[2024-01-25 19:47:50,962] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:50,963] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:50,963] [INFO] DQC Reference Directory: /var/lib/cwl/stg010ca38b-5688-4a61-9ff2-bfcf3338bc45/dqc_reference
[2024-01-25 19:47:52,070] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:52,071] [INFO] Task started: Prodigal
[2024-01-25 19:47:52,071] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5a11cd8-3b16-4457-8c43-b4f483c89440/GCF_012931845.1_ASM1293184v1_genomic.fna.gz | prodigal -d GCF_012931845.1_ASM1293184v1_genomic.fna/cds.fna -a GCF_012931845.1_ASM1293184v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:48:01,093] [INFO] Task succeeded: Prodigal
[2024-01-25 19:48:01,093] [INFO] Task started: HMMsearch
[2024-01-25 19:48:01,093] [INFO] Running command: hmmsearch --tblout GCF_012931845.1_ASM1293184v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg010ca38b-5688-4a61-9ff2-bfcf3338bc45/dqc_reference/reference_markers.hmm GCF_012931845.1_ASM1293184v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:48:01,320] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:48:01,323] [INFO] Found 6/6 markers.
[2024-01-25 19:48:01,350] [INFO] Query marker FASTA was written to GCF_012931845.1_ASM1293184v1_genomic.fna/markers.fasta
[2024-01-25 19:48:01,350] [INFO] Task started: Blastn
[2024-01-25 19:48:01,351] [INFO] Running command: blastn -query GCF_012931845.1_ASM1293184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg010ca38b-5688-4a61-9ff2-bfcf3338bc45/dqc_reference/reference_markers.fasta -out GCF_012931845.1_ASM1293184v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:02,687] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:02,690] [INFO] Selected 16 target genomes.
[2024-01-25 19:48:02,690] [INFO] Target genome list was writen to GCF_012931845.1_ASM1293184v1_genomic.fna/target_genomes.txt
[2024-01-25 19:48:02,705] [INFO] Task started: fastANI
[2024-01-25 19:48:02,705] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5a11cd8-3b16-4457-8c43-b4f483c89440/GCF_012931845.1_ASM1293184v1_genomic.fna.gz --refList GCF_012931845.1_ASM1293184v1_genomic.fna/target_genomes.txt --output GCF_012931845.1_ASM1293184v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:48:15,344] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:15,344] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg010ca38b-5688-4a61-9ff2-bfcf3338bc45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:48:15,345] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg010ca38b-5688-4a61-9ff2-bfcf3338bc45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:48:15,355] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:48:15,355] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:48:15,355] [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 taurus	strain=P40-2	GCA_012931845.1	2729175	2729175	type	True	100.0	1143	1145	95	conclusive
Cellulomonas denverensis	strain=ATCC BAA-788	GCA_012396125.1	264297	264297	type	True	87.0567	908	1145	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	81.8121	746	1145	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	81.6543	730	1145	95	below_threshold
Cellulomonas timonensis	strain=SN7	GCA_900046455.1	1689271	1689271	type	True	79.5708	542	1145	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	79.4207	488	1145	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	79.4175	506	1145	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	79.2457	517	1145	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.2383	468	1145	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	79.2285	512	1145	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	79.1554	501	1145	95	below_threshold
Cellulomonas oligotrophica	strain=DSM 24482	GCA_013409875.1	931536	931536	type	True	79.1265	546	1145	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	78.9625	462	1145	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	78.3897	430	1145	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	78.3619	385	1145	95	below_threshold
Tsukamurella spumae	strain=DSM 44113	GCA_012396015.1	44753	44753	type	True	76.5985	211	1145	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:48:15,356] [INFO] DFAST Taxonomy check result was written to GCF_012931845.1_ASM1293184v1_genomic.fna/tc_result.tsv
[2024-01-25 19:48:15,357] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:48:15,357] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:48:15,357] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg010ca38b-5688-4a61-9ff2-bfcf3338bc45/dqc_reference/checkm_data
[2024-01-25 19:48:15,358] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:48:15,400] [INFO] Task started: CheckM
[2024-01-25 19:48:15,400] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012931845.1_ASM1293184v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012931845.1_ASM1293184v1_genomic.fna/checkm_input GCF_012931845.1_ASM1293184v1_genomic.fna/checkm_result
[2024-01-25 19:49:43,457] [INFO] Task succeeded: CheckM
[2024-01-25 19:49:43,458] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:49:43,475] [INFO] ===== Completeness check finished =====
[2024-01-25 19:49:43,475] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:49:43,476] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012931845.1_ASM1293184v1_genomic.fna/markers.fasta)
[2024-01-25 19:49:43,476] [INFO] Task started: Blastn
[2024-01-25 19:49:43,476] [INFO] Running command: blastn -query GCF_012931845.1_ASM1293184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg010ca38b-5688-4a61-9ff2-bfcf3338bc45/dqc_reference/reference_markers_gtdb.fasta -out GCF_012931845.1_ASM1293184v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:45,676] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:45,678] [INFO] Selected 17 target genomes.
[2024-01-25 19:49:45,678] [INFO] Target genome list was writen to GCF_012931845.1_ASM1293184v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:49:45,703] [INFO] Task started: fastANI
[2024-01-25 19:49:45,703] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5a11cd8-3b16-4457-8c43-b4f483c89440/GCF_012931845.1_ASM1293184v1_genomic.fna.gz --refList GCF_012931845.1_ASM1293184v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012931845.1_ASM1293184v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:50:01,424] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:01,435] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:50:01,435] [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
GCF_012931845.1	s__Cellulomonas taurus	100.0	1144	1145	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_012396125.1	s__Cellulomonas denverensis	87.0568	908	1145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_011603975.1	s__Cellulomonas sp011603975	82.3759	687	1145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005239125.1	s__Cellulomonas hominis_A	82.1189	689	1145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679345.1	s__Cellulomonas cellulans_A	82.0421	779	1145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862755.1	s__Cellulomonas pakistanensis	81.8608	738	1145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409475.1	s__Cellulomonas hominis_B	81.8343	746	1145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201095.1	s__Cellulomonas hominis	81.7682	751	1145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.15	98.63	0.95	0.92	4	-
GCF_003696205.1	s__Cellulomonas sp003696205	81.6733	702	1145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901521055.1	s__Cellulomonas hominis_C	81.611	700	1145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763765.1	s__Cellulomonas sp014763765	81.1632	639	1145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000212695.1	s__Cellulomonas fimi	79.1896	518	1145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	99.99	1.00	1.00	3	-
GCF_006386485.1	s__Cellulomonas oligotrophica	78.9738	548	1145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCA_016771945.1	s__Leucobacter sulfamidivorax	76.9266	172	1145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396015.1	s__Tsukamurella spumae	76.6091	210	1145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900631615.1	s__Tsukamurella paurometabola_A	76.605	231	1145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331005.1	s__Streptomyces turgidiscabies	76.4598	295	1145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.67	0.92	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:50:01,437] [INFO] GTDB search result was written to GCF_012931845.1_ASM1293184v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:50:01,437] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:50:01,444] [INFO] DFAST_QC result json was written to GCF_012931845.1_ASM1293184v1_genomic.fna/dqc_result.json
[2024-01-25 19:50:01,444] [INFO] DFAST_QC completed!
[2024-01-25 19:50:01,444] [INFO] Total running time: 0h2m10s