[2024-01-24 15:26:38,225] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:38,228] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:38,228] [INFO] DQC Reference Directory: /var/lib/cwl/stga837367a-db18-4552-af8e-d4267fd946a5/dqc_reference
[2024-01-24 15:26:39,659] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:39,660] [INFO] Task started: Prodigal
[2024-01-24 15:26:39,660] [INFO] Running command: gunzip -c /var/lib/cwl/stga0ccd699-c57a-48bd-84cb-52aaf30df17d/GCF_002995785.1_ASM299578v1_genomic.fna.gz | prodigal -d GCF_002995785.1_ASM299578v1_genomic.fna/cds.fna -a GCF_002995785.1_ASM299578v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:44,405] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:44,405] [INFO] Task started: HMMsearch
[2024-01-24 15:26:44,405] [INFO] Running command: hmmsearch --tblout GCF_002995785.1_ASM299578v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga837367a-db18-4552-af8e-d4267fd946a5/dqc_reference/reference_markers.hmm GCF_002995785.1_ASM299578v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:44,688] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:44,690] [INFO] Found 6/6 markers.
[2024-01-24 15:26:44,719] [INFO] Query marker FASTA was written to GCF_002995785.1_ASM299578v1_genomic.fna/markers.fasta
[2024-01-24 15:26:44,720] [INFO] Task started: Blastn
[2024-01-24 15:26:44,720] [INFO] Running command: blastn -query GCF_002995785.1_ASM299578v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga837367a-db18-4552-af8e-d4267fd946a5/dqc_reference/reference_markers.fasta -out GCF_002995785.1_ASM299578v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:46,794] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:46,797] [INFO] Selected 18 target genomes.
[2024-01-24 15:26:46,797] [INFO] Target genome list was writen to GCF_002995785.1_ASM299578v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:46,820] [INFO] Task started: fastANI
[2024-01-24 15:26:46,820] [INFO] Running command: fastANI --query /var/lib/cwl/stga0ccd699-c57a-48bd-84cb-52aaf30df17d/GCF_002995785.1_ASM299578v1_genomic.fna.gz --refList GCF_002995785.1_ASM299578v1_genomic.fna/target_genomes.txt --output GCF_002995785.1_ASM299578v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:26:59,797] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:59,798] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga837367a-db18-4552-af8e-d4267fd946a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:26:59,798] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga837367a-db18-4552-af8e-d4267fd946a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:26:59,815] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:26:59,815] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:26:59,815] [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 liquoris	strain=DSM 100320	GCA_002995785.1	1289519	1289519	type	True	100.0	917	921	95	conclusive
Clostridium lundense	strain=DSM 17049	GCA_000619945.1	319475	319475	type	True	83.6762	673	921	95	below_threshold
Clostridium tetanomorphum	strain=DSM 4474	GCA_017873215.1	1553	1553	type	True	81.3642	568	921	95	below_threshold
Clostridium rectalis	strain=Marseille-P4200	GCA_900626095.1	2040295	2040295	type	True	78.3732	312	921	95	below_threshold
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	78.3211	271	921	95	below_threshold
Clostridium cochlearium	strain=NCTC13027	GCA_900187165.1	1494	1494	type	True	78.3086	258	921	95	below_threshold
Clostridium tepidum	strain=IEH 97212	GCA_002008345.1	1962263	1962263	type	True	78.178	212	921	95	below_threshold
Clostridium tetani	strain=ATCC 19406	GCA_900167265.1	1513	1513	type	True	77.4816	242	921	95	below_threshold
Clostridium botulinum	strain=ATCC 25763	GCA_011017965.1	1491	1491	type	True	77.1057	213	921	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	76.9837	221	921	95	below_threshold
Clostridium senegalense	strain=type strain: JC122	GCA_000285575.1	1465809	1465809	type	True	76.7345	127	921	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	76.1665	113	921	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=ATCC 27021	GCA_000334435.1	36745	36745	type	True	76.1581	107	921	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=N1-4(HMT)	GCA_000340885.1	36745	36745	type	True	76.1379	107	921	95	below_threshold
Clostridium massiliamazoniense	strain=ND2	GCA_001403635.1	1347366	1347366	type	True	76.0187	102	921	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:26:59,817] [INFO] DFAST Taxonomy check result was written to GCF_002995785.1_ASM299578v1_genomic.fna/tc_result.tsv
[2024-01-24 15:26:59,818] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:26:59,818] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:26:59,818] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga837367a-db18-4552-af8e-d4267fd946a5/dqc_reference/checkm_data
[2024-01-24 15:26:59,819] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:26:59,852] [INFO] Task started: CheckM
[2024-01-24 15:26:59,852] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002995785.1_ASM299578v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002995785.1_ASM299578v1_genomic.fna/checkm_input GCF_002995785.1_ASM299578v1_genomic.fna/checkm_result
[2024-01-24 15:27:21,254] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:21,256] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:21,274] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:21,275] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:21,275] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002995785.1_ASM299578v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:21,276] [INFO] Task started: Blastn
[2024-01-24 15:27:21,276] [INFO] Running command: blastn -query GCF_002995785.1_ASM299578v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga837367a-db18-4552-af8e-d4267fd946a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_002995785.1_ASM299578v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:22,100] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:22,109] [INFO] Selected 12 target genomes.
[2024-01-24 15:27:22,110] [INFO] Target genome list was writen to GCF_002995785.1_ASM299578v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:22,119] [INFO] Task started: fastANI
[2024-01-24 15:27:22,119] [INFO] Running command: fastANI --query /var/lib/cwl/stga0ccd699-c57a-48bd-84cb-52aaf30df17d/GCF_002995785.1_ASM299578v1_genomic.fna.gz --refList GCF_002995785.1_ASM299578v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002995785.1_ASM299578v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:30,511] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:30,527] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:30,527] [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_002995785.1	s__Clostridium_AO liquoris	100.0	917	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AO	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000619945.1	s__Clostridium_AO lundense	83.6693	673	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873215.1	s__Clostridium_AO tetanomorphum	81.3498	569	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AO	95.0	99.85	99.71	0.98	0.97	5	-
GCF_900626095.1	s__Clostridium_AS rectalis	78.3483	314	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AS	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018918285.1	s__MSJ-11 sp018918285	78.3353	270	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__MSJ-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187165.1	s__Clostridium_G cochlearium	78.2798	260	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_G	95.0	99.06	98.56	0.90	0.85	10	-
GCF_002008345.1	s__Clostridium_F tepidum	78.1772	212	921	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_900185645.1	s__Clostridium_AK sp900185645	78.0418	255	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AK	95.0	96.24	95.22	0.84	0.82	3	-
GCF_900167265.1	s__Clostridium_G tetani	77.4694	243	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_G	95.0	99.11	96.49	0.94	0.90	43	-
GCF_012926525.1	s__Clostridium_AM sp012926525	76.9837	221	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001276215.1	s__Clostridium_F sp001276215	76.8829	191	921	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_000789395.1	s__Clostridium baratii	75.9695	107	921	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.53	95.37	0.92	0.89	15	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:30,529] [INFO] GTDB search result was written to GCF_002995785.1_ASM299578v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:30,530] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:30,534] [INFO] DFAST_QC result json was written to GCF_002995785.1_ASM299578v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:30,534] [INFO] DFAST_QC completed!
[2024-01-24 15:27:30,534] [INFO] Total running time: 0h0m52s