[2024-01-25 20:05:50,477] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:05:50,482] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:05:50,482] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bc49d16-ea34-4cff-9cd3-a569ad7172d3/dqc_reference
[2024-01-25 20:05:51,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:05:51,643] [INFO] Task started: Prodigal
[2024-01-25 20:05:51,643] [INFO] Running command: gunzip -c /var/lib/cwl/stg37085fe0-68e5-4bdd-ac23-9be1b09433dc/GCF_020736665.1_ASM2073666v1_genomic.fna.gz | prodigal -d GCF_020736665.1_ASM2073666v1_genomic.fna/cds.fna -a GCF_020736665.1_ASM2073666v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:56,043] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:56,044] [INFO] Task started: HMMsearch
[2024-01-25 20:05:56,044] [INFO] Running command: hmmsearch --tblout GCF_020736665.1_ASM2073666v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bc49d16-ea34-4cff-9cd3-a569ad7172d3/dqc_reference/reference_markers.hmm GCF_020736665.1_ASM2073666v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:56,316] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:56,317] [INFO] Found 6/6 markers.
[2024-01-25 20:05:56,345] [INFO] Query marker FASTA was written to GCF_020736665.1_ASM2073666v1_genomic.fna/markers.fasta
[2024-01-25 20:05:56,345] [INFO] Task started: Blastn
[2024-01-25 20:05:56,346] [INFO] Running command: blastn -query GCF_020736665.1_ASM2073666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bc49d16-ea34-4cff-9cd3-a569ad7172d3/dqc_reference/reference_markers.fasta -out GCF_020736665.1_ASM2073666v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:56,907] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:56,910] [INFO] Selected 17 target genomes.
[2024-01-25 20:05:56,910] [INFO] Target genome list was writen to GCF_020736665.1_ASM2073666v1_genomic.fna/target_genomes.txt
[2024-01-25 20:05:56,915] [INFO] Task started: fastANI
[2024-01-25 20:05:56,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg37085fe0-68e5-4bdd-ac23-9be1b09433dc/GCF_020736665.1_ASM2073666v1_genomic.fna.gz --refList GCF_020736665.1_ASM2073666v1_genomic.fna/target_genomes.txt --output GCF_020736665.1_ASM2073666v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:06:11,103] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:11,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bc49d16-ea34-4cff-9cd3-a569ad7172d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:06:11,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bc49d16-ea34-4cff-9cd3-a569ad7172d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:06:11,114] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:06:11,114] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:06:11,114] [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 septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	100.0	1133	1133	95	conclusive
Clostridium septicum	strain=DSM 7534	GCA_003606265.1	1504	1504	type	True	99.9945	1130	1133	95	conclusive
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	85.177	773	1133	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	79.3827	421	1133	95	below_threshold
Clostridium tertium	strain=DSM 2485	GCA_017873245.1	1559	1559	type	True	79.2377	448	1133	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	78.9725	411	1133	95	below_threshold
Clostridium paraputrificum	strain=NCTC11833	GCA_900447045.1	29363	29363	type	True	78.5877	269	1133	95	below_threshold
Clostridium gasigenes	strain=DSM 12272	GCA_900104115.1	94869	94869	type	True	78.4393	396	1133	95	below_threshold
Clostridium diolis	strain=DSM 15410	GCA_008705175.1	223919	223919	suspected-type	True	78.2896	258	1133	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	78.0917	272	1133	95	below_threshold
Clostridium manihotivorum	strain=CT4	GCA_004015185.1	2320868	2320868	type	True	77.9127	188	1133	95	below_threshold
Clostridium mediterraneense	strain=Marseille-P2434	GCA_900091705.1	1805472	1805472	type	True	77.6907	224	1133	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	77.5372	243	1133	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	77.5153	244	1133	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_002006445.1	1520	1520	suspected-type	True	77.3629	254	1133	95	below_threshold
Clostridium diolis	strain=DSM 15410	GCA_008580445.1	223919	223919	suspected-type	True	77.2971	256	1133	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	76.4862	146	1133	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:06:11,116] [INFO] DFAST Taxonomy check result was written to GCF_020736665.1_ASM2073666v1_genomic.fna/tc_result.tsv
[2024-01-25 20:06:11,116] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:06:11,116] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:06:11,117] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bc49d16-ea34-4cff-9cd3-a569ad7172d3/dqc_reference/checkm_data
[2024-01-25 20:06:11,117] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:06:11,153] [INFO] Task started: CheckM
[2024-01-25 20:06:11,153] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020736665.1_ASM2073666v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020736665.1_ASM2073666v1_genomic.fna/checkm_input GCF_020736665.1_ASM2073666v1_genomic.fna/checkm_result
[2024-01-25 20:06:29,835] [INFO] Task succeeded: CheckM
[2024-01-25 20:06:29,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:06:29,851] [INFO] ===== Completeness check finished =====
[2024-01-25 20:06:29,852] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:06:29,852] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020736665.1_ASM2073666v1_genomic.fna/markers.fasta)
[2024-01-25 20:06:29,852] [INFO] Task started: Blastn
[2024-01-25 20:06:29,852] [INFO] Running command: blastn -query GCF_020736665.1_ASM2073666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bc49d16-ea34-4cff-9cd3-a569ad7172d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_020736665.1_ASM2073666v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:30,654] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:30,656] [INFO] Selected 14 target genomes.
[2024-01-25 20:06:30,656] [INFO] Target genome list was writen to GCF_020736665.1_ASM2073666v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:06:30,664] [INFO] Task started: fastANI
[2024-01-25 20:06:30,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg37085fe0-68e5-4bdd-ac23-9be1b09433dc/GCF_020736665.1_ASM2073666v1_genomic.fna.gz --refList GCF_020736665.1_ASM2073666v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020736665.1_ASM2073666v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:41,547] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:41,558] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:06:41,558] [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_003606265.1	s__Clostridium septicum	99.9945	1130	1133	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.65	99.48	0.94	0.92	5	conclusive
GCF_002327185.1	s__Clostridium chauvoei	85.1675	773	1133	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.96	99.88	0.99	0.99	5	-
GCF_017873245.1	s__Clostridium tertium	79.2277	449	1133	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.32	97.37	0.91	0.89	19	-
GCF_015550425.1	s__Clostridium sp015550425	79.1185	465	1133	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.01	99.01	0.93	0.93	2	-
GCF_000401215.1	s__Clostridium sartagoforme_A	79.0612	402	1133	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.25	98.25	0.85	0.85	2	-
GCA_017888565.1	s__Clostridium sp017888565	78.9061	449	1133	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_900759995.1	s__Clostridium sp900759995	78.7933	362	1133	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.46	98.18	0.80	0.79	3	-
GCF_004794105.1	s__Clostridium sartagoforme_B	78.626	384	1133	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.58	98.58	0.90	0.90	2	-
GCA_018372555.1	s__Clostridium sp018372555	78.2839	310	1133	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_001405015.1	s__Clostridium disporicum	78.1655	309	1133	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.24	98.87	0.93	0.88	4	-
GCA_900547475.1	s__Clostridium sp900547475	78.1651	355	1133	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.47	95.30	0.88	0.84	3	-
GCF_015667795.1	s__Clostridium sp015667795	78.012	384	1133	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_900543325.1	s__Clostridium sp900543325	77.8836	311	1133	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_017383505.1	s__Clostridium sp017383505	77.6862	178	1133	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:06:41,559] [INFO] GTDB search result was written to GCF_020736665.1_ASM2073666v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:41,560] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:41,563] [INFO] DFAST_QC result json was written to GCF_020736665.1_ASM2073666v1_genomic.fna/dqc_result.json
[2024-01-25 20:06:41,564] [INFO] DFAST_QC completed!
[2024-01-25 20:06:41,564] [INFO] Total running time: 0h0m51s