[2024-01-24 12:39:48,048] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:48,051] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:48,051] [INFO] DQC Reference Directory: /var/lib/cwl/stg4739cef3-e12a-4416-810d-bbb8d0fdd7f9/dqc_reference
[2024-01-24 12:39:49,247] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:49,248] [INFO] Task started: Prodigal
[2024-01-24 12:39:49,248] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0fa094c-e089-4c4b-aa76-d2baf4387d54/GCF_009755355.1_ASM975535v1_genomic.fna.gz | prodigal -d GCF_009755355.1_ASM975535v1_genomic.fna/cds.fna -a GCF_009755355.1_ASM975535v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:02,221] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:02,222] [INFO] Task started: HMMsearch
[2024-01-24 12:40:02,222] [INFO] Running command: hmmsearch --tblout GCF_009755355.1_ASM975535v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4739cef3-e12a-4416-810d-bbb8d0fdd7f9/dqc_reference/reference_markers.hmm GCF_009755355.1_ASM975535v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:02,454] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:02,456] [INFO] Found 6/6 markers.
[2024-01-24 12:40:02,500] [INFO] Query marker FASTA was written to GCF_009755355.1_ASM975535v1_genomic.fna/markers.fasta
[2024-01-24 12:40:02,501] [INFO] Task started: Blastn
[2024-01-24 12:40:02,501] [INFO] Running command: blastn -query GCF_009755355.1_ASM975535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4739cef3-e12a-4416-810d-bbb8d0fdd7f9/dqc_reference/reference_markers.fasta -out GCF_009755355.1_ASM975535v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:03,135] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:03,138] [INFO] Selected 22 target genomes.
[2024-01-24 12:40:03,138] [INFO] Target genome list was writen to GCF_009755355.1_ASM975535v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:03,152] [INFO] Task started: fastANI
[2024-01-24 12:40:03,152] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0fa094c-e089-4c4b-aa76-d2baf4387d54/GCF_009755355.1_ASM975535v1_genomic.fna.gz --refList GCF_009755355.1_ASM975535v1_genomic.fna/target_genomes.txt --output GCF_009755355.1_ASM975535v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:21,191] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:21,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4739cef3-e12a-4416-810d-bbb8d0fdd7f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:21,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4739cef3-e12a-4416-810d-bbb8d0fdd7f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:21,207] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:40:21,207] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:40:21,207] [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
Deinococcus multiflagellatus	strain=KACC 19287	GCA_020166415.1	1656887	1656887	type	True	83.2526	921	1532	95	below_threshold
Deinococcus arcticus	strain=OD32	GCA_003028415.1	2136176	2136176	type	True	83.0439	893	1532	95	below_threshold
Deinococcus aquaedulcis	strain=SYSU M42101	GCA_019693445.1	2840455	2840455	type	True	82.8931	919	1532	95	below_threshold
Deinococcus actinosclerus	strain=BM2	GCA_001507665.1	1768108	1768108	type	True	79.8054	651	1532	95	below_threshold
Deinococcus arenae	strain=JCM 31047	GCA_014647995.1	1452751	1452751	type	True	79.5784	680	1532	95	below_threshold
Deinococcus kurensis	strain=KR-1	GCA_009687825.1	2662757	2662757	type	True	79.5497	707	1532	95	below_threshold
Deinococcus soli (ex Cha et al. 2016)	strain=N5	GCA_001007995.1	1309411	1309411	type	True	79.4618	642	1532	95	below_threshold
Deinococcus radiotolerans	strain=JCM 19173	GCA_014647435.1	1309407	1309407	type	True	79.4242	663	1532	95	below_threshold
Deinococcus gobiensis	strain=I-0	GCA_000252445.1	502394	502394	type	True	79.4092	582	1532	95	below_threshold
Deinococcus aerophilus	strain=JCM 15443	GCA_014647075.1	522488	522488	type	True	79.3905	569	1532	95	below_threshold
Deinococcus saudiensis	strain=CGMCC 1.15089	GCA_014640655.1	1765963	1765963	type	True	79.3762	696	1532	95	below_threshold
Deinococcus radiopugnans	strain=ATCC 19172	GCA_006335125.1	57497	57497	type	True	79.3002	611	1532	95	below_threshold
Deinococcus radiopugnans	strain=DSM 12027	GCA_014201625.1	57497	57497	type	True	79.2881	615	1532	95	below_threshold
Deinococcus daejeonensis	strain=JCM 16918	GCA_014647175.1	1007098	1007098	type	True	79.2814	667	1532	95	below_threshold
Deinococcus aerolatus	strain=JCM 15442	GCA_014647055.1	522487	522487	type	True	79.0785	574	1532	95	below_threshold
Deinococcus malanensis	strain=JCM 30331	GCA_014647655.1	1706855	1706855	type	True	78.9237	485	1532	95	below_threshold
Deinococcus deserti	strain=VCD115	GCA_000020685.1	310783	310783	type	True	78.6638	437	1532	95	below_threshold
Deinococcus radiodurans	strain=DSM 20539	GCA_000685985.1	1299	1299	type	True	78.4276	459	1532	95	below_threshold
Deinococcus radiodurans	strain=R1	GCA_000008565.1	1299	1299	type	True	78.3392	478	1532	95	below_threshold
Deinobacterium chartae	strain=DSM 21458	GCA_014202645.1	521158	521158	type	True	76.6759	207	1532	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:21,209] [INFO] DFAST Taxonomy check result was written to GCF_009755355.1_ASM975535v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:21,210] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:21,210] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:21,210] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4739cef3-e12a-4416-810d-bbb8d0fdd7f9/dqc_reference/checkm_data
[2024-01-24 12:40:21,211] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:21,258] [INFO] Task started: CheckM
[2024-01-24 12:40:21,258] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009755355.1_ASM975535v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009755355.1_ASM975535v1_genomic.fna/checkm_input GCF_009755355.1_ASM975535v1_genomic.fna/checkm_result
[2024-01-24 12:41:00,434] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:00,435] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:00,454] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:00,455] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:00,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009755355.1_ASM975535v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:00,455] [INFO] Task started: Blastn
[2024-01-24 12:41:00,455] [INFO] Running command: blastn -query GCF_009755355.1_ASM975535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4739cef3-e12a-4416-810d-bbb8d0fdd7f9/dqc_reference/reference_markers_gtdb.fasta -out GCF_009755355.1_ASM975535v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:01,338] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:01,341] [INFO] Selected 21 target genomes.
[2024-01-24 12:41:01,342] [INFO] Target genome list was writen to GCF_009755355.1_ASM975535v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:01,369] [INFO] Task started: fastANI
[2024-01-24 12:41:01,370] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0fa094c-e089-4c4b-aa76-d2baf4387d54/GCF_009755355.1_ASM975535v1_genomic.fna.gz --refList GCF_009755355.1_ASM975535v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009755355.1_ASM975535v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:20,795] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:20,811] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:20,811] [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_009755355.1	s__Deinococcus sp009755355	100.0	1529	1532	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003028415.1	s__Deinococcus sp003028415	83.0125	896	1532	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507665.1	s__Deinococcus actinosclerus	79.808	652	1532	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.26	96.21	0.94	0.94	4	-
GCF_002017875.1	s__Deinococcus sp002017875	79.6766	702	1532	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.85	96.85	0.84	0.84	2	-
GCF_002198095.1	s__Deinococcus indicus	79.6152	692	1532	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.28	99.28	0.90	0.90	2	-
GCF_001007995.1	s__Deinococcus soli	79.4925	638	1532	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.09	98.03	0.94	0.93	3	-
GCF_014647435.1	s__Deinococcus radiotolerans	79.4332	663	1532	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000252445.1	s__Deinococcus gobiensis	79.4212	580	1532	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647075.1	s__Deinococcus aerophilus	79.4175	566	1532	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001485435.1	s__Deinococcus grandis	79.376	686	1532	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.65	95.40	0.88	0.83	5	-
GCF_014648135.1	s__Deinococcus sedimenti	79.3516	666	1532	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335125.1	s__Deinococcus radiopugnans	79.2772	613	1532	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.45	97.61	0.92	0.87	4	-
GCF_014201805.1	s__Deinococcus metalli	78.9376	607	1532	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014647655.1	s__Deinococcus malanensis	78.9228	486	1532	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020685.1	s__Deinococcus deserti	78.6413	440	1532	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201875.1	s__Deinococcus humi	78.4368	505	1532	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000008565.1	s__Deinococcus radiodurans	78.3446	478	1532	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.94	99.91	0.99	0.99	8	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:20,813] [INFO] GTDB search result was written to GCF_009755355.1_ASM975535v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:20,813] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:20,817] [INFO] DFAST_QC result json was written to GCF_009755355.1_ASM975535v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:20,817] [INFO] DFAST_QC completed!
[2024-01-24 12:41:20,817] [INFO] Total running time: 0h1m33s