[2024-01-24 14:19:45,305] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:45,348] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:45,348] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7f81153-0373-4029-a522-7b7a1ff56ef3/dqc_reference
[2024-01-24 14:19:47,128] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:47,132] [INFO] Task started: Prodigal
[2024-01-24 14:19:47,132] [INFO] Running command: gunzip -c /var/lib/cwl/stg0bd10896-3fbf-49f4-91f8-70e5f681b3cc/GCF_025149125.1_ASM2514912v1_genomic.fna.gz | prodigal -d GCF_025149125.1_ASM2514912v1_genomic.fna/cds.fna -a GCF_025149125.1_ASM2514912v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:09,525] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:09,525] [INFO] Task started: HMMsearch
[2024-01-24 14:20:09,525] [INFO] Running command: hmmsearch --tblout GCF_025149125.1_ASM2514912v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7f81153-0373-4029-a522-7b7a1ff56ef3/dqc_reference/reference_markers.hmm GCF_025149125.1_ASM2514912v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:09,848] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:09,849] [INFO] Found 6/6 markers.
[2024-01-24 14:20:09,897] [INFO] Query marker FASTA was written to GCF_025149125.1_ASM2514912v1_genomic.fna/markers.fasta
[2024-01-24 14:20:09,897] [INFO] Task started: Blastn
[2024-01-24 14:20:09,897] [INFO] Running command: blastn -query GCF_025149125.1_ASM2514912v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7f81153-0373-4029-a522-7b7a1ff56ef3/dqc_reference/reference_markers.fasta -out GCF_025149125.1_ASM2514912v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:10,546] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:10,549] [INFO] Selected 18 target genomes.
[2024-01-24 14:20:10,549] [INFO] Target genome list was writen to GCF_025149125.1_ASM2514912v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:10,555] [INFO] Task started: fastANI
[2024-01-24 14:20:10,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bd10896-3fbf-49f4-91f8-70e5f681b3cc/GCF_025149125.1_ASM2514912v1_genomic.fna.gz --refList GCF_025149125.1_ASM2514912v1_genomic.fna/target_genomes.txt --output GCF_025149125.1_ASM2514912v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:29,815] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:29,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7f81153-0373-4029-a522-7b7a1ff56ef3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:29,815] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7f81153-0373-4029-a522-7b7a1ff56ef3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:29,826] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:20:29,826] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:29,826] [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
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	100.0	2117	2117	95	conclusive
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	99.783	2068	2117	95	conclusive
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	78.5218	418	2117	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	78.4853	418	2117	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	78.4417	253	2117	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	78.3789	50	2117	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002234575.2	208479	208479	type	True	78.3027	428	2117	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	78.2988	398	2117	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	78.292	429	2117	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	77.9618	421	2117	95	below_threshold
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	77.7857	122	2117	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	77.1567	110	2117	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	77.0539	95	2117	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	76.9993	233	2117	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	76.9224	104	2117	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	76.4068	103	2117	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	76.2645	55	2117	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:29,828] [INFO] DFAST Taxonomy check result was written to GCF_025149125.1_ASM2514912v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:29,828] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:29,828] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:29,829] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7f81153-0373-4029-a522-7b7a1ff56ef3/dqc_reference/checkm_data
[2024-01-24 14:20:29,829] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:29,888] [INFO] Task started: CheckM
[2024-01-24 14:20:29,888] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025149125.1_ASM2514912v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025149125.1_ASM2514912v1_genomic.fna/checkm_input GCF_025149125.1_ASM2514912v1_genomic.fna/checkm_result
[2024-01-24 14:21:30,326] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:30,327] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.57%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:30,344] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:30,344] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:30,345] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025149125.1_ASM2514912v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:30,345] [INFO] Task started: Blastn
[2024-01-24 14:21:30,345] [INFO] Running command: blastn -query GCF_025149125.1_ASM2514912v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7f81153-0373-4029-a522-7b7a1ff56ef3/dqc_reference/reference_markers_gtdb.fasta -out GCF_025149125.1_ASM2514912v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:31,497] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:31,500] [INFO] Selected 8 target genomes.
[2024-01-24 14:21:31,500] [INFO] Target genome list was writen to GCF_025149125.1_ASM2514912v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:31,504] [INFO] Task started: fastANI
[2024-01-24 14:21:31,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bd10896-3fbf-49f4-91f8-70e5f681b3cc/GCF_025149125.1_ASM2514912v1_genomic.fna.gz --refList GCF_025149125.1_ASM2514912v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025149125.1_ASM2514912v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:41,076] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:41,082] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:41,082] [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_000158075.1	s__Enterocloster asparagiformis	99.783	2068	2117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.72	98.33	0.90	0.88	5	conclusive
GCF_902364025.1	s__Enterocloster lavalensis	94.5829	1697	2117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.58	98.12	0.90	0.83	6	-
GCA_018380885.1	s__Enterocloster sp900555905	86.4067	1330	2117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.89	98.89	0.95	0.95	2	-
GCA_900555045.1	s__Enterocloster sp900555045	83.1532	862	2117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551225.1	s__Enterocloster sp900551225	80.092	680	2117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000233455.1	s__Enterocloster citroniae	78.6437	419	2117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.23	99.13	0.87	0.84	10	-
GCA_019114845.1	s__Lachnoclostridium_A stercoripullorum	78.4634	282	2117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	98.44	98.44	0.80	0.80	2	-
GCA_900547035.1	s__Enterocloster excrementigallinarum	78.0654	289	2117	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.35	98.28	0.80	0.77	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:41,083] [INFO] GTDB search result was written to GCF_025149125.1_ASM2514912v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:41,084] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:41,087] [INFO] DFAST_QC result json was written to GCF_025149125.1_ASM2514912v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:41,087] [INFO] DFAST_QC completed!
[2024-01-24 14:21:41,087] [INFO] Total running time: 0h1m56s