[2024-01-24 14:55:06,150] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:06,152] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:06,152] [INFO] DQC Reference Directory: /var/lib/cwl/stg37b76031-dcd8-42e3-b069-090e09052078/dqc_reference
[2024-01-24 14:55:09,461] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:09,464] [INFO] Task started: Prodigal
[2024-01-24 14:55:09,464] [INFO] Running command: gunzip -c /var/lib/cwl/stga8c08212-3ac2-47cb-94d6-453ed1962bc2/GCF_014635665.1_ASM1463566v1_genomic.fna.gz | prodigal -d GCF_014635665.1_ASM1463566v1_genomic.fna/cds.fna -a GCF_014635665.1_ASM1463566v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:21,647] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:21,648] [INFO] Task started: HMMsearch
[2024-01-24 14:55:21,648] [INFO] Running command: hmmsearch --tblout GCF_014635665.1_ASM1463566v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37b76031-dcd8-42e3-b069-090e09052078/dqc_reference/reference_markers.hmm GCF_014635665.1_ASM1463566v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:21,942] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:21,943] [INFO] Found 6/6 markers.
[2024-01-24 14:55:21,981] [INFO] Query marker FASTA was written to GCF_014635665.1_ASM1463566v1_genomic.fna/markers.fasta
[2024-01-24 14:55:21,981] [INFO] Task started: Blastn
[2024-01-24 14:55:21,981] [INFO] Running command: blastn -query GCF_014635665.1_ASM1463566v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37b76031-dcd8-42e3-b069-090e09052078/dqc_reference/reference_markers.fasta -out GCF_014635665.1_ASM1463566v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:23,311] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:23,315] [INFO] Selected 19 target genomes.
[2024-01-24 14:55:23,316] [INFO] Target genome list was writen to GCF_014635665.1_ASM1463566v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:23,326] [INFO] Task started: fastANI
[2024-01-24 14:55:23,326] [INFO] Running command: fastANI --query /var/lib/cwl/stga8c08212-3ac2-47cb-94d6-453ed1962bc2/GCF_014635665.1_ASM1463566v1_genomic.fna.gz --refList GCF_014635665.1_ASM1463566v1_genomic.fna/target_genomes.txt --output GCF_014635665.1_ASM1463566v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:42,406] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:42,407] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37b76031-dcd8-42e3-b069-090e09052078/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:42,407] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37b76031-dcd8-42e3-b069-090e09052078/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:42,423] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:55:42,423] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:55:42,423] [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	81.5442	812	1474	95	below_threshold
Isoptericola dokdonensis	strain=DS-3	GCA_001636295.1	372663	372663	type	True	81.5172	823	1474	95	below_threshold
Isoptericola sediminis	strain=JC619	GCA_013085345.1	2733572	2733572	type	True	81.1092	680	1474	95	below_threshold
Isoptericola chiayiensis	strain=KCTC 19740	GCA_013149805.1	579446	579446	type	True	81.101	772	1474	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	80.3522	774	1474	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	80.2858	757	1474	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	80.2594	724	1474	95	below_threshold
Promicromonospora citrea	strain=JCM 3051	GCA_014647735.1	43677	43677	type	True	80.0719	778	1474	95	below_threshold
Promicromonospora sukumoe	strain=DSM 44121	GCA_014137995.1	88382	88382	type	True	79.9374	825	1474	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	79.7277	621	1474	95	below_threshold
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	79.7035	624	1474	95	below_threshold
Promicromonospora soli	strain=CGMCC 4.7398	GCA_014653785.1	2035533	2035533	type	True	79.6004	722	1474	95	below_threshold
Promicromonospora umidemergens	strain=DSM 22081	GCA_024171995.1	629679	629679	type	True	79.5073	767	1474	95	below_threshold
Myceligenerans xiligouense	strain=DSM 15700	GCA_003814695.1	253184	253184	type	True	79.3923	644	1474	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	79.3779	630	1474	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	79.171	670	1474	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.7484	589	1474	95	below_threshold
Cellulomonas shaoxiangyii	strain=Z28	GCA_004798685.1	2566013	2566013	type	True	78.4706	600	1474	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	78.2507	619	1474	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:42,425] [INFO] DFAST Taxonomy check result was written to GCF_014635665.1_ASM1463566v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:42,426] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:42,426] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:42,426] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37b76031-dcd8-42e3-b069-090e09052078/dqc_reference/checkm_data
[2024-01-24 14:55:42,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:42,472] [INFO] Task started: CheckM
[2024-01-24 14:55:42,472] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635665.1_ASM1463566v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635665.1_ASM1463566v1_genomic.fna/checkm_input GCF_014635665.1_ASM1463566v1_genomic.fna/checkm_result
[2024-01-24 14:56:50,093] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:50,094] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:50,115] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:50,116] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:50,116] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635665.1_ASM1463566v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:50,117] [INFO] Task started: Blastn
[2024-01-24 14:56:50,117] [INFO] Running command: blastn -query GCF_014635665.1_ASM1463566v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37b76031-dcd8-42e3-b069-090e09052078/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635665.1_ASM1463566v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:52,282] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:52,285] [INFO] Selected 16 target genomes.
[2024-01-24 14:56:52,286] [INFO] Target genome list was writen to GCF_014635665.1_ASM1463566v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:52,303] [INFO] Task started: fastANI
[2024-01-24 14:56:52,303] [INFO] Running command: fastANI --query /var/lib/cwl/stga8c08212-3ac2-47cb-94d6-453ed1962bc2/GCF_014635665.1_ASM1463566v1_genomic.fna.gz --refList GCF_014635665.1_ASM1463566v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635665.1_ASM1463566v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:09,150] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:09,163] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:09,164] [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_014635665.1	s__Isoptericola cucumis	100.0	1474	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900167525.1	s__Isoptericola flava	84.3927	1121	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011634835.1	s__Isoptericola sp011634835	83.6603	1018	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215105.1	s__Isoptericola variabilis_A	82.4226	795	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	99.96	99.96	0.98	0.98	2	-
GCA_009663185.1	s__Isoptericola sp009663185	81.7701	769	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636295.1	s__Isoptericola dokdonensis	81.5088	824	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001750215.1	s__Xylanimonas variabilis_A	81.4413	596	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013149805.1	s__Isoptericola chiayiensis	81.2022	760	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003075.1	s__Isoptericola halotolerans_A	81.1623	803	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013149785.1	s__Isoptericola halotolerans	80.7988	784	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009783295.1	s__Xylanimonas sp009783295	80.5277	649	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519295.1	s__Cellulosimicrobium funkei	80.3752	771	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	98.03	96.84	0.93	0.88	18	-
GCF_013004695.1	s__Promicromonospora citrea	80.1921	731	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	99.97	99.97	0.99	0.99	2	-
GCF_006539945.1	s__Cellulosimicrobium cellulans	80.0215	780	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552375.1	s__Cellulomonas iranensis	78.694	607	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.21	97.89	0.91	0.88	6	-
GCF_004798685.1	s__Cellulomonas shaoxiangyii	78.468	601	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:09,165] [INFO] GTDB search result was written to GCF_014635665.1_ASM1463566v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:09,166] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:09,171] [INFO] DFAST_QC result json was written to GCF_014635665.1_ASM1463566v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:09,171] [INFO] DFAST_QC completed!
[2024-01-24 14:57:09,172] [INFO] Total running time: 0h2m3s