[2024-01-25 19:31:51,523] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:31:51,524] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:31:51,524] [INFO] DQC Reference Directory: /var/lib/cwl/stg71635fac-6224-4a16-94dd-da884b420fb0/dqc_reference
[2024-01-25 19:31:52,680] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:31:52,681] [INFO] Task started: Prodigal
[2024-01-25 19:31:52,681] [INFO] Running command: gunzip -c /var/lib/cwl/stg30558711-fb16-498b-ada0-a57907ecb383/GCF_900240335.1_PRJEB20164_genomic.fna.gz | prodigal -d GCF_900240335.1_PRJEB20164_genomic.fna/cds.fna -a GCF_900240335.1_PRJEB20164_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:32:00,190] [INFO] Task succeeded: Prodigal
[2024-01-25 19:32:00,191] [INFO] Task started: HMMsearch
[2024-01-25 19:32:00,191] [INFO] Running command: hmmsearch --tblout GCF_900240335.1_PRJEB20164_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71635fac-6224-4a16-94dd-da884b420fb0/dqc_reference/reference_markers.hmm GCF_900240335.1_PRJEB20164_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:32:00,384] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:32:00,385] [INFO] Found 6/6 markers.
[2024-01-25 19:32:00,411] [INFO] Query marker FASTA was written to GCF_900240335.1_PRJEB20164_genomic.fna/markers.fasta
[2024-01-25 19:32:00,411] [INFO] Task started: Blastn
[2024-01-25 19:32:00,411] [INFO] Running command: blastn -query GCF_900240335.1_PRJEB20164_genomic.fna/markers.fasta -db /var/lib/cwl/stg71635fac-6224-4a16-94dd-da884b420fb0/dqc_reference/reference_markers.fasta -out GCF_900240335.1_PRJEB20164_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:01,593] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:01,597] [INFO] Selected 26 target genomes.
[2024-01-25 19:32:01,597] [INFO] Target genome list was writen to GCF_900240335.1_PRJEB20164_genomic.fna/target_genomes.txt
[2024-01-25 19:32:01,605] [INFO] Task started: fastANI
[2024-01-25 19:32:01,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg30558711-fb16-498b-ada0-a57907ecb383/GCF_900240335.1_PRJEB20164_genomic.fna.gz --refList GCF_900240335.1_PRJEB20164_genomic.fna/target_genomes.txt --output GCF_900240335.1_PRJEB20164_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:32:20,469] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:20,470] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71635fac-6224-4a16-94dd-da884b420fb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:32:20,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71635fac-6224-4a16-94dd-da884b420fb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:32:20,486] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:32:20,486] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:32:20,486] [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
Flavimobilis marinus	strain=DSM 19083	GCA_900113055.1	285351	285351	type	True	79.939	481	1014	95	below_threshold
Flavimobilis marinus	strain=CGMCC 1.3457	GCA_014653315.1	285351	285351	type	True	79.8587	493	1014	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	79.5497	519	1014	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	79.4776	537	1014	95	below_threshold
Oerskovia turbata	strain=JCM3160	GCA_004121315.1	1713	1713	type	True	79.3748	484	1014	95	below_threshold
Oerskovia turbata	strain=NRRL B-8019	GCA_000718325.1	1713	1713	type	True	79.3737	478	1014	95	below_threshold
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	79.3668	477	1014	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	79.33	480	1014	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	79.2943	460	1014	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.2443	491	1014	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	79.244	490	1014	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	79.1457	467	1014	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	79.0517	522	1014	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	78.9816	510	1014	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	78.9498	462	1014	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	78.9098	513	1014	95	below_threshold
Cellulomonas persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	78.8462	493	1014	95	below_threshold
Cellulomonas carbonis	strain=T26	GCA_000767175.1	1386092	1386092	type	True	78.8184	452	1014	95	below_threshold
Cellulomonas carbonis	strain=CGMCC 1.10786	GCA_014636275.1	1386092	1386092	type	True	78.8125	483	1014	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	78.7869	510	1014	95	below_threshold
Sanguibacter gelidistatuariae	strain=ISLP-3	GCA_900096585.1	1814289	1814289	type	True	78.7625	407	1014	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	78.677	435	1014	95	below_threshold
Cellulomonas timonensis	strain=SN7	GCA_900046455.1	1689271	1689271	type	True	78.5203	407	1014	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	78.5202	446	1014	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	78.2796	415	1014	95	below_threshold
Cellulomonas denverensis	strain=ATCC BAA-788	GCA_012396125.1	264297	264297	type	True	77.465	269	1014	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:32:20,488] [INFO] DFAST Taxonomy check result was written to GCF_900240335.1_PRJEB20164_genomic.fna/tc_result.tsv
[2024-01-25 19:32:20,488] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:32:20,488] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:32:20,488] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71635fac-6224-4a16-94dd-da884b420fb0/dqc_reference/checkm_data
[2024-01-25 19:32:20,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:32:20,526] [INFO] Task started: CheckM
[2024-01-25 19:32:20,526] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900240335.1_PRJEB20164_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900240335.1_PRJEB20164_genomic.fna/checkm_input GCF_900240335.1_PRJEB20164_genomic.fna/checkm_result
[2024-01-25 19:33:02,593] [INFO] Task succeeded: CheckM
[2024-01-25 19:33:02,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:33:02,614] [INFO] ===== Completeness check finished =====
[2024-01-25 19:33:02,614] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:33:02,616] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900240335.1_PRJEB20164_genomic.fna/markers.fasta)
[2024-01-25 19:33:02,616] [INFO] Task started: Blastn
[2024-01-25 19:33:02,616] [INFO] Running command: blastn -query GCF_900240335.1_PRJEB20164_genomic.fna/markers.fasta -db /var/lib/cwl/stg71635fac-6224-4a16-94dd-da884b420fb0/dqc_reference/reference_markers_gtdb.fasta -out GCF_900240335.1_PRJEB20164_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:33:04,514] [INFO] Task succeeded: Blastn
[2024-01-25 19:33:04,517] [INFO] Selected 17 target genomes.
[2024-01-25 19:33:04,518] [INFO] Target genome list was writen to GCF_900240335.1_PRJEB20164_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:33:04,527] [INFO] Task started: fastANI
[2024-01-25 19:33:04,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg30558711-fb16-498b-ada0-a57907ecb383/GCF_900240335.1_PRJEB20164_genomic.fna.gz --refList GCF_900240335.1_PRJEB20164_genomic.fna/target_genomes_gtdb.txt --output GCF_900240335.1_PRJEB20164_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:33:17,924] [INFO] Task succeeded: fastANI
[2024-01-25 19:33:17,935] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:33:17,935] [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_014852685.1	s__Flavimobilis rhizosphaerae	95.2033	827	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	95.20	95.20	0.83	0.83	2	conclusive
GCF_011300875.1	s__Flavimobilis sp011300875	88.5341	825	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002564025.1	s__Flavimobilis soli	82.0362	603	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396185.1	s__Flavimobilis hominis	81.5568	596	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113055.1	s__Flavimobilis marinus	79.8945	485	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004519295.1	s__Cellulosimicrobium funkei	79.5721	527	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	98.03	96.84	0.93	0.88	18	-
GCF_009708005.2	s__Cellulosimicrobium sp009708005	79.3356	532	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538745.1	s__Cellulomonas cellasea	79.0189	526	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.79	95.59	0.95	0.91	3	-
GCF_014042015.1	s__Actinotalea sp014042015	78.9038	443	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	99.62	99.62	0.98	0.98	2	-
GCF_007989825.1	s__Cellulomonas persica	78.8716	490	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018388445.1	s__Cellulomonas sp018388445	78.8014	447	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.55	99.30	0.98	0.97	4	-
GCF_003470205.1	s__Cellulomonas rhizosphaerae	78.7743	412	1014	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	78.7011	427	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696205.1	s__Cellulomonas sp003696205	78.6064	406	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715865.1	s__Cellulomonas sp006715865	78.5771	456	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018388465.1	s__Cellulomonas sp018388465	78.2952	403	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.65	99.29	0.98	0.97	3	-
GCF_012396125.1	s__Cellulomonas denverensis	77.4742	269	1014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:33:17,936] [INFO] GTDB search result was written to GCF_900240335.1_PRJEB20164_genomic.fna/result_gtdb.tsv
[2024-01-25 19:33:17,938] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:33:17,941] [INFO] DFAST_QC result json was written to GCF_900240335.1_PRJEB20164_genomic.fna/dqc_result.json
[2024-01-25 19:33:17,941] [INFO] DFAST_QC completed!
[2024-01-25 19:33:17,942] [INFO] Total running time: 0h1m26s