[2024-01-24 14:28:08,504] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:08,511] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:08,511] [INFO] DQC Reference Directory: /var/lib/cwl/stg468d4308-535a-4c4e-9a13-b51fdea1c793/dqc_reference
[2024-01-24 14:28:10,419] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:10,421] [INFO] Task started: Prodigal
[2024-01-24 14:28:10,422] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe89a3f4-4976-43bb-88b3-a3920d7aeac2/GCF_001636295.1_ASM163629v1_genomic.fna.gz | prodigal -d GCF_001636295.1_ASM163629v1_genomic.fna/cds.fna -a GCF_001636295.1_ASM163629v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:21,966] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:21,966] [INFO] Task started: HMMsearch
[2024-01-24 14:28:21,966] [INFO] Running command: hmmsearch --tblout GCF_001636295.1_ASM163629v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg468d4308-535a-4c4e-9a13-b51fdea1c793/dqc_reference/reference_markers.hmm GCF_001636295.1_ASM163629v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:22,274] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:22,275] [INFO] Found 6/6 markers.
[2024-01-24 14:28:22,314] [INFO] Query marker FASTA was written to GCF_001636295.1_ASM163629v1_genomic.fna/markers.fasta
[2024-01-24 14:28:22,314] [INFO] Task started: Blastn
[2024-01-24 14:28:22,314] [INFO] Running command: blastn -query GCF_001636295.1_ASM163629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg468d4308-535a-4c4e-9a13-b51fdea1c793/dqc_reference/reference_markers.fasta -out GCF_001636295.1_ASM163629v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:23,769] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:23,772] [INFO] Selected 16 target genomes.
[2024-01-24 14:28:23,773] [INFO] Target genome list was writen to GCF_001636295.1_ASM163629v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:23,784] [INFO] Task started: fastANI
[2024-01-24 14:28:23,785] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe89a3f4-4976-43bb-88b3-a3920d7aeac2/GCF_001636295.1_ASM163629v1_genomic.fna.gz --refList GCF_001636295.1_ASM163629v1_genomic.fna/target_genomes.txt --output GCF_001636295.1_ASM163629v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:40,918] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:40,919] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg468d4308-535a-4c4e-9a13-b51fdea1c793/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:40,919] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg468d4308-535a-4c4e-9a13-b51fdea1c793/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:40,933] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:40,934] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:40,934] [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 dokdonensis	strain=DS-3	GCA_001636295.1	372663	372663	type	True	100.0	1275	1275	95	conclusive
Isoptericola jiangsuensis	strain=DSM 21863	GCA_002563715.1	548579	548579	type	True	88.5139	1085	1275	95	below_threshold
Isoptericola chiayiensis	strain=KCTC 19740	GCA_013149805.1	579446	579446	type	True	83.2018	879	1275	95	below_threshold
Isoptericola sediminis	strain=JC619	GCA_013085345.1	2733572	2733572	type	True	82.4011	745	1275	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	80.157	651	1275	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	80.1327	691	1275	95	below_threshold
Promicromonospora sukumoe	strain=DSM 44121	GCA_014137995.1	88382	88382	type	True	80.0892	735	1275	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	80.0725	717	1275	95	below_threshold
Promicromonospora citrea	strain=JCM 3051	GCA_014647735.1	43677	43677	type	True	80.0639	701	1275	95	below_threshold
Oerskovia turbata	strain=JCM3160	GCA_004121315.1	1713	1713	type	True	79.4371	599	1275	95	below_threshold
Oerskovia turbata	strain=NRRL B-8019	GCA_000718325.1	1713	1713	type	True	79.4087	594	1275	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	79.3345	618	1275	95	below_threshold
Promicromonospora umidemergens	strain=DSM 22081	GCA_024171995.1	629679	629679	type	True	79.2496	674	1275	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	79.1306	609	1275	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.0785	562	1275	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	78.3222	585	1275	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:40,936] [INFO] DFAST Taxonomy check result was written to GCF_001636295.1_ASM163629v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:40,936] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:40,937] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:40,937] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg468d4308-535a-4c4e-9a13-b51fdea1c793/dqc_reference/checkm_data
[2024-01-24 14:28:40,938] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:40,979] [INFO] Task started: CheckM
[2024-01-24 14:28:40,980] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001636295.1_ASM163629v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001636295.1_ASM163629v1_genomic.fna/checkm_input GCF_001636295.1_ASM163629v1_genomic.fna/checkm_result
[2024-01-24 14:29:52,027] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:52,028] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:52,047] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:52,048] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:52,048] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001636295.1_ASM163629v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:52,049] [INFO] Task started: Blastn
[2024-01-24 14:29:52,049] [INFO] Running command: blastn -query GCF_001636295.1_ASM163629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg468d4308-535a-4c4e-9a13-b51fdea1c793/dqc_reference/reference_markers_gtdb.fasta -out GCF_001636295.1_ASM163629v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:53,992] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:53,997] [INFO] Selected 14 target genomes.
[2024-01-24 14:29:53,997] [INFO] Target genome list was writen to GCF_001636295.1_ASM163629v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:54,012] [INFO] Task started: fastANI
[2024-01-24 14:29:54,012] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe89a3f4-4976-43bb-88b3-a3920d7aeac2/GCF_001636295.1_ASM163629v1_genomic.fna.gz --refList GCF_001636295.1_ASM163629v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001636295.1_ASM163629v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:30:08,866] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:08,890] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:30:08,890] [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_001636295.1	s__Isoptericola dokdonensis	100.0	1275	1275	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_002563715.1	s__Isoptericola jiangsuensis	88.5159	1083	1275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013149805.1	s__Isoptericola chiayiensis	83.1528	884	1275	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	82.775	847	1275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013085345.1	s__Isoptericola sediminis	82.4225	743	1275	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	82.1895	758	1275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	99.96	99.96	0.98	0.98	2	-
GCF_013149785.1	s__Isoptericola halotolerans	82.1807	863	1275	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	81.8293	806	1275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167525.1	s__Isoptericola flava	81.7263	847	1275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635665.1	s__Isoptericola cucumis	81.5992	827	1275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004695.1	s__Promicromonospora citrea	80.2368	641	1275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	99.97	99.97	0.99	0.99	2	-
GCF_004519295.1	s__Cellulosimicrobium funkei	80.1179	711	1275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	98.03	96.84	0.93	0.88	18	-
GCF_014137995.1	s__Promicromonospora sukumoe	80.0054	742	1275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014803435.1	s__Cellulosimicrobium terreum	79.9666	707	1275	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:30:08,892] [INFO] GTDB search result was written to GCF_001636295.1_ASM163629v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:30:08,893] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:30:08,897] [INFO] DFAST_QC result json was written to GCF_001636295.1_ASM163629v1_genomic.fna/dqc_result.json
[2024-01-24 14:30:08,897] [INFO] DFAST_QC completed!
[2024-01-24 14:30:08,897] [INFO] Total running time: 0h2m0s