[2024-01-24 13:59:42,530] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:59:42,534] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:59:42,534] [INFO] DQC Reference Directory: /var/lib/cwl/stgeaab8ff5-e7d3-4aa3-b39e-bc5f335fb4e4/dqc_reference
[2024-01-24 13:59:43,773] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:59:43,774] [INFO] Task started: Prodigal
[2024-01-24 13:59:43,774] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1a3aacf-b7cb-41c3-96f1-8cb758568e5b/GCF_001047375.1_ASM104737v1_genomic.fna.gz | prodigal -d GCF_001047375.1_ASM104737v1_genomic.fna/cds.fna -a GCF_001047375.1_ASM104737v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:47,933] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:47,934] [INFO] Task started: HMMsearch
[2024-01-24 13:59:47,934] [INFO] Running command: hmmsearch --tblout GCF_001047375.1_ASM104737v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeaab8ff5-e7d3-4aa3-b39e-bc5f335fb4e4/dqc_reference/reference_markers.hmm GCF_001047375.1_ASM104737v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:48,169] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:48,171] [INFO] Found 6/6 markers.
[2024-01-24 13:59:48,202] [INFO] Query marker FASTA was written to GCF_001047375.1_ASM104737v1_genomic.fna/markers.fasta
[2024-01-24 13:59:48,202] [INFO] Task started: Blastn
[2024-01-24 13:59:48,202] [INFO] Running command: blastn -query GCF_001047375.1_ASM104737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeaab8ff5-e7d3-4aa3-b39e-bc5f335fb4e4/dqc_reference/reference_markers.fasta -out GCF_001047375.1_ASM104737v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:48,799] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:48,802] [INFO] Selected 17 target genomes.
[2024-01-24 13:59:48,802] [INFO] Target genome list was writen to GCF_001047375.1_ASM104737v1_genomic.fna/target_genomes.txt
[2024-01-24 13:59:48,813] [INFO] Task started: fastANI
[2024-01-24 13:59:48,814] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1a3aacf-b7cb-41c3-96f1-8cb758568e5b/GCF_001047375.1_ASM104737v1_genomic.fna.gz --refList GCF_001047375.1_ASM104737v1_genomic.fna/target_genomes.txt --output GCF_001047375.1_ASM104737v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:57,799] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:57,800] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeaab8ff5-e7d3-4aa3-b39e-bc5f335fb4e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:57,801] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeaab8ff5-e7d3-4aa3-b39e-bc5f335fb4e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:57,824] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:57,825] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:57,825] [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 cylindrosporum	strain=DSM 605	GCA_001047375.1	1495	1495	type	True	99.9718	901	902	95	conclusive
Clostridium niameyense	strain=MT5	GCA_001243045.1	1622073	1622073	type	True	76.2676	60	902	95	below_threshold
Clostridium paraputrificum	strain=NCTC11833	GCA_900447045.1	29363	29363	type	True	76.2293	56	902	95	below_threshold
Caloramator australicus	strain=RC3	GCA_000297115.1	515264	515264	type	True	75.9813	53	902	95	below_threshold
Clostridium perfringens	strain=FDAARGOS_903	GCA_016027375.1	1502	1502	type	True	75.9761	71	902	95	below_threshold
Clostridium magnum	strain=DSM 2767	GCA_001623875.1	33954	33954	type	True	75.969	78	902	95	below_threshold
Clostridium perfringens	strain=ATCC 13124	GCA_000013285.1	1502	1502	type	True	75.9376	66	902	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	75.9212	77	902	95	below_threshold
Clostridium pasteurianum	strain=ATCC 6013	GCA_001856645.1	1501	1501	type	True	75.8795	56	902	95	below_threshold
Clostridium pasteurianum	strain=DSM 525	GCA_000807255.1	1501	1501	type	True	75.8348	58	902	95	below_threshold
Clostridium pasteurianum	strain=DSM 525	GCA_000330945.1	1501	1501	type	True	75.8183	57	902	95	below_threshold
Clostridium hydrogeniformans	strain=DSM 21757	GCA_000686705.1	349933	349933	type	True	75.7785	81	902	95	below_threshold
Clostridium magnum	strain=DSM 2767	GCA_900129955.1	33954	33954	type	True	75.5848	75	902	95	below_threshold
Clostridium arbusti	strain=SL206	GCA_000246895.2	1137848	1137848	type	True	75.5463	57	902	95	below_threshold
Clostridium lundense	strain=DSM 17049	GCA_000619945.1	319475	319475	type	True	75.5313	65	902	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:57,826] [INFO] DFAST Taxonomy check result was written to GCF_001047375.1_ASM104737v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:57,827] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:57,827] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:57,827] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeaab8ff5-e7d3-4aa3-b39e-bc5f335fb4e4/dqc_reference/checkm_data
[2024-01-24 13:59:57,828] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:57,859] [INFO] Task started: CheckM
[2024-01-24 13:59:57,860] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001047375.1_ASM104737v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001047375.1_ASM104737v1_genomic.fna/checkm_input GCF_001047375.1_ASM104737v1_genomic.fna/checkm_result
[2024-01-24 14:00:17,571] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:17,573] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:17,592] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:17,592] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:17,593] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001047375.1_ASM104737v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:17,593] [INFO] Task started: Blastn
[2024-01-24 14:00:17,593] [INFO] Running command: blastn -query GCF_001047375.1_ASM104737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeaab8ff5-e7d3-4aa3-b39e-bc5f335fb4e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_001047375.1_ASM104737v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:18,400] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:18,404] [INFO] Selected 20 target genomes.
[2024-01-24 14:00:18,404] [INFO] Target genome list was writen to GCF_001047375.1_ASM104737v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:18,418] [INFO] Task started: fastANI
[2024-01-24 14:00:18,419] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1a3aacf-b7cb-41c3-96f1-8cb758568e5b/GCF_001047375.1_ASM104737v1_genomic.fna.gz --refList GCF_001047375.1_ASM104737v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001047375.1_ASM104737v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:27,382] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:27,398] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:27,399] [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_001047375.1	s__Clostridium_AB cylindrosporum	100.0	900	902	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Clostridium_AB	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000430995.1	s__Thermobrachium celere	77.288	68	902	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Thermobrachium	95.0	98.16	98.16	0.91	0.91	2	-
GCF_017100085.1	s__Clostridium_H botulinum_A	76.3899	50	902	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0162	99.30	99.03	0.94	0.90	14	-
GCF_016908015.1	s__Clostridium_AK pascui	76.3204	52	902	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AK	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001243045.1	s__Clostridium_F niameyense	76.2968	59	902	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	-
GCF_006016075.1	s__Caloramator_B sp006016075	76.2438	63	902	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900447045.1	s__Clostridium paraputrificum	76.2292	56	902	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.58	95.42	0.89	0.83	29	-
GCF_000297115.1	s__Caloramator australicus	75.9813	53	902	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000204565.1	s__Clostridium_H botulinum_B	75.9717	54	902	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0162	99.87	99.52	0.98	0.95	19	-
GCF_000013285.1	s__Clostridium_P perfringens	75.9376	66	902	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	98.05	95.74	0.91	0.81	315	-
GCF_000686705.1	s__Clostridium_Z hydrogeniformans	75.7628	82	902	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004794105.1	s__Clostridium sartagoforme_B	75.6878	79	902	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.58	98.58	0.90	0.90	2	-
GCF_000619945.1	s__Clostridium_AO lundense	75.5606	63	902	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_000246895.1	s__Clostridium_I arbusti	75.5505	57	902	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_I	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:27,400] [INFO] GTDB search result was written to GCF_001047375.1_ASM104737v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:27,401] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:27,404] [INFO] DFAST_QC result json was written to GCF_001047375.1_ASM104737v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:27,404] [INFO] DFAST_QC completed!
[2024-01-24 14:00:27,404] [INFO] Total running time: 0h0m45s