[2024-01-24 13:32:41,143] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,145] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,146] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c1812b3-2277-4bc2-b34c-758cefea1412/dqc_reference
[2024-01-24 13:32:42,443] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:42,443] [INFO] Task started: Prodigal
[2024-01-24 13:32:42,443] [INFO] Running command: gunzip -c /var/lib/cwl/stg703e017f-2c44-48f9-8743-d5e276846511/GCF_018919175.1_ASM1891917v1_genomic.fna.gz | prodigal -d GCF_018919175.1_ASM1891917v1_genomic.fna/cds.fna -a GCF_018919175.1_ASM1891917v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:47,691] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:47,691] [INFO] Task started: HMMsearch
[2024-01-24 13:32:47,692] [INFO] Running command: hmmsearch --tblout GCF_018919175.1_ASM1891917v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c1812b3-2277-4bc2-b34c-758cefea1412/dqc_reference/reference_markers.hmm GCF_018919175.1_ASM1891917v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:48,024] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:48,025] [INFO] Found 6/6 markers.
[2024-01-24 13:32:48,053] [INFO] Query marker FASTA was written to GCF_018919175.1_ASM1891917v1_genomic.fna/markers.fasta
[2024-01-24 13:32:48,053] [INFO] Task started: Blastn
[2024-01-24 13:32:48,053] [INFO] Running command: blastn -query GCF_018919175.1_ASM1891917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c1812b3-2277-4bc2-b34c-758cefea1412/dqc_reference/reference_markers.fasta -out GCF_018919175.1_ASM1891917v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:48,605] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:48,608] [INFO] Selected 23 target genomes.
[2024-01-24 13:32:48,608] [INFO] Target genome list was writen to GCF_018919175.1_ASM1891917v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:48,748] [INFO] Task started: fastANI
[2024-01-24 13:32:48,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg703e017f-2c44-48f9-8743-d5e276846511/GCF_018919175.1_ASM1891917v1_genomic.fna.gz --refList GCF_018919175.1_ASM1891917v1_genomic.fna/target_genomes.txt --output GCF_018919175.1_ASM1891917v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:04,678] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:04,679] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c1812b3-2277-4bc2-b34c-758cefea1412/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:04,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c1812b3-2277-4bc2-b34c-758cefea1412/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:04,704] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:04,704] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:04,705] [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 simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	100.0	1245	1246	95	conclusive
Clostridium algidicarnis	strain=DSM 15099	GCA_002934235.1	37659	37659	type	True	79.6732	505	1246	95	below_threshold
Clostridium putrefaciens	strain=NCTC9836	GCA_900461105.1	99675	99675	type	True	79.4474	489	1246	95	below_threshold
Clostridium amylolyticum	strain=DSM 21864	GCA_900142075.1	1121298	1121298	type	True	78.2783	181	1246	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	77.8389	207	1246	95	below_threshold
Clostridium sporogenes	strain=NCIMB 10696	GCA_000973705.1	1509	1509	type	True	77.6712	208	1246	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_001020205.1	1509	1509	type	True	77.6372	203	1246	95	below_threshold
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	77.6191	208	1246	95	below_threshold
Clostridium frigidicarnis	strain=DSM 12271	GCA_900111985.1	84698	84698	type	True	77.5486	218	1246	95	below_threshold
Clostridium lundense	strain=DSM 17049	GCA_000619945.1	319475	319475	type	True	76.9544	193	1246	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	76.8691	190	1246	95	below_threshold
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	76.7765	190	1246	95	below_threshold
Clostridium ihumii	strain=AP5	GCA_000612845.1	1470356	1470356	type	True	76.5998	176	1246	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	76.5477	150	1246	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	76.5203	188	1246	95	below_threshold
Clostridium cavendishii	strain=DSM 21758	GCA_900141845.1	349931	349931	type	True	76.5026	205	1246	95	below_threshold
Clostridium senegalense	strain=type strain: JC122	GCA_000285575.1	1465809	1465809	type	True	76.4587	173	1246	95	below_threshold
Clostridium acidisoli	strain=DSM 12555	GCA_900176305.1	91624	91624	type	True	76.4106	113	1246	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	76.4034	158	1246	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	76.3359	163	1246	95	below_threshold
Clostridium mediterraneense	strain=Marseille-P2434	GCA_900091705.1	1805472	1805472	type	True	75.9639	121	1246	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:04,706] [INFO] DFAST Taxonomy check result was written to GCF_018919175.1_ASM1891917v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:04,707] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:04,707] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:04,707] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c1812b3-2277-4bc2-b34c-758cefea1412/dqc_reference/checkm_data
[2024-01-24 13:33:04,708] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:04,747] [INFO] Task started: CheckM
[2024-01-24 13:33:04,747] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018919175.1_ASM1891917v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018919175.1_ASM1891917v1_genomic.fna/checkm_input GCF_018919175.1_ASM1891917v1_genomic.fna/checkm_result
[2024-01-24 13:33:25,805] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:25,806] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:25,823] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:25,824] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:25,824] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018919175.1_ASM1891917v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:25,824] [INFO] Task started: Blastn
[2024-01-24 13:33:25,824] [INFO] Running command: blastn -query GCF_018919175.1_ASM1891917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c1812b3-2277-4bc2-b34c-758cefea1412/dqc_reference/reference_markers_gtdb.fasta -out GCF_018919175.1_ASM1891917v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:26,626] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:26,629] [INFO] Selected 23 target genomes.
[2024-01-24 13:33:26,629] [INFO] Target genome list was writen to GCF_018919175.1_ASM1891917v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:26,641] [INFO] Task started: fastANI
[2024-01-24 13:33:26,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg703e017f-2c44-48f9-8743-d5e276846511/GCF_018919175.1_ASM1891917v1_genomic.fna.gz --refList GCF_018919175.1_ASM1891917v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018919175.1_ASM1891917v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:41,877] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:41,891] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:41,891] [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
GCA_000753435.1	s__Clostridium_L amazonitimonense	97.9388	1155	1246	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_L	95.0	99.33	97.98	0.97	0.93	4	conclusive
GCF_002934235.1	s__Clostridium_L algidicarnis	79.6732	505	1246	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_L	95.0	97.66	96.15	0.89	0.86	14	-
GCF_900461105.1	s__Clostridium_L putrefaciens	79.428	491	1246	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142075.1	s__Clostridium_AA amylolyticum	78.2997	180	1246	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AA	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001276985.1	s__Clostridium_F botulinum	77.769	229	1246	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_001020205.1	s__Clostridium_F sporogenes	77.6527	202	1246	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_900111985.1	s__Clostridium_Z frigidicarnis	77.5503	219	1246	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	-
GCA_002423705.1	s__Clostridium_X sp002423705	77.2017	168	1246	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	-
GCF_001276215.1	s__Clostridium_F sp001276215	76.9983	223	1246	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_000619945.1	s__Clostridium_AO lundense	76.9611	192	1246	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_000424205.1	s__Clostridium_X cadaveris	76.8254	149	1246	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_X	95.0	99.52	99.40	0.92	0.82	7	-
GCF_900129365.1	s__Clostridium_AH fallax	76.7872	189	1246	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AH	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016316925.1	s__Clostridium_AM aciditolerans	76.7113	173	1246	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	95.27	95.27	0.80	0.80	2	-
GCF_001735765.2	s__Clostridium taeniosporum	76.6813	164	1246	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_000612845.1	s__Clostridium_J ihumii	76.5998	176	1246	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000401215.1	s__Clostridium sartagoforme_A	76.5703	158	1246	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.25	98.25	0.85	0.85	2	-
GCF_014836325.1	s__Clostridium sp014836325	76.3345	162	1246	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	76.2575	150	1246	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_002008345.1	s__Clostridium_F tepidum	76.2292	190	1246	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_014050525.1	s__Clostridium_B sp014050525	76.215	98	1246	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091705.1	s__Clostridium_P mediterraneense	75.9639	121	1246	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000498355.1	s__Clostridium sp000498355	75.8921	170	1246	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:41,893] [INFO] GTDB search result was written to GCF_018919175.1_ASM1891917v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:41,894] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:41,897] [INFO] DFAST_QC result json was written to GCF_018919175.1_ASM1891917v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:41,897] [INFO] DFAST_QC completed!
[2024-01-24 13:33:41,897] [INFO] Total running time: 0h1m1s