[2024-01-24 13:41:20,477] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:20,480] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:20,481] [INFO] DQC Reference Directory: /var/lib/cwl/stg613e0e50-a05e-4c52-bd8e-c4d9e641f035/dqc_reference
[2024-01-24 13:41:21,858] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:21,859] [INFO] Task started: Prodigal
[2024-01-24 13:41:21,860] [INFO] Running command: gunzip -c /var/lib/cwl/stg698235fa-3d7c-4624-83fa-261f58763900/GCF_014287635.1_ASM1428763v1_genomic.fna.gz | prodigal -d GCF_014287635.1_ASM1428763v1_genomic.fna/cds.fna -a GCF_014287635.1_ASM1428763v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:29,782] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:29,782] [INFO] Task started: HMMsearch
[2024-01-24 13:41:29,782] [INFO] Running command: hmmsearch --tblout GCF_014287635.1_ASM1428763v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg613e0e50-a05e-4c52-bd8e-c4d9e641f035/dqc_reference/reference_markers.hmm GCF_014287635.1_ASM1428763v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:30,140] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:30,141] [INFO] Found 6/6 markers.
[2024-01-24 13:41:30,177] [INFO] Query marker FASTA was written to GCF_014287635.1_ASM1428763v1_genomic.fna/markers.fasta
[2024-01-24 13:41:30,177] [INFO] Task started: Blastn
[2024-01-24 13:41:30,178] [INFO] Running command: blastn -query GCF_014287635.1_ASM1428763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg613e0e50-a05e-4c52-bd8e-c4d9e641f035/dqc_reference/reference_markers.fasta -out GCF_014287635.1_ASM1428763v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:30,819] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:30,822] [INFO] Selected 25 target genomes.
[2024-01-24 13:41:30,823] [INFO] Target genome list was writen to GCF_014287635.1_ASM1428763v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:30,832] [INFO] Task started: fastANI
[2024-01-24 13:41:30,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg698235fa-3d7c-4624-83fa-261f58763900/GCF_014287635.1_ASM1428763v1_genomic.fna.gz --refList GCF_014287635.1_ASM1428763v1_genomic.fna/target_genomes.txt --output GCF_014287635.1_ASM1428763v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:47,641] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:47,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg613e0e50-a05e-4c52-bd8e-c4d9e641f035/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:47,642] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg613e0e50-a05e-4c52-bd8e-c4d9e641f035/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:47,660] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:47,660] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:47,661] [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
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	83.5204	249	1127	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	83.0037	179	1127	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	82.8568	314	1127	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	82.8126	317	1127	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	82.6677	306	1127	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	81.373	116	1127	95	below_threshold
Jutongia hominis	strain=BX3	GCA_014384965.1	2763664	2763664	type	True	80.8565	110	1127	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	80.7343	118	1127	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	80.6866	115	1127	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	80.6274	143	1127	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	80.4973	153	1127	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	80.1968	97	1127	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	79.8644	106	1127	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	79.7046	102	1127	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	79.6617	109	1127	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	78.8432	105	1127	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	78.7156	103	1127	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	78.628	168	1127	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	78.0349	66	1127	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	77.8062	71	1127	95	below_threshold
Faecalimonas umbilicata	strain=EGH7	GCA_003402615.1	1912855	1912855	type	True	77.7606	71	1127	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	77.649	69	1127	95	below_threshold
Sellimonas caecigallum	strain=SW451	GCA_019754295.1	2592333	2592333	type	True	77.2616	55	1127	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	76.3006	63	1127	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:47,663] [INFO] DFAST Taxonomy check result was written to GCF_014287635.1_ASM1428763v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:47,664] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:47,664] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:47,664] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg613e0e50-a05e-4c52-bd8e-c4d9e641f035/dqc_reference/checkm_data
[2024-01-24 13:41:47,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:47,704] [INFO] Task started: CheckM
[2024-01-24 13:41:47,704] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014287635.1_ASM1428763v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014287635.1_ASM1428763v1_genomic.fna/checkm_input GCF_014287635.1_ASM1428763v1_genomic.fna/checkm_result
[2024-01-24 13:42:18,525] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:18,526] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:18,551] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:18,551] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:18,552] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014287635.1_ASM1428763v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:18,552] [INFO] Task started: Blastn
[2024-01-24 13:42:18,552] [INFO] Running command: blastn -query GCF_014287635.1_ASM1428763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg613e0e50-a05e-4c52-bd8e-c4d9e641f035/dqc_reference/reference_markers_gtdb.fasta -out GCF_014287635.1_ASM1428763v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:19,625] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:19,629] [INFO] Selected 19 target genomes.
[2024-01-24 13:42:19,629] [INFO] Target genome list was writen to GCF_014287635.1_ASM1428763v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:19,642] [INFO] Task started: fastANI
[2024-01-24 13:42:19,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg698235fa-3d7c-4624-83fa-261f58763900/GCF_014287635.1_ASM1428763v1_genomic.fna.gz --refList GCF_014287635.1_ASM1428763v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014287635.1_ASM1428763v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:30,028] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:30,047] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:30,048] [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_014287635.1	s__1XD42-69 sp014287635	100.0	1123	1127	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	98.20	98.20	0.93	0.93	2	conclusive
GCF_000174195.1	s__Roseburia inulinivorans	83.4597	251	1127	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	95.90	0.77	0.61	28	-
GCF_900537995.1	s__Roseburia intestinalis	82.9087	313	1127	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.51	98.07	0.86	0.80	21	-
GCF_003470905.1	s__Roseburia sp003470905	81.0392	279	1127	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.69	98.30	0.90	0.82	7	-
GCF_003479605.1	s__RUG115 sp900066395	80.6586	213	1127	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	98.27	97.78	0.88	0.83	29	-
GCF_001940165.1	s__Roseburia sp001940165	78.9485	179	1127	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017624495.1	s__1XD42-69 sp017624495	78.6855	192	1127	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017625255.1	s__1XD42-69 sp017625255	78.3987	255	1127	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003483745.1	s__Roseburia sp003483745	78.3735	181	1127	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	97.41	0.84	0.84	3	-
GCA_900550935.1	s__Roseburia sp900550935	77.9512	168	1127	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.33	98.19	0.83	0.82	3	-
GCA_902782995.1	s__RUG115 sp902782995	77.8514	157	1127	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585825.1	s__1XD42-69 sp910585825	77.8122	218	1127	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003507655.1	s__UBA11774 sp003507655	77.6945	182	1127	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA11774	95.0	98.49	98.09	0.91	0.83	6	-
GCA_900771955.1	s__CAG-45 sp900771955	77.5752	147	1127	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-45	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011959925.1	s__1XD42-69 sp011959925	77.5612	177	1127	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	98.99	98.99	0.83	0.83	2	-
GCA_910586355.1	s__1XD42-69 sp910586355	77.1447	179	1127	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588565.1	s__1XD42-69 sp910588565	77.1431	193	1127	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586725.1	s__1XD42-69 sp910586725	76.9253	152	1127	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:30,050] [INFO] GTDB search result was written to GCF_014287635.1_ASM1428763v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:30,050] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:30,055] [INFO] DFAST_QC result json was written to GCF_014287635.1_ASM1428763v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:30,055] [INFO] DFAST_QC completed!
[2024-01-24 13:42:30,056] [INFO] Total running time: 0h1m10s