[2024-01-24 13:40:42,179] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:42,180] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:42,181] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f2780ec-7856-415c-91fd-5379516a36a8/dqc_reference
[2024-01-24 13:40:43,568] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:43,569] [INFO] Task started: Prodigal
[2024-01-24 13:40:43,569] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5a30d09-67f5-402d-a3d0-3c93b667c1d3/GCF_002029255.1_ASM202925v1_genomic.fna.gz | prodigal -d GCF_002029255.1_ASM202925v1_genomic.fna/cds.fna -a GCF_002029255.1_ASM202925v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:52,557] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:52,557] [INFO] Task started: HMMsearch
[2024-01-24 13:40:52,557] [INFO] Running command: hmmsearch --tblout GCF_002029255.1_ASM202925v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f2780ec-7856-415c-91fd-5379516a36a8/dqc_reference/reference_markers.hmm GCF_002029255.1_ASM202925v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:52,972] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:52,974] [INFO] Found 6/6 markers.
[2024-01-24 13:40:53,023] [INFO] Query marker FASTA was written to GCF_002029255.1_ASM202925v1_genomic.fna/markers.fasta
[2024-01-24 13:40:53,024] [INFO] Task started: Blastn
[2024-01-24 13:40:53,024] [INFO] Running command: blastn -query GCF_002029255.1_ASM202925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f2780ec-7856-415c-91fd-5379516a36a8/dqc_reference/reference_markers.fasta -out GCF_002029255.1_ASM202925v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:53,655] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:53,658] [INFO] Selected 16 target genomes.
[2024-01-24 13:40:53,659] [INFO] Target genome list was writen to GCF_002029255.1_ASM202925v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:53,667] [INFO] Task started: fastANI
[2024-01-24 13:40:53,667] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5a30d09-67f5-402d-a3d0-3c93b667c1d3/GCF_002029255.1_ASM202925v1_genomic.fna.gz --refList GCF_002029255.1_ASM202925v1_genomic.fna/target_genomes.txt --output GCF_002029255.1_ASM202925v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:12,596] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:12,596] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f2780ec-7856-415c-91fd-5379516a36a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:12,596] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f2780ec-7856-415c-91fd-5379516a36a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:12,609] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:12,609] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:12,609] [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 chromiireducens	strain=DSM 23318	GCA_002029255.1	225345	225345	type	True	100.0	1720	1727	95	conclusive
Clostridium diolis	strain=DSM 15410	GCA_008705175.1	223919	223919	suspected-type	True	82.7184	1057	1727	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	82.5818	1015	1727	95	below_threshold
Clostridium diolis	strain=DSM 15410	GCA_008580445.1	223919	223919	suspected-type	True	82.581	1048	1727	95	below_threshold
Clostridium beijerinckii	strain=NCTC13035	GCA_900447025.1	1520	1520	suspected-type	True	82.5786	1004	1727	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_002006445.1	1520	1520	suspected-type	True	82.4725	990	1727	95	below_threshold
Clostridium puniceum	strain=DSM 2619	GCA_002006345.1	29367	29367	type	True	81.2879	822	1727	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	81.1945	916	1727	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=N1-4(HMT)	GCA_000340885.1	36745	36745	type	True	80.8367	865	1727	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=ATCC 27021	GCA_000334435.1	36745	36745	type	True	80.7281	849	1727	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_000473995.1	169679	169679	type	True	80.3956	681	1727	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_001657435.1	169679	169679	type	True	80.3882	620	1727	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	77.3864	286	1727	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	76.34	210	1727	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:12,611] [INFO] DFAST Taxonomy check result was written to GCF_002029255.1_ASM202925v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:12,611] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:12,611] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:12,611] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f2780ec-7856-415c-91fd-5379516a36a8/dqc_reference/checkm_data
[2024-01-24 13:41:12,613] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:12,667] [INFO] Task started: CheckM
[2024-01-24 13:41:12,667] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002029255.1_ASM202925v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002029255.1_ASM202925v1_genomic.fna/checkm_input GCF_002029255.1_ASM202925v1_genomic.fna/checkm_result
[2024-01-24 13:41:45,518] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:45,519] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:45,551] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:45,551] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:45,552] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002029255.1_ASM202925v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:45,552] [INFO] Task started: Blastn
[2024-01-24 13:41:45,552] [INFO] Running command: blastn -query GCF_002029255.1_ASM202925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f2780ec-7856-415c-91fd-5379516a36a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002029255.1_ASM202925v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:46,401] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:46,404] [INFO] Selected 11 target genomes.
[2024-01-24 13:41:46,405] [INFO] Target genome list was writen to GCF_002029255.1_ASM202925v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:46,434] [INFO] Task started: fastANI
[2024-01-24 13:41:46,434] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5a30d09-67f5-402d-a3d0-3c93b667c1d3/GCF_002029255.1_ASM202925v1_genomic.fna.gz --refList GCF_002029255.1_ASM202925v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002029255.1_ASM202925v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:59,044] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:59,057] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:59,057] [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_002029255.1	s__Clostridium chromiireducens	100.0	1720	1727	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.07	97.40	0.90	0.87	3	conclusive
GCF_002760435.1	s__Clostridium sp002760435	82.9649	1022	1727	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_018223745.1	s__Clostridium beijerinckii	82.5573	1018	1727	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.01	95.18	0.85	0.79	244	-
GCF_000621745.1	s__Clostridium beijerinckii_A	82.4712	974	1727	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003129525.1	s__Clostridium beijerinckii_D	81.5473	826	1727	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000230835.1	s__Clostridium sp000230835	81.456	929	1727	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.12	96.12	0.82	0.82	2	-
GCF_002006345.1	s__Clostridium puniceum	81.3659	813	1727	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000340885.1	s__Clostridium saccharoperbutylacetonicum	80.8107	866	1727	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.35	98.00	0.96	0.89	7	-
GCF_000473995.1	s__Clostridium saccharobutylicum	80.3865	685	1727	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.89	95.82	0.99	0.83	65	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:59,059] [INFO] GTDB search result was written to GCF_002029255.1_ASM202925v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:59,059] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:59,063] [INFO] DFAST_QC result json was written to GCF_002029255.1_ASM202925v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:59,063] [INFO] DFAST_QC completed!
[2024-01-24 13:41:59,063] [INFO] Total running time: 0h1m17s