 sp007694915	84.2083	620	1060	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007135755.1	s__NIES-981 sp007135755	84.1234	590	1060	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	99.54	99.54	0.92	0.92	2	-
GCF_000155635.1	s__NIES-981 sp000155635	83.0388	608	1060	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900088535.1	s__NIES-981 sp900088535	83.0037	628	1060	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001039265.1	s__NIES-981 sp001039265	82.9157	476	1060	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903862155.1	s__UBA5018 sp903862155	82.4039	417	1060	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__UBA5018	95.0	99.05	99.00	0.85	0.80	5	-
GCF_003003925.1	s__Cyanobium minutissimum	81.7957	596	1060	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	95.57	95.57	0.88	0.88	2	-
GCA_003249115.1	s__QBMD01 sp003249115	79.9065	455	1060	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__QBMD01	95.0	98.24	98.24	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-06-18 11:27:16,347] [INFO] GTDB search result was written to GCA_018399015.1_ASM1839901v1_genomic.fna/result_gtdb.tsv
[2023-06-18 11:27:16,348] [INFO] ===== GTDB Search completed =====
[2023-06-18 11:27:16,352] [INFO] DFAST_QC result json was written to GCA_018399015.1_ASM1839901v1_genomic.fna/dqc_result.json
[2023-06-18 11:27:16,352] [INFO] DFAST_QC completed!
[2023-06-18 11:27:16,352] [INFO] Total running time: 0h1m50s