[2024-01-25 20:03:50,608] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:50,610] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:50,610] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3fd1c22-f48a-401d-80e9-f461c9588b5d/dqc_reference
[2024-01-25 20:03:51,921] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:51,922] [INFO] Task started: Prodigal
[2024-01-25 20:03:51,922] [INFO] Running command: gunzip -c /var/lib/cwl/stg0375e436-53fd-41b6-9258-11ecf3f1b58f/GCF_017569225.1_ASM1756922v1_genomic.fna.gz | prodigal -d GCF_017569225.1_ASM1756922v1_genomic.fna/cds.fna -a GCF_017569225.1_ASM1756922v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:04:02,594] [INFO] Task succeeded: Prodigal
[2024-01-25 20:04:02,594] [INFO] Task started: HMMsearch
[2024-01-25 20:04:02,594] [INFO] Running command: hmmsearch --tblout GCF_017569225.1_ASM1756922v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3fd1c22-f48a-401d-80e9-f461c9588b5d/dqc_reference/reference_markers.hmm GCF_017569225.1_ASM1756922v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:04:02,838] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:04:02,839] [INFO] Found 6/6 markers.
[2024-01-25 20:04:02,881] [INFO] Query marker FASTA was written to GCF_017569225.1_ASM1756922v1_genomic.fna/markers.fasta
[2024-01-25 20:04:02,881] [INFO] Task started: Blastn
[2024-01-25 20:04:02,881] [INFO] Running command: blastn -query GCF_017569225.1_ASM1756922v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3fd1c22-f48a-401d-80e9-f461c9588b5d/dqc_reference/reference_markers.fasta -out GCF_017569225.1_ASM1756922v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:04,152] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:04,155] [INFO] Selected 27 target genomes.
[2024-01-25 20:04:04,155] [INFO] Target genome list was writen to GCF_017569225.1_ASM1756922v1_genomic.fna/target_genomes.txt
[2024-01-25 20:04:04,181] [INFO] Task started: fastANI
[2024-01-25 20:04:04,181] [INFO] Running command: fastANI --query /var/lib/cwl/stg0375e436-53fd-41b6-9258-11ecf3f1b58f/GCF_017569225.1_ASM1756922v1_genomic.fna.gz --refList GCF_017569225.1_ASM1756922v1_genomic.fna/target_genomes.txt --output GCF_017569225.1_ASM1756922v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:04:29,341] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:29,342] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3fd1c22-f48a-401d-80e9-f461c9588b5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:04:29,342] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3fd1c22-f48a-401d-80e9-f461c9588b5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:04:29,358] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:04:29,358] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:04:29,358] [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
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	80.0524	742	1465	95	below_threshold
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	79.9972	609	1465	95	below_threshold
Cellulomonas timonensis	strain=SN7	GCA_900046455.1	1689271	1689271	type	True	79.7573	608	1465	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	79.7162	621	1465	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	79.7079	596	1465	95	below_threshold
Cellulomonas rhizosphaerae	strain=NEAU-TCZ24	GCA_003470205.1	2293719	2293719	type	True	79.6419	561	1465	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.6007	627	1465	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	79.4956	607	1465	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	79.4936	600	1465	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.4597	685	1465	95	below_threshold
Cellulomonas humilata	strain=ATCC 25174	GCA_013359775.1	144055	144055	type	True	79.3758	658	1465	95	below_threshold
Cellulomonas uda	strain=NBRC 3747	GCA_006538705.1	1714	1714	type	True	79.3541	580	1465	95	below_threshold
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	79.283	618	1465	95	below_threshold
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	79.1715	552	1465	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	79.1325	546	1465	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	79.1015	606	1465	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	79.0532	608	1465	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	79.0054	636	1465	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	78.9688	632	1465	95	below_threshold
Sanguibacter keddieii	strain=DSM 10542	GCA_000024925.1	60920	60920	type	True	78.9502	540	1465	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	78.8284	549	1465	95	below_threshold
Cellulosimicrobium arenosum	strain=KCTC 49039	GCA_014837295.1	2708133	2708133	type	True	78.6988	545	1465	95	below_threshold
Sanguibacter inulinus	strain=DSM 100099	GCA_013415325.1	60922	60922	type	True	78.5743	496	1465	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.7861	428	1465	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	77.2519	431	1465	95	below_threshold
Sinomonas mesophila	strain=MPKL 26	GCA_001999765.1	1531955	1531955	type	True	77.0513	337	1465	95	below_threshold
Actinophytocola oryzae	strain=DSM 45499	GCA_004364325.1	502181	502181	type	True	75.7863	417	1465	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:04:29,360] [INFO] DFAST Taxonomy check result was written to GCF_017569225.1_ASM1756922v1_genomic.fna/tc_result.tsv
[2024-01-25 20:04:29,360] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:04:29,360] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:04:29,360] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3fd1c22-f48a-401d-80e9-f461c9588b5d/dqc_reference/checkm_data
[2024-01-25 20:04:29,361] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:04:29,403] [INFO] Task started: CheckM
[2024-01-25 20:04:29,403] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017569225.1_ASM1756922v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017569225.1_ASM1756922v1_genomic.fna/checkm_input GCF_017569225.1_ASM1756922v1_genomic.fna/checkm_result
[2024-01-25 20:05:13,940] [INFO] Task succeeded: CheckM
[2024-01-25 20:05:13,941] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:05:13,956] [INFO] ===== Completeness check finished =====
[2024-01-25 20:05:13,957] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:05:13,957] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017569225.1_ASM1756922v1_genomic.fna/markers.fasta)
[2024-01-25 20:05:13,957] [INFO] Task started: Blastn
[2024-01-25 20:05:13,957] [INFO] Running command: blastn -query GCF_017569225.1_ASM1756922v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3fd1c22-f48a-401d-80e9-f461c9588b5d/dqc_reference/reference_markers_gtdb.fasta -out GCF_017569225.1_ASM1756922v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:15,920] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:15,923] [INFO] Selected 16 target genomes.
[2024-01-25 20:05:15,923] [INFO] Target genome list was writen to GCF_017569225.1_ASM1756922v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:05:15,945] [INFO] Task started: fastANI
[2024-01-25 20:05:15,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg0375e436-53fd-41b6-9258-11ecf3f1b58f/GCF_017569225.1_ASM1756922v1_genomic.fna.gz --refList GCF_017569225.1_ASM1756922v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017569225.1_ASM1756922v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:31,019] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:31,029] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:05:31,029] [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_017569225.1	s__Cellulomonas sp017569225	100.0	1465	1465	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004168625.1	s__Cellulomonas sp004168625	82.464	792	1465	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012952065.1	s__Cellulomonas fimi_A	81.0779	654	1465	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538745.1	s__Cellulomonas cellasea	80.1465	730	1465	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.79	95.59	0.95	0.91	3	-
GCF_003115775.1	s__Cellulomonas sp003115775	80.0734	642	1465	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991755.1	s__Cellulomonas aerilata	80.0642	619	1465	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409305.1	s__Cellulomonas soli	79.7221	616	1465	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004306155.1	s__Cellulomonas biazotea	79.7213	594	1465	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900046455.1	s__Cellulomonas timonensis	79.7064	613	1465	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003470205.1	s__Cellulomonas rhizosphaerae	79.6597	559	1465	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359775.1	s__Cellulomonas humilata	79.406	654	1465	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538705.1	s__Cellulomonas uda	79.3756	578	1465	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.69	98.01	0.94	0.90	4	-
GCF_007989805.1	s__Cellulomonas xylanilytica	79.25	624	1465	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010287905.1	s__Cellulosimicrobium fucosivorans	78.9948	628	1465	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.84	98.55	0.94	0.90	6	-
GCF_000024925.1	s__Sanguibacter keddieii	78.9362	540	1465	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013415325.1	s__Sanguibacter inulinus	78.5913	493	1465	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sanguibacter	95.0	98.94	97.89	0.97	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:05:31,037] [INFO] GTDB search result was written to GCF_017569225.1_ASM1756922v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:31,037] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:31,041] [INFO] DFAST_QC result json was written to GCF_017569225.1_ASM1756922v1_genomic.fna/dqc_result.json
[2024-01-25 20:05:31,041] [INFO] DFAST_QC completed!
[2024-01-25 20:05:31,041] [INFO] Total running time: 0h1m40s