[2024-01-24 13:57:45,308] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:45,310] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:45,310] [INFO] DQC Reference Directory: /var/lib/cwl/stg3484fedf-c4b4-4e36-ac39-b0fc9099943e/dqc_reference
[2024-01-24 13:57:46,717] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:46,718] [INFO] Task started: Prodigal
[2024-01-24 13:57:46,719] [INFO] Running command: gunzip -c /var/lib/cwl/stg6bb0d347-e06c-460c-af6f-f5df0efce185/GCF_001243045.1_Clostridium_niameyense_genomic.fna.gz | prodigal -d GCF_001243045.1_Clostridium_niameyense_genomic.fna/cds.fna -a GCF_001243045.1_Clostridium_niameyense_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:50,744] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:50,745] [INFO] Task started: HMMsearch
[2024-01-24 13:57:50,745] [INFO] Running command: hmmsearch --tblout GCF_001243045.1_Clostridium_niameyense_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3484fedf-c4b4-4e36-ac39-b0fc9099943e/dqc_reference/reference_markers.hmm GCF_001243045.1_Clostridium_niameyense_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:51,035] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:51,036] [INFO] Found 6/6 markers.
[2024-01-24 13:57:51,066] [INFO] Query marker FASTA was written to GCF_001243045.1_Clostridium_niameyense_genomic.fna/markers.fasta
[2024-01-24 13:57:51,067] [INFO] Task started: Blastn
[2024-01-24 13:57:51,067] [INFO] Running command: blastn -query GCF_001243045.1_Clostridium_niameyense_genomic.fna/markers.fasta -db /var/lib/cwl/stg3484fedf-c4b4-4e36-ac39-b0fc9099943e/dqc_reference/reference_markers.fasta -out GCF_001243045.1_Clostridium_niameyense_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:51,741] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:51,745] [INFO] Selected 18 target genomes.
[2024-01-24 13:57:51,746] [INFO] Target genome list was writen to GCF_001243045.1_Clostridium_niameyense_genomic.fna/target_genomes.txt
[2024-01-24 13:57:51,788] [INFO] Task started: fastANI
[2024-01-24 13:57:51,789] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bb0d347-e06c-460c-af6f-f5df0efce185/GCF_001243045.1_Clostridium_niameyense_genomic.fna.gz --refList GCF_001243045.1_Clostridium_niameyense_genomic.fna/target_genomes.txt --output GCF_001243045.1_Clostridium_niameyense_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:05,290] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:05,290] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3484fedf-c4b4-4e36-ac39-b0fc9099943e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:05,291] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3484fedf-c4b4-4e36-ac39-b0fc9099943e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:05,306] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:05,306] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:05,307] [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
Clostridium niameyense	strain=MT5	GCA_001243045.1	1622073	1622073	type	True	100.0	845	845	95	conclusive
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	79.4991	457	845	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_001020205.1	1509	1509	type	True	79.4915	458	845	95	below_threshold
Clostridium sporogenes	strain=NCIMB 10696	GCA_000973705.1	1509	1509	type	True	79.4618	455	845	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_000685115.1	1509	1509	type	True	79.426	466	845	95	below_threshold
Clostridium botulinum	strain=ATCC 25763	GCA_001276985.1	1491	1491	type	True	79.2345	458	845	95	below_threshold
Clostridium tepidum	strain=IEH 97212	GCA_002008345.1	1962263	1962263	type	True	79.1931	440	845	95	below_threshold
Clostridium botulinum	strain=ATCC 25763	GCA_011017965.1	1491	1491	type	True	79.1841	462	845	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	77.2235	232	845	95	below_threshold
Clostridium autoethanogenum	strain=DSM 10061	GCA_000484505.2	84023	84023	suspected-type	True	76.8122	159	845	95	below_threshold
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	76.6428	173	845	95	below_threshold
Clostridium felsineum	strain=DSM 794	GCA_002006355.2	36839	36839	type	True	76.5952	141	845	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	76.491	174	845	95	below_threshold
Clostridium swellfunianum	strain=CICC 10730	GCA_023656515.1	1367462	1367462	type	True	76.4259	88	845	95	below_threshold
Clostridium saudiense	strain=JCC	GCA_000577815.1	1414720	1414720	type	True	75.9282	144	845	95	below_threshold
Anaeromicrobium sediminis	strain=DY2726D	GCA_002270055.1	1478221	1478221	type	True	75.2409	66	845	95	below_threshold
Maledivibacter halophilus	strain=M1	GCA_900167445.1	36842	36842	type	True	74.7104	88	845	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:05,308] [INFO] DFAST Taxonomy check result was written to GCF_001243045.1_Clostridium_niameyense_genomic.fna/tc_result.tsv
[2024-01-24 13:58:05,309] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:05,309] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:05,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3484fedf-c4b4-4e36-ac39-b0fc9099943e/dqc_reference/checkm_data
[2024-01-24 13:58:05,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:05,341] [INFO] Task started: CheckM
[2024-01-24 13:58:05,341] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001243045.1_Clostridium_niameyense_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001243045.1_Clostridium_niameyense_genomic.fna/checkm_input GCF_001243045.1_Clostridium_niameyense_genomic.fna/checkm_result
[2024-01-24 13:58:25,298] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:25,302] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:25,332] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:25,332] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:25,333] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001243045.1_Clostridium_niameyense_genomic.fna/markers.fasta)
[2024-01-24 13:58:25,333] [INFO] Task started: Blastn
[2024-01-24 13:58:25,333] [INFO] Running command: blastn -query GCF_001243045.1_Clostridium_niameyense_genomic.fna/markers.fasta -db /var/lib/cwl/stg3484fedf-c4b4-4e36-ac39-b0fc9099943e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001243045.1_Clostridium_niameyense_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:26,150] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:26,156] [INFO] Selected 9 target genomes.
[2024-01-24 13:58:26,156] [INFO] Target genome list was writen to GCF_001243045.1_Clostridium_niameyense_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:26,166] [INFO] Task started: fastANI
[2024-01-24 13:58:26,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bb0d347-e06c-460c-af6f-f5df0efce185/GCF_001243045.1_Clostridium_niameyense_genomic.fna.gz --refList GCF_001243045.1_Clostridium_niameyense_genomic.fna/target_genomes_gtdb.txt --output GCF_001243045.1_Clostridium_niameyense_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:32,823] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:32,831] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:32,832] [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_001243045.1	s__Clostridium_F niameyense	100.0	845	845	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.56	99.11	0.96	0.92	3	conclusive
GCF_001020205.1	s__Clostridium_F sporogenes	79.458	461	845	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.24	98.80	0.94	0.88	81	-
GCF_001889325.1	s__Clostridium_F botulinum_A	79.2849	468	845	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	95.92	95.51	0.89	0.85	52	-
GCF_001276985.1	s__Clostridium_F botulinum	79.2468	456	845	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.69	95.97	0.92	0.83	213	-
GCF_002008345.1	s__Clostridium_F tepidum	79.1769	441	845	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.70	99.54	0.93	0.92	5	-
GCF_001276215.1	s__Clostridium_F sp001276215	79.1154	456	845	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.32	95.44	0.88	0.82	10	-
GCF_000968375.1	s__Clostridium_AM scatologenes	77.1954	249	845	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	96.092	N/A	N/A	N/A	N/A	1	-
GCA_002423705.1	s__Clostridium_X sp002423705	76.153	123	845	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_X	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:32,833] [INFO] GTDB search result was written to GCF_001243045.1_Clostridium_niameyense_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:32,834] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:32,838] [INFO] DFAST_QC result json was written to GCF_001243045.1_Clostridium_niameyense_genomic.fna/dqc_result.json
[2024-01-24 13:58:32,839] [INFO] DFAST_QC completed!
[2024-01-24 13:58:32,839] [INFO] Total running time: 0h0m48s