[2024-01-24 12:57:50,174] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:57:50,176] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:57:50,176] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8e9be47-dca4-4700-9454-78873ae6ae7b/dqc_reference
[2024-01-24 12:57:51,340] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:57:51,341] [INFO] Task started: Prodigal
[2024-01-24 12:57:51,341] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b03682e-4f1f-4411-8faa-6e1346096bb8/GCF_000024965.1_ASM2496v1_genomic.fna.gz | prodigal -d GCF_000024965.1_ASM2496v1_genomic.fna/cds.fna -a GCF_000024965.1_ASM2496v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:58:02,093] [INFO] Task succeeded: Prodigal
[2024-01-24 12:58:02,093] [INFO] Task started: HMMsearch
[2024-01-24 12:58:02,093] [INFO] Running command: hmmsearch --tblout GCF_000024965.1_ASM2496v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8e9be47-dca4-4700-9454-78873ae6ae7b/dqc_reference/reference_markers.hmm GCF_000024965.1_ASM2496v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:58:02,295] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:58:02,297] [INFO] Found 6/6 markers.
[2024-01-24 12:58:02,326] [INFO] Query marker FASTA was written to GCF_000024965.1_ASM2496v1_genomic.fna/markers.fasta
[2024-01-24 12:58:02,326] [INFO] Task started: Blastn
[2024-01-24 12:58:02,326] [INFO] Running command: blastn -query GCF_000024965.1_ASM2496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8e9be47-dca4-4700-9454-78873ae6ae7b/dqc_reference/reference_markers.fasta -out GCF_000024965.1_ASM2496v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:58:03,569] [INFO] Task succeeded: Blastn
[2024-01-24 12:58:03,574] [INFO] Selected 24 target genomes.
[2024-01-24 12:58:03,574] [INFO] Target genome list was writen to GCF_000024965.1_ASM2496v1_genomic.fna/target_genomes.txt
[2024-01-24 12:58:03,602] [INFO] Task started: fastANI
[2024-01-24 12:58:03,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b03682e-4f1f-4411-8faa-6e1346096bb8/GCF_000024965.1_ASM2496v1_genomic.fna.gz --refList GCF_000024965.1_ASM2496v1_genomic.fna/target_genomes.txt --output GCF_000024965.1_ASM2496v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:58:23,818] [INFO] Task succeeded: fastANI
[2024-01-24 12:58:23,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8e9be47-dca4-4700-9454-78873ae6ae7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:58:23,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8e9be47-dca4-4700-9454-78873ae6ae7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:58:23,836] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:58:23,836] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:58:23,836] [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
Isoptericola jiangsuensis	strain=DSM 21863	GCA_002563715.1	548579	548579	type	True	80.5105	664	1276	95	below_threshold
Isoptericola dokdonensis	strain=DS-3	GCA_001636295.1	372663	372663	type	True	80.4988	646	1276	95	below_threshold
Isoptericola chiayiensis	strain=KCTC 19740	GCA_013149805.1	579446	579446	type	True	80.1286	619	1276	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	80.0874	615	1276	95	below_threshold
Promicromonospora citrea	strain=JCM 3051	GCA_014647735.1	43677	43677	type	True	80.069	652	1276	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	80.0111	626	1276	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	80.0024	612	1276	95	below_threshold
Promicromonospora sukumoe	strain=DSM 44121	GCA_014137995.1	88382	88382	type	True	79.8883	683	1276	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	79.7517	540	1276	95	below_threshold
Promicromonospora kroppenstedtii	strain=DSM 19349	GCA_000515355.1	440482	440482	type	True	79.7259	602	1276	95	below_threshold
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	79.6544	548	1276	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	79.4016	560	1276	95	below_threshold
Cellulosimicrobium arenosum	strain=KCTC 49039	GCA_014837295.1	2708133	2708133	type	True	79.3791	554	1276	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.3363	527	1276	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	79.3144	566	1276	95	below_threshold
Myceligenerans xiligouense	strain=DSM 15700	GCA_003814695.1	253184	253184	type	True	79.2908	552	1276	95	below_threshold
Promicromonospora umidemergens	strain=DSM 22081	GCA_024171995.1	629679	629679	type	True	79.2182	602	1276	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	79.1452	550	1276	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	79.1369	525	1276	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	79.1266	522	1276	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	79.0174	568	1276	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	78.9177	582	1276	95	below_threshold
Sanguibacter suarezii	strain=NBRC 16159	GCA_001552735.1	60921	60921	type	True	78.8068	433	1276	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	78.6273	513	1276	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:58:23,838] [INFO] DFAST Taxonomy check result was written to GCF_000024965.1_ASM2496v1_genomic.fna/tc_result.tsv
[2024-01-24 12:58:23,838] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:58:23,838] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:58:23,839] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8e9be47-dca4-4700-9454-78873ae6ae7b/dqc_reference/checkm_data
[2024-01-24 12:58:23,840] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:58:23,875] [INFO] Task started: CheckM
[2024-01-24 12:58:23,876] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024965.1_ASM2496v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024965.1_ASM2496v1_genomic.fna/checkm_input GCF_000024965.1_ASM2496v1_genomic.fna/checkm_result
[2024-01-24 12:59:30,343] [INFO] Task succeeded: CheckM
[2024-01-24 12:59:30,344] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:59:30,363] [INFO] ===== Completeness check finished =====
[2024-01-24 12:59:30,364] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:59:30,364] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024965.1_ASM2496v1_genomic.fna/markers.fasta)
[2024-01-24 12:59:30,364] [INFO] Task started: Blastn
[2024-01-24 12:59:30,364] [INFO] Running command: blastn -query GCF_000024965.1_ASM2496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8e9be47-dca4-4700-9454-78873ae6ae7b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024965.1_ASM2496v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:59:32,344] [INFO] Task succeeded: Blastn
[2024-01-24 12:59:32,350] [INFO] Selected 9 target genomes.
[2024-01-24 12:59:32,350] [INFO] Target genome list was writen to GCF_000024965.1_ASM2496v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:59:32,406] [INFO] Task started: fastANI
[2024-01-24 12:59:32,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b03682e-4f1f-4411-8faa-6e1346096bb8/GCF_000024965.1_ASM2496v1_genomic.fna.gz --refList GCF_000024965.1_ASM2496v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024965.1_ASM2496v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:59:41,045] [INFO] Task succeeded: fastANI
[2024-01-24 12:59:41,053] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:59:41,054] [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_000024965.1	s__Xylanimonas cellulosilytica	100.0	1276	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004135385.1	s__Xylanimonas sp004135385	86.3846	893	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009783295.1	s__Xylanimonas sp009783295	84.3274	780	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001592145.1	s__Xylanimonas pachnodae	83.8289	792	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216535.1	s__Xylanimonas ulmi	83.7943	789	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135345.1	s__Xylanimonas allomyrinae	83.5183	758	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001750215.1	s__Xylanimonas variabilis_A	82.1353	518	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003244315.1	s__Xylanimonas oleitrophica	81.9962	683	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009846865.1	s__Xylanimonas puerhi	81.771	671	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:59:41,055] [INFO] GTDB search result was written to GCF_000024965.1_ASM2496v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:59:41,058] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:59:41,061] [INFO] DFAST_QC result json was written to GCF_000024965.1_ASM2496v1_genomic.fna/dqc_result.json
[2024-01-24 12:59:41,062] [INFO] DFAST_QC completed!
[2024-01-24 12:59:41,062] [INFO] Total running time: 0h1m51s