[2024-01-24 13:41:20,737] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:20,739] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:20,739] [INFO] DQC Reference Directory: /var/lib/cwl/stgac390f3a-6d3f-434e-84ef-3a5b33ff398e/dqc_reference
[2024-01-24 13:41:22,039] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:22,048] [INFO] Task started: Prodigal
[2024-01-24 13:41:22,048] [INFO] Running command: gunzip -c /var/lib/cwl/stg3eb9f609-7f36-4789-8d8c-0454bb160739/GCF_030161555.1_ASM3016155v1_genomic.fna.gz | prodigal -d GCF_030161555.1_ASM3016155v1_genomic.fna/cds.fna -a GCF_030161555.1_ASM3016155v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:33,673] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:33,674] [INFO] Task started: HMMsearch
[2024-01-24 13:41:33,674] [INFO] Running command: hmmsearch --tblout GCF_030161555.1_ASM3016155v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac390f3a-6d3f-434e-84ef-3a5b33ff398e/dqc_reference/reference_markers.hmm GCF_030161555.1_ASM3016155v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:33,970] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:33,972] [INFO] Found 6/6 markers.
[2024-01-24 13:41:34,010] [INFO] Query marker FASTA was written to GCF_030161555.1_ASM3016155v1_genomic.fna/markers.fasta
[2024-01-24 13:41:34,010] [INFO] Task started: Blastn
[2024-01-24 13:41:34,011] [INFO] Running command: blastn -query GCF_030161555.1_ASM3016155v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac390f3a-6d3f-434e-84ef-3a5b33ff398e/dqc_reference/reference_markers.fasta -out GCF_030161555.1_ASM3016155v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:35,301] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:35,305] [INFO] Selected 24 target genomes.
[2024-01-24 13:41:35,306] [INFO] Target genome list was writen to GCF_030161555.1_ASM3016155v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:35,314] [INFO] Task started: fastANI
[2024-01-24 13:41:35,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eb9f609-7f36-4789-8d8c-0454bb160739/GCF_030161555.1_ASM3016155v1_genomic.fna.gz --refList GCF_030161555.1_ASM3016155v1_genomic.fna/target_genomes.txt --output GCF_030161555.1_ASM3016155v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:57,287] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:57,288] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac390f3a-6d3f-434e-84ef-3a5b33ff398e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:57,288] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac390f3a-6d3f-434e-84ef-3a5b33ff398e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:57,308] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:57,308] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:57,308] [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
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	80.0394	668	1394	95	below_threshold
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	80.0328	592	1394	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	79.9751	598	1394	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	79.9475	699	1394	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	79.7302	645	1394	95	below_threshold
Oerskovia jenensis	strain=DSM 46000	GCA_016907235.1	162169	162169	type	True	79.5548	608	1394	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	79.4838	616	1394	95	below_threshold
Oerskovia enterophila	strain=DSM 43852	GCA_001692445.1	43678	43678	type	True	79.4445	612	1394	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	79.398	609	1394	95	below_threshold
Cellulosimicrobium arenosum	strain=KCTC 49039	GCA_014837295.1	2708133	2708133	type	True	79.3222	617	1394	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.2345	583	1394	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	79.2212	559	1394	95	below_threshold
Cellulomonas uda	strain=NBRC 3747	GCA_006538705.1	1714	1714	type	True	79.1693	545	1394	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	79.0581	596	1394	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	78.9365	623	1394	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	78.9061	560	1394	95	below_threshold
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	78.8948	511	1394	95	below_threshold
Cellulomonas flavigena	strain=DSM 20109	GCA_000092865.1	1711	1711	type	True	78.8292	554	1394	95	below_threshold
Promicromonospora citrea	strain=JCM 3051	GCA_014647735.1	43677	43677	type	True	78.8053	593	1394	95	below_threshold
Isoptericola chiayiensis	strain=KCTC 19740	GCA_013149805.1	579446	579446	type	True	78.684	526	1394	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	78.4079	526	1394	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	78.2853	568	1394	95	below_threshold
Ruania albidiflava	strain=DSM 18029	GCA_000421225.1	366586	366586	type	True	77.0646	241	1394	95	below_threshold
Nonomuraea mesophila	strain=6K102	GCA_004352805.1	2530382	2530382	type	True	75.9443	395	1394	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:57,310] [INFO] DFAST Taxonomy check result was written to GCF_030161555.1_ASM3016155v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:57,311] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:57,311] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:57,311] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac390f3a-6d3f-434e-84ef-3a5b33ff398e/dqc_reference/checkm_data
[2024-01-24 13:41:57,313] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:57,361] [INFO] Task started: CheckM
[2024-01-24 13:41:57,361] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030161555.1_ASM3016155v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030161555.1_ASM3016155v1_genomic.fna/checkm_input GCF_030161555.1_ASM3016155v1_genomic.fna/checkm_result
[2024-01-24 13:42:54,525] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:54,526] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:54,550] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:54,550] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:54,551] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030161555.1_ASM3016155v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:54,551] [INFO] Task started: Blastn
[2024-01-24 13:42:54,551] [INFO] Running command: blastn -query GCF_030161555.1_ASM3016155v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac390f3a-6d3f-434e-84ef-3a5b33ff398e/dqc_reference/reference_markers_gtdb.fasta -out GCF_030161555.1_ASM3016155v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:56,595] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:56,600] [INFO] Selected 24 target genomes.
[2024-01-24 13:42:56,600] [INFO] Target genome list was writen to GCF_030161555.1_ASM3016155v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:56,634] [INFO] Task started: fastANI
[2024-01-24 13:42:56,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eb9f609-7f36-4789-8d8c-0454bb160739/GCF_030161555.1_ASM3016155v1_genomic.fna.gz --refList GCF_030161555.1_ASM3016155v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030161555.1_ASM3016155v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:19,935] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:19,959] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:43:19,959] [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_009429125.1	s__Luteimicrobium xylanilyticum	90.5828	1087	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Luteimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002798015.1	s__Luteimicrobium subarcticum	81.7068	772	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Luteimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722485.1	s__Cellulosimicrobium cellulans_A	80.1359	570	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797595.1	s__Sediminihabitans luteus	80.1208	583	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010287905.1	s__Cellulosimicrobium fucosivorans	80.0405	662	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.84	98.55	0.94	0.90	6	-
GCF_016907755.1	s__Cellulosimicrobium cellulans_D	79.9952	732	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	99.18	99.18	0.97	0.97	2	-
GCF_004519295.1	s__Cellulosimicrobium funkei	79.9455	698	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	98.03	96.84	0.93	0.88	18	-
GCF_016921195.1	s__Cellulosimicrobium cellulans_F	79.9024	694	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215105.1	s__Isoptericola variabilis_A	79.8184	596	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	99.96	99.96	0.98	0.98	2	-
GCF_001692445.1	s__Oerskovia enterophila	79.4429	612	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	98.35	97.89	0.90	0.89	4	-
GCF_014837295.1	s__Cellulosimicrobium arenosum	79.3768	610	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009783295.1	s__Xylanimonas sp009783295	79.3456	532	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009663185.1	s__Isoptericola sp009663185	79.2927	558	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004306155.1	s__Cellulomonas biazotea	79.2767	552	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216535.1	s__Xylanimonas ulmi	79.1607	547	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004695.1	s__Promicromonospora citrea	78.9919	547	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	99.97	99.97	0.99	0.99	2	-
GCF_006538745.1	s__Cellulomonas cellasea	78.9728	617	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.79	95.59	0.95	0.91	3	-
GCF_003696205.1	s__Cellulomonas sp003696205	78.9606	517	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409475.1	s__Cellulomonas hominis_B	78.8696	542	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114185.1	s__Cellulomonas sp900114185	78.7438	522	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013149805.1	s__Isoptericola chiayiensis	78.7264	520	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715865.1	s__Cellulomonas sp006715865	78.6865	565	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014892515.1	s__Myceligenerans sp014892515	78.374	534	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Myceligenerans	95.0	100.00	100.00	0.99	0.99	2	-
GCA_015234515.1	s__Cellulomonas sp015234515	78.2565	531	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:19,961] [INFO] GTDB search result was written to GCF_030161555.1_ASM3016155v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:19,962] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:19,967] [INFO] DFAST_QC result json was written to GCF_030161555.1_ASM3016155v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:19,968] [INFO] DFAST_QC completed!
[2024-01-24 13:43:19,968] [INFO] Total running time: 0h1m59s