[2024-01-25 19:39:50,522] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:39:50,523] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:39:50,524] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5055cef-3cc9-4c7a-b8b8-5efd76b224c9/dqc_reference
[2024-01-25 19:39:51,660] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:39:51,661] [INFO] Task started: Prodigal
[2024-01-25 19:39:51,661] [INFO] Running command: gunzip -c /var/lib/cwl/stg65d134ac-6024-49b0-8e5e-8a40fd14fb0b/GCF_017873185.1_ASM1787318v1_genomic.fna.gz | prodigal -d GCF_017873185.1_ASM1787318v1_genomic.fna/cds.fna -a GCF_017873185.1_ASM1787318v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:39:56,031] [INFO] Task succeeded: Prodigal
[2024-01-25 19:39:56,031] [INFO] Task started: HMMsearch
[2024-01-25 19:39:56,031] [INFO] Running command: hmmsearch --tblout GCF_017873185.1_ASM1787318v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5055cef-3cc9-4c7a-b8b8-5efd76b224c9/dqc_reference/reference_markers.hmm GCF_017873185.1_ASM1787318v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:39:56,293] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:39:56,294] [INFO] Found 6/6 markers.
[2024-01-25 19:39:56,320] [INFO] Query marker FASTA was written to GCF_017873185.1_ASM1787318v1_genomic.fna/markers.fasta
[2024-01-25 19:39:56,320] [INFO] Task started: Blastn
[2024-01-25 19:39:56,320] [INFO] Running command: blastn -query GCF_017873185.1_ASM1787318v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5055cef-3cc9-4c7a-b8b8-5efd76b224c9/dqc_reference/reference_markers.fasta -out GCF_017873185.1_ASM1787318v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:56,865] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:56,867] [INFO] Selected 17 target genomes.
[2024-01-25 19:39:56,868] [INFO] Target genome list was writen to GCF_017873185.1_ASM1787318v1_genomic.fna/target_genomes.txt
[2024-01-25 19:39:56,894] [INFO] Task started: fastANI
[2024-01-25 19:39:56,895] [INFO] Running command: fastANI --query /var/lib/cwl/stg65d134ac-6024-49b0-8e5e-8a40fd14fb0b/GCF_017873185.1_ASM1787318v1_genomic.fna.gz --refList GCF_017873185.1_ASM1787318v1_genomic.fna/target_genomes.txt --output GCF_017873185.1_ASM1787318v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:40:07,514] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:07,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5055cef-3cc9-4c7a-b8b8-5efd76b224c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:40:07,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5055cef-3cc9-4c7a-b8b8-5efd76b224c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:40:07,528] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:40:07,528] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:40:07,528] [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
Clostridioides mangenotii	strain=DSM 1289	GCA_017873185.1	1540	1540	suspected-type	True	100.0	979	980	95	conclusive
Paraclostridium dentum	strain=SKVG24	GCA_012922555.1	2662455	2662455	type	True	77.9893	178	980	95	below_threshold
Clostridioides difficile	strain=DSM 1296	GCA_000438845.1	1496	1496	type	True	77.9824	241	980	95	below_threshold
Terrisporobacter mayombei	strain=DSM 6539	GCA_020748465.1	1541	1541	type	True	77.9344	163	980	95	below_threshold
Clostridioides difficile	strain=ATCC 9689	GCA_000376285.1	1496	1496	type	True	77.8998	238	980	95	below_threshold
[Clostridium] dakarense	strain=FF1	GCA_000499525.1	1301100	1301100	type	True	77.8987	194	980	95	below_threshold
Terrisporobacter petrolearius	strain=LAM0A37	GCA_020748185.1	1460447	1460447	type	True	77.8213	134	980	95	below_threshold
Paeniclostridium sordellii	strain=ATCC9714	GCA_000953675.1	1505	1505	type	True	77.7725	168	980	95	below_threshold
Romboutsia ilealis	strain=CRIB	GCA_900015215.1	1115758	1115758	type	True	77.6336	142	980	95	below_threshold
Romboutsia hominis	strain=FRIFI	GCA_900002575.1	1507512	1507512	type	True	77.6178	168	980	95	below_threshold
Romboutsia lituseburensis	strain=A25K	GCA_900002825.1	1537	1537	type	True	77.5843	181	980	95	below_threshold
Romboutsia lituseburensis	strain=DSM 797	GCA_900103615.1	1537	1537	type	True	77.4931	186	980	95	below_threshold
Romboutsia weinsteinii	strain=CCRI-19649	GCA_002250835.2	2020949	2020949	type	True	77.4426	200	980	95	below_threshold
Terrisporobacter glycolicus	strain=DSM 1288	GCA_000439105.1	36841	36841	suspected-type	True	77.441	152	980	95	below_threshold
Romboutsia timonensis	strain=Marseille-P326	GCA_900106845.1	1776391	1776391	type	True	77.3828	153	980	95	below_threshold
Peptacetobacter hominis	strain=ZHW00191	GCA_006861675.1	2743610	2743610	type	True	77.2131	96	980	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:40:07,531] [INFO] DFAST Taxonomy check result was written to GCF_017873185.1_ASM1787318v1_genomic.fna/tc_result.tsv
[2024-01-25 19:40:07,532] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:40:07,532] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:40:07,532] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5055cef-3cc9-4c7a-b8b8-5efd76b224c9/dqc_reference/checkm_data
[2024-01-25 19:40:07,533] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:40:07,571] [INFO] Task started: CheckM
[2024-01-25 19:40:07,571] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873185.1_ASM1787318v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873185.1_ASM1787318v1_genomic.fna/checkm_input GCF_017873185.1_ASM1787318v1_genomic.fna/checkm_result
[2024-01-25 19:40:26,178] [INFO] Task succeeded: CheckM
[2024-01-25 19:40:26,179] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:40:26,195] [INFO] ===== Completeness check finished =====
[2024-01-25 19:40:26,195] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:40:26,196] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873185.1_ASM1787318v1_genomic.fna/markers.fasta)
[2024-01-25 19:40:26,196] [INFO] Task started: Blastn
[2024-01-25 19:40:26,196] [INFO] Running command: blastn -query GCF_017873185.1_ASM1787318v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5055cef-3cc9-4c7a-b8b8-5efd76b224c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873185.1_ASM1787318v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:26,905] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:26,908] [INFO] Selected 13 target genomes.
[2024-01-25 19:40:26,908] [INFO] Target genome list was writen to GCF_017873185.1_ASM1787318v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:40:26,927] [INFO] Task started: fastANI
[2024-01-25 19:40:26,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg65d134ac-6024-49b0-8e5e-8a40fd14fb0b/GCF_017873185.1_ASM1787318v1_genomic.fna.gz --refList GCF_017873185.1_ASM1787318v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873185.1_ASM1787318v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:40:34,648] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:34,657] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:40:34,657] [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_017873185.1	s__Clostridioides_A mangenotii	100.0	979	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridioides_A	95.0	96.86	96.86	0.88	0.88	2	conclusive
GCF_000498755.1	s__Clostridioides_A mangenotii_A	93.9746	827	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridioides_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018917235.1	s__Clostridioides_A sp002390935	83.8671	754	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridioides_A	95.0	96.42	96.30	0.91	0.89	4	-
GCF_017590215.1	s__CCUG-7971 sp017590215	78.0238	186	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__CCUG-7971	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002251085.2	s__Romboutsia_B maritimum	77.9622	163	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000499525.1	s__CCUG-7971 spG000499525	77.8987	194	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__CCUG-7971	95.0	100.00	100.00	0.99	0.99	2	-
GCA_018336475.1	s__Romboutsia sp018336475	77.7622	148	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015668515.1	s__Paraclostridium tenue	77.7092	156	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	98.58	97.73	0.92	0.87	8	-
GCF_900103615.1	s__Romboutsia_D lituseburensis	77.5111	185	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia_D	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002250835.2	s__Romboutsia_A weinsteinii	77.4414	201	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015667935.1	s__Intestinibacter sp900540355	77.1624	110	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Intestinibacter	95.0	99.12	98.96	0.88	0.87	4	-
GCA_017425305.1	s__Paraclostridium sp017425305	77.036	84	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	97.54	97.54	0.79	0.79	2	-
GCA_900557165.1	s__Terrisporobacter sp900557165	76.4147	92	980	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	99.06	99.06	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:40:34,658] [INFO] GTDB search result was written to GCF_017873185.1_ASM1787318v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:40:34,659] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:40:34,661] [INFO] DFAST_QC result json was written to GCF_017873185.1_ASM1787318v1_genomic.fna/dqc_result.json
[2024-01-25 19:40:34,662] [INFO] DFAST_QC completed!
[2024-01-25 19:40:34,662] [INFO] Total running time: 0h0m44s