[2024-01-24 11:58:20,620] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:20,621] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:20,622] [INFO] DQC Reference Directory: /var/lib/cwl/stg13b0fb8b-6a73-42f7-a214-2225ef254ba9/dqc_reference
[2024-01-24 11:58:21,831] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:21,831] [INFO] Task started: Prodigal
[2024-01-24 11:58:21,832] [INFO] Running command: gunzip -c /var/lib/cwl/stg66ae1f35-bd5e-4818-855c-e5c34349f171/GCF_004786095.1_ASM478609v1_genomic.fna.gz | prodigal -d GCF_004786095.1_ASM478609v1_genomic.fna/cds.fna -a GCF_004786095.1_ASM478609v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:58:30,979] [INFO] Task succeeded: Prodigal
[2024-01-24 11:58:30,980] [INFO] Task started: HMMsearch
[2024-01-24 11:58:30,980] [INFO] Running command: hmmsearch --tblout GCF_004786095.1_ASM478609v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13b0fb8b-6a73-42f7-a214-2225ef254ba9/dqc_reference/reference_markers.hmm GCF_004786095.1_ASM478609v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:58:31,232] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:58:31,234] [INFO] Found 6/6 markers.
[2024-01-24 11:58:31,267] [INFO] Query marker FASTA was written to GCF_004786095.1_ASM478609v1_genomic.fna/markers.fasta
[2024-01-24 11:58:31,267] [INFO] Task started: Blastn
[2024-01-24 11:58:31,267] [INFO] Running command: blastn -query GCF_004786095.1_ASM478609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13b0fb8b-6a73-42f7-a214-2225ef254ba9/dqc_reference/reference_markers.fasta -out GCF_004786095.1_ASM478609v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:58:32,508] [INFO] Task succeeded: Blastn
[2024-01-24 11:58:32,512] [INFO] Selected 27 target genomes.
[2024-01-24 11:58:32,513] [INFO] Target genome list was writen to GCF_004786095.1_ASM478609v1_genomic.fna/target_genomes.txt
[2024-01-24 11:58:32,561] [INFO] Task started: fastANI
[2024-01-24 11:58:32,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg66ae1f35-bd5e-4818-855c-e5c34349f171/GCF_004786095.1_ASM478609v1_genomic.fna.gz --refList GCF_004786095.1_ASM478609v1_genomic.fna/target_genomes.txt --output GCF_004786095.1_ASM478609v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:58:55,084] [INFO] Task succeeded: fastANI
[2024-01-24 11:58:55,084] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13b0fb8b-6a73-42f7-a214-2225ef254ba9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:58:55,085] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13b0fb8b-6a73-42f7-a214-2225ef254ba9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:58:55,107] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:58:55,108] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:58:55,108] [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
Beutenbergia cavernae	strain=DSM 12333	GCA_000023105.1	84757	84757	type	True	78.2649	525	1142	95	below_threshold
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	78.2136	410	1142	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.1637	440	1142	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	78.14	427	1142	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	78.08	473	1142	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	78.0515	427	1142	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	78.0332	439	1142	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	78.0307	514	1142	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	77.9816	424	1142	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	77.96	506	1142	95	below_threshold
Georgenia thermotolerans	strain=DSM 21501	GCA_009299305.1	527326	527326	type	True	77.9164	403	1142	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	77.9138	463	1142	95	below_threshold
Georgenia thermotolerans	strain=NBRC 104148	GCA_009193185.1	527326	527326	type	True	77.9104	425	1142	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	77.8876	469	1142	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	77.8808	438	1142	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	77.8526	459	1142	95	below_threshold
Cellulomonas oligotrophica	strain=DSM 24482	GCA_013409875.1	931536	931536	type	True	77.8275	493	1142	95	below_threshold
Cellulomonas carbonis	strain=T26	GCA_000767175.1	1386092	1386092	type	True	77.7913	430	1142	95	below_threshold
Georgenia ruanii	strain=JCM 15130	GCA_009193175.1	348442	348442	type	True	77.7705	427	1142	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.7503	487	1142	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.7415	388	1142	95	below_threshold
Sanguibacter suarezii	strain=NBRC 16159	GCA_001552735.1	60921	60921	type	True	77.7121	370	1142	95	below_threshold
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	77.5264	404	1142	95	below_threshold
Microbispora camponoti	strain=2C-HV3	GCA_014712745.1	1677852	1677852	type	True	76.0452	304	1142	95	below_threshold
Microbispora siamensis	strain=NBRC 104113	GCA_016863095.1	564413	564413	type	True	75.8958	362	1142	95	below_threshold
Microbispora catharanthi	strain=CR1-09	GCA_006334915.2	1712871	1712871	type	True	75.8214	345	1142	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	75.6686	390	1142	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:58:55,109] [INFO] DFAST Taxonomy check result was written to GCF_004786095.1_ASM478609v1_genomic.fna/tc_result.tsv
[2024-01-24 11:58:55,110] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:58:55,110] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:58:55,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13b0fb8b-6a73-42f7-a214-2225ef254ba9/dqc_reference/checkm_data
[2024-01-24 11:58:55,111] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:58:55,144] [INFO] Task started: CheckM
[2024-01-24 11:58:55,144] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004786095.1_ASM478609v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004786095.1_ASM478609v1_genomic.fna/checkm_input GCF_004786095.1_ASM478609v1_genomic.fna/checkm_result
[2024-01-24 11:59:43,247] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:43,248] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:43,266] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:43,266] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:43,267] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004786095.1_ASM478609v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:43,267] [INFO] Task started: Blastn
[2024-01-24 11:59:43,267] [INFO] Running command: blastn -query GCF_004786095.1_ASM478609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13b0fb8b-6a73-42f7-a214-2225ef254ba9/dqc_reference/reference_markers_gtdb.fasta -out GCF_004786095.1_ASM478609v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:45,182] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:45,185] [INFO] Selected 13 target genomes.
[2024-01-24 11:59:45,186] [INFO] Target genome list was writen to GCF_004786095.1_ASM478609v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:45,197] [INFO] Task started: fastANI
[2024-01-24 11:59:45,198] [INFO] Running command: fastANI --query /var/lib/cwl/stg66ae1f35-bd5e-4818-855c-e5c34349f171/GCF_004786095.1_ASM478609v1_genomic.fna.gz --refList GCF_004786095.1_ASM478609v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004786095.1_ASM478609v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:59:56,587] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:56,600] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:59:56,600] [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_004786095.1	s__Serinibacter_A arcticus	100.0	1142	1142	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Serinibacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003121705.1	s__Serinibacter_A sp003121705	84.4408	885	1142	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Serinibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006351005.1	s__Miniimonas arenae	80.6771	582	1142	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Miniimonas	95.0	98.18	97.40	0.91	0.83	3	-
GCF_003751805.1	s__Salana multivorans	79.7543	581	1142	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Salana	95.0	99.05	99.05	0.93	0.93	2	-
GCF_002563925.1	s__Serinibacter salmoneus	79.1121	453	1142	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Serinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696205.1	s__Cellulomonas sp003696205	78.0466	472	1142	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116375.1	s__Oceanitalea nanhaiensis	78.013	430	1142	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Oceanitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000767215.1	s__Actinotalea fermentans	77.9247	303	1142	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009193185.1	s__Georgenia thermotolerans	77.8857	428	1142	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_006538705.1	s__Cellulomonas uda	77.8857	419	1142	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.69	98.01	0.94	0.90	4	-
GCF_009193175.1	s__Georgenia ruanii	77.7372	432	1142	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006352065.1	s__Georgenia sp006352065	77.7097	390	1142	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	95.59	95.59	0.82	0.82	2	-
GCF_011634835.1	s__Isoptericola sp011634835	77.6228	447	1142	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:59:56,602] [INFO] GTDB search result was written to GCF_004786095.1_ASM478609v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:59:56,602] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:59:56,606] [INFO] DFAST_QC result json was written to GCF_004786095.1_ASM478609v1_genomic.fna/dqc_result.json
[2024-01-24 11:59:56,607] [INFO] DFAST_QC completed!
[2024-01-24 11:59:56,607] [INFO] Total running time: 0h1m36s