[2024-01-24 13:55:19,854] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:19,856] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:19,856] [INFO] DQC Reference Directory: /var/lib/cwl/stg9999282a-8280-465d-b02c-7cf5b9e5b38d/dqc_reference
[2024-01-24 13:55:21,152] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:21,153] [INFO] Task started: Prodigal
[2024-01-24 13:55:21,153] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c66f4a8-fa6d-4666-8c28-5f31cb739773/GCF_000350145.1_ASM35014v1_genomic.fna.gz | prodigal -d GCF_000350145.1_ASM35014v1_genomic.fna/cds.fna -a GCF_000350145.1_ASM35014v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:32,976] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:32,976] [INFO] Task started: HMMsearch
[2024-01-24 13:55:32,976] [INFO] Running command: hmmsearch --tblout GCF_000350145.1_ASM35014v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9999282a-8280-465d-b02c-7cf5b9e5b38d/dqc_reference/reference_markers.hmm GCF_000350145.1_ASM35014v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:33,287] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:33,288] [INFO] Found 6/6 markers.
[2024-01-24 13:55:33,328] [INFO] Query marker FASTA was written to GCF_000350145.1_ASM35014v1_genomic.fna/markers.fasta
[2024-01-24 13:55:33,329] [INFO] Task started: Blastn
[2024-01-24 13:55:33,329] [INFO] Running command: blastn -query GCF_000350145.1_ASM35014v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9999282a-8280-465d-b02c-7cf5b9e5b38d/dqc_reference/reference_markers.fasta -out GCF_000350145.1_ASM35014v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:34,242] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:34,245] [INFO] Selected 16 target genomes.
[2024-01-24 13:55:34,245] [INFO] Target genome list was writen to GCF_000350145.1_ASM35014v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:34,254] [INFO] Task started: fastANI
[2024-01-24 13:55:34,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c66f4a8-fa6d-4666-8c28-5f31cb739773/GCF_000350145.1_ASM35014v1_genomic.fna.gz --refList GCF_000350145.1_ASM35014v1_genomic.fna/target_genomes.txt --output GCF_000350145.1_ASM35014v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:49,871] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:49,872] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9999282a-8280-465d-b02c-7cf5b9e5b38d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:49,872] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9999282a-8280-465d-b02c-7cf5b9e5b38d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:49,884] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:49,884] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:49,885] [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
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	100.0	1237	1253	95	conclusive
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	79.6758	628	1253	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	77.65	410	1253	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	77.2842	327	1253	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.6418	162	1253	95	below_threshold
Propionibacterium australiense	strain=NML98A072	GCA_003666605.1	119981	119981	type	True	75.4867	52	1253	95	below_threshold
Nocardioides pelophilus	strain=CGMCC 4.7388	GCA_014180685.1	2172019	2172019	type	True	75.4798	122	1253	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	75.4624	58	1253	95	below_threshold
Nocardioides albus	strain=JCM 3185	GCA_014648255.1	1841	1841	type	True	75.4511	101	1253	95	below_threshold
Tessaracoccus bendigoensis	strain=DSM 12906	GCA_900141915.1	72764	72764	type	True	75.3264	63	1253	95	below_threshold
Micromonospora maritima		GCA_902825405.1	986711	986711	type	True	75.3143	91	1253	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	75.3072	164	1253	95	below_threshold
Micromonospora marina	strain=DSM 45555	GCA_900091565.1	307120	307120	type	True	75.2439	122	1253	95	below_threshold
Tenggerimyces flavus	strain=DSM 28944	GCA_016907715.1	1708749	1708749	type	True	75.1567	138	1253	95	below_threshold
Actinomadura namibiensis	strain=DSM 44197	GCA_014138665.1	182080	182080	type	True	75.0353	150	1253	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:49,886] [INFO] DFAST Taxonomy check result was written to GCF_000350145.1_ASM35014v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:49,887] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:49,887] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:49,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9999282a-8280-465d-b02c-7cf5b9e5b38d/dqc_reference/checkm_data
[2024-01-24 13:55:49,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:49,934] [INFO] Task started: CheckM
[2024-01-24 13:55:49,934] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000350145.1_ASM35014v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000350145.1_ASM35014v1_genomic.fna/checkm_input GCF_000350145.1_ASM35014v1_genomic.fna/checkm_result
[2024-01-24 13:57:02,151] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:02,152] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:02,174] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:02,175] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:02,175] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000350145.1_ASM35014v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:02,176] [INFO] Task started: Blastn
[2024-01-24 13:57:02,176] [INFO] Running command: blastn -query GCF_000350145.1_ASM35014v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9999282a-8280-465d-b02c-7cf5b9e5b38d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000350145.1_ASM35014v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:03,473] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:03,478] [INFO] Selected 13 target genomes.
[2024-01-24 13:57:03,478] [INFO] Target genome list was writen to GCF_000350145.1_ASM35014v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:03,529] [INFO] Task started: fastANI
[2024-01-24 13:57:03,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c66f4a8-fa6d-4666-8c28-5f31cb739773/GCF_000350145.1_ASM35014v1_genomic.fna.gz --refList GCF_000350145.1_ASM35014v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000350145.1_ASM35014v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:12,616] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:12,627] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:12,627] [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_000350145.1	s__Ilumatobacter_A nonamiensis	100.0	1237	1253	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000348785.1	s__Ilumatobacter_A coccineus	79.6838	627	1253	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002175.1	s__Ilumatobacter_A sp013002175	78.8596	404	1253	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480335.1	s__Ilumatobacter_A sp905480335	78.4376	364	1253	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666235.1	s__Ilumatobacter_A sp018666235	78.0483	281	1253	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	99.79	99.78	0.94	0.93	4	-
GCA_013213745.1	s__JABSQH01 sp013213745	77.9053	298	1253	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JABSQH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693335.1	s__SKSP01 sp007693335	77.6927	283	1253	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007122945.1	s__SKSP01 sp007122945	77.6754	283	1253	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	99.05	99.05	0.83	0.83	2	-
GCF_004364865.1	s__Ilumatobacter fluminis	77.6497	410	1253	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182555.1	s__Ilumatobacter_A sp905182555	77.3915	205	1253	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016700055.1	s__Kalu-18 sp016700055	77.1842	247	1253	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Kalu-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009702045.1	s__UBA668 sp009702045	76.9546	162	1253	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	99.96	99.94	0.98	0.97	6	-
GCA_016185275.1	s__JACPNX01 sp016185275	76.4113	152	1253	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JACPNX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:12,629] [INFO] GTDB search result was written to GCF_000350145.1_ASM35014v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:12,630] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:12,633] [INFO] DFAST_QC result json was written to GCF_000350145.1_ASM35014v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:12,634] [INFO] DFAST_QC completed!
[2024-01-24 13:57:12,634] [INFO] Total running time: 0h1m53s