[2024-01-24 14:19:32,049] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:32,051] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:32,051] [INFO] DQC Reference Directory: /var/lib/cwl/stg769eac81-e089-474d-b552-42c93f608147/dqc_reference
[2024-01-24 14:19:33,442] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:33,447] [INFO] Task started: Prodigal
[2024-01-24 14:19:33,448] [INFO] Running command: gunzip -c /var/lib/cwl/stg03861405-f6d1-4299-a086-4f7635cbb3e9/GCF_006716265.1_ASM671626v1_genomic.fna.gz | prodigal -d GCF_006716265.1_ASM671626v1_genomic.fna/cds.fna -a GCF_006716265.1_ASM671626v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:42,536] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:42,536] [INFO] Task started: HMMsearch
[2024-01-24 14:19:42,536] [INFO] Running command: hmmsearch --tblout GCF_006716265.1_ASM671626v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg769eac81-e089-474d-b552-42c93f608147/dqc_reference/reference_markers.hmm GCF_006716265.1_ASM671626v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:42,857] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:42,858] [INFO] Found 6/6 markers.
[2024-01-24 14:19:42,897] [INFO] Query marker FASTA was written to GCF_006716265.1_ASM671626v1_genomic.fna/markers.fasta
[2024-01-24 14:19:42,898] [INFO] Task started: Blastn
[2024-01-24 14:19:42,898] [INFO] Running command: blastn -query GCF_006716265.1_ASM671626v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg769eac81-e089-474d-b552-42c93f608147/dqc_reference/reference_markers.fasta -out GCF_006716265.1_ASM671626v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:44,039] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:44,045] [INFO] Selected 26 target genomes.
[2024-01-24 14:19:44,045] [INFO] Target genome list was writen to GCF_006716265.1_ASM671626v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:44,064] [INFO] Task started: fastANI
[2024-01-24 14:19:44,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg03861405-f6d1-4299-a086-4f7635cbb3e9/GCF_006716265.1_ASM671626v1_genomic.fna.gz --refList GCF_006716265.1_ASM671626v1_genomic.fna/target_genomes.txt --output GCF_006716265.1_ASM671626v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:03,075] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:03,075] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg769eac81-e089-474d-b552-42c93f608147/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:03,075] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg769eac81-e089-474d-b552-42c93f608147/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:03,097] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:03,097] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:03,098] [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
Rarobacter faecitabidus	strain=DSM 4813	GCA_006716265.1	13243	13243	type	True	100.0	930	932	95	conclusive
Rarobacter incanus	strain=DSM 10596	GCA_006715765.1	153494	153494	type	True	78.9419	250	932	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.2219	237	932	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	78.1423	225	932	95	below_threshold
Promicromonospora kroppenstedtii	strain=DSM 19349	GCA_000515355.1	440482	440482	type	True	78.1148	190	932	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	78.0604	215	932	95	below_threshold
Cellulomonas gilvus	strain=ATCC 13127	GCA_000218545.1	11	11	type	True	78.0333	214	932	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	78.0197	215	932	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	77.9463	235	932	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	77.9443	207	932	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	77.8589	206	932	95	below_threshold
Cellulomonas oligotrophica	strain=DSM 24482	GCA_013409875.1	931536	931536	type	True	77.8167	207	932	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	77.8096	241	932	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	77.8052	237	932	95	below_threshold
Cellulomonas rhizosphaerae	strain=NEAU-TCZ24	GCA_003470205.1	2293719	2293719	type	True	77.8046	201	932	95	below_threshold
Sanguibacter suarezii	strain=NBRC 16159	GCA_001552735.1	60921	60921	type	True	77.7756	194	932	95	below_threshold
Promicromonospora sukumoe	strain=DSM 44121	GCA_014137995.1	88382	88382	type	True	77.7619	217	932	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	77.6521	202	932	95	below_threshold
Cellulomonas timonensis	strain=SN7	GCA_900046455.1	1689271	1689271	type	True	77.6415	206	932	95	below_threshold
Cellulomonas denverensis	strain=ATCC BAA-788	GCA_012396125.1	264297	264297	type	True	77.5314	193	932	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.4615	217	932	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	77.3763	120	932	95	below_threshold
Serinicoccus chungangensis	strain=CCUG 59777	GCA_006337125.1	767452	767452	type	True	76.5172	110	932	95	below_threshold
Nocardioides pelophilus	strain=CGMCC 4.7388	GCA_014180685.1	2172019	2172019	type	True	76.453	90	932	95	below_threshold
Nakamurella endophytica	strain=CGMCC 4.7308	GCA_014646215.1	1748367	1748367	type	True	76.2698	100	932	95	below_threshold
Streptosporangium amethystogenes	strain=NRRL B-2639	GCA_000721075.1	2002	2002	type	True	75.8752	115	932	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:03,099] [INFO] DFAST Taxonomy check result was written to GCF_006716265.1_ASM671626v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:03,100] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:03,100] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:03,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg769eac81-e089-474d-b552-42c93f608147/dqc_reference/checkm_data
[2024-01-24 14:20:03,101] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:03,132] [INFO] Task started: CheckM
[2024-01-24 14:20:03,132] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006716265.1_ASM671626v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006716265.1_ASM671626v1_genomic.fna/checkm_input GCF_006716265.1_ASM671626v1_genomic.fna/checkm_result
[2024-01-24 14:20:33,918] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:33,919] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.93%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:33,939] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:33,940] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:33,940] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006716265.1_ASM671626v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:33,940] [INFO] Task started: Blastn
[2024-01-24 14:20:33,941] [INFO] Running command: blastn -query GCF_006716265.1_ASM671626v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg769eac81-e089-474d-b552-42c93f608147/dqc_reference/reference_markers_gtdb.fasta -out GCF_006716265.1_ASM671626v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:35,523] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:35,527] [INFO] Selected 27 target genomes.
[2024-01-24 14:20:35,528] [INFO] Target genome list was writen to GCF_006716265.1_ASM671626v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:35,587] [INFO] Task started: fastANI
[2024-01-24 14:20:35,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg03861405-f6d1-4299-a086-4f7635cbb3e9/GCF_006716265.1_ASM671626v1_genomic.fna.gz --refList GCF_006716265.1_ASM671626v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006716265.1_ASM671626v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:51,640] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:51,667] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:51,668] [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_006716265.1	s__Rarobacter faecitabidus	100.0	930	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Rarobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006715765.1	s__Rarobacter incanus	78.9419	250	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Rarobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942335.1	s__Cellulosimicrobium sp001942335	78.4443	207	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009429125.1	s__Luteimicrobium xylanilyticum	78.3297	210	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Luteimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797595.1	s__Sediminihabitans luteus	78.1656	214	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000215105.1	s__Isoptericola variabilis_A	78.1423	219	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	99.96	99.96	0.98	0.98	2	-
GCF_001722485.1	s__Cellulosimicrobium cellulans_A	78.1198	203	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000218545.1	s__Cellulomonas gilvus	78.1111	214	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014852685.1	s__Flavimobilis rhizosphaerae	78.0503	194	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	95.20	95.20	0.83	0.83	2	-
GCF_001462455.1	s__Cellulomonas sp001462455	77.8998	211	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033115.1	s__Cellulomonas sp008033115	77.8874	236	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	96.34	96.34	0.91	0.91	2	-
GCF_003752595.1	s__Sediminihabitans sp003752595	77.8703	211	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004886325.1	s__Cellulomonas telluris	77.8424	207	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001750215.1	s__Xylanimonas variabilis_A	77.8288	196	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763765.1	s__Cellulomonas sp014763765	77.8229	191	932	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	77.7753	246	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.84	98.55	0.94	0.90	6	-
GCF_001552375.1	s__Cellulomonas iranensis	77.723	220	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.21	97.89	0.91	0.88	6	-
GCF_001019615.1	s__Cellulosimicrobium cellulans_E	77.7016	245	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.64	98.58	0.94	0.93	3	-
GCF_009996735.1	s__Actinotalea sp009996735	77.6643	191	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550025.1	s__Promicromonospora thailandica	77.6577	213	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862675.1	s__Cellulomonas chitinilytica	77.6492	220	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539945.1	s__Cellulosimicrobium cellulans	77.6243	226	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744555.1	s__Cellulomonas sp017744555	77.3795	200	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018275325.1	s__Nocardioides sp018275325	77.0665	116	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297305.1	s__FW305-bin1 sp004297305	76.5572	74	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__FW305-bin1;g__FW305-bin1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644415.1	s__Marmoricola endophyticus	76.5411	97	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014180685.1	s__Nocardioides pelophilus	76.4306	91	932	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:51,670] [INFO] GTDB search result was written to GCF_006716265.1_ASM671626v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:51,670] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:51,675] [INFO] DFAST_QC result json was written to GCF_006716265.1_ASM671626v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:51,676] [INFO] DFAST_QC completed!
[2024-01-24 14:20:51,676] [INFO] Total running time: 0h1m20s