[2024-01-24 13:25:31,268] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:31,269] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:31,270] [INFO] DQC Reference Directory: /var/lib/cwl/stg9599bf58-7138-4c29-a511-b66c813b0fa3/dqc_reference
[2024-01-24 13:25:32,601] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:32,602] [INFO] Task started: Prodigal
[2024-01-24 13:25:32,602] [INFO] Running command: gunzip -c /var/lib/cwl/stga162e505-5fed-45d3-a1c6-19cdcc354836/GCF_004793545.1_ASM479354v1_genomic.fna.gz | prodigal -d GCF_004793545.1_ASM479354v1_genomic.fna/cds.fna -a GCF_004793545.1_ASM479354v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:47,105] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:47,105] [INFO] Task started: HMMsearch
[2024-01-24 13:25:47,105] [INFO] Running command: hmmsearch --tblout GCF_004793545.1_ASM479354v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9599bf58-7138-4c29-a511-b66c813b0fa3/dqc_reference/reference_markers.hmm GCF_004793545.1_ASM479354v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:47,494] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:47,496] [INFO] Found 6/6 markers.
[2024-01-24 13:25:47,548] [INFO] Query marker FASTA was written to GCF_004793545.1_ASM479354v1_genomic.fna/markers.fasta
[2024-01-24 13:25:47,548] [INFO] Task started: Blastn
[2024-01-24 13:25:47,549] [INFO] Running command: blastn -query GCF_004793545.1_ASM479354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9599bf58-7138-4c29-a511-b66c813b0fa3/dqc_reference/reference_markers.fasta -out GCF_004793545.1_ASM479354v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:48,167] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:48,170] [INFO] Selected 28 target genomes.
[2024-01-24 13:25:48,170] [INFO] Target genome list was writen to GCF_004793545.1_ASM479354v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:48,178] [INFO] Task started: fastANI
[2024-01-24 13:25:48,178] [INFO] Running command: fastANI --query /var/lib/cwl/stga162e505-5fed-45d3-a1c6-19cdcc354836/GCF_004793545.1_ASM479354v1_genomic.fna.gz --refList GCF_004793545.1_ASM479354v1_genomic.fna/target_genomes.txt --output GCF_004793545.1_ASM479354v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:04,510] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:04,511] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9599bf58-7138-4c29-a511-b66c813b0fa3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:04,512] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9599bf58-7138-4c29-a511-b66c813b0fa3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:04,535] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:26:04,535] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:26:04,535] [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
Sellimonas intestinalis	strain=BR72	GCA_001280875.1	1653434	1653434	type	True	81.9909	70	1832	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	79.5782	87	1832	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	79.5308	107	1832	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	79.3978	100	1832	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	79.2807	92	1832	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	78.6206	84	1832	95	below_threshold
Lactonifactor longoviformis	strain=DSM 17459	GCA_900129135.1	341220	341220	suspected-type	True	78.5078	91	1832	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	78.2967	82	1832	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	77.9125	55	1832	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	77.4514	65	1832	95	below_threshold
Lactonifactor longoviformis	strain=DSM 17459	GCA_002915525.1	341220	341220	suspected-type	True	77.3431	69	1832	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	77.3124	65	1832	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	77.0553	73	1832	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	76.9147	98	1832	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	76.7081	71	1832	95	below_threshold
Blautia argi	strain=KCTC 15426	GCA_003287895.1	1912897	1912897	type	True	76.7067	85	1832	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	76.5972	69	1832	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_025151995.1	438033	438033	type	True	76.5168	54	1832	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_000425525.1	438033	438033	type	True	76.4873	50	1832	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	76.3217	64	1832	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	76.1981	55	1832	95	below_threshold
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	75.8638	64	1832	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:04,537] [INFO] DFAST Taxonomy check result was written to GCF_004793545.1_ASM479354v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:04,538] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:04,538] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:04,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9599bf58-7138-4c29-a511-b66c813b0fa3/dqc_reference/checkm_data
[2024-01-24 13:26:04,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:04,602] [INFO] Task started: CheckM
[2024-01-24 13:26:04,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004793545.1_ASM479354v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004793545.1_ASM479354v1_genomic.fna/checkm_input GCF_004793545.1_ASM479354v1_genomic.fna/checkm_result
[2024-01-24 13:26:49,051] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:49,053] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:49,078] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:49,078] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:49,079] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004793545.1_ASM479354v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:49,079] [INFO] Task started: Blastn
[2024-01-24 13:26:49,079] [INFO] Running command: blastn -query GCF_004793545.1_ASM479354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9599bf58-7138-4c29-a511-b66c813b0fa3/dqc_reference/reference_markers_gtdb.fasta -out GCF_004793545.1_ASM479354v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:49,869] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:49,873] [INFO] Selected 8 target genomes.
[2024-01-24 13:26:49,874] [INFO] Target genome list was writen to GCF_004793545.1_ASM479354v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:49,895] [INFO] Task started: fastANI
[2024-01-24 13:26:49,896] [INFO] Running command: fastANI --query /var/lib/cwl/stga162e505-5fed-45d3-a1c6-19cdcc354836/GCF_004793545.1_ASM479354v1_genomic.fna.gz --refList GCF_004793545.1_ASM479354v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004793545.1_ASM479354v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:58,878] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:58,889] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:58,890] [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
GCA_004793545.1	s__14-2 sp004793545	100.0	1824	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910575555.1	s__14-2 sp011960065	85.0821	1070	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	99.61	97.67	0.95	0.76	7	-
GCA_910584585.1	s__14-2 sp910584585	83.5958	897	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000403255.2	s__14-2 sp000403255	81.9068	742	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	99.01	99.01	0.96	0.96	2	-
GCF_000403845.2	s__14-2 sp000403845	80.7127	649	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585295.1	s__14-2 sp009774455	79.4681	484	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	99.41	99.41	0.81	0.81	2	-
GCA_910580195.1	s__14-2 sp910580195	78.7817	489	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910580015.1	s__14-2 sp910580015	77.5772	219	1832	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:58,891] [INFO] GTDB search result was written to GCF_004793545.1_ASM479354v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:58,892] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:58,895] [INFO] DFAST_QC result json was written to GCF_004793545.1_ASM479354v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:58,895] [INFO] DFAST_QC completed!
[2024-01-24 13:26:58,896] [INFO] Total running time: 0h1m28s