[2023-06-13 15:14:34,190] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:14:34,193] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:14:34,193] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f778afc-1a20-4e52-90e8-af08b3122a86/dqc_reference
[2023-06-13 15:14:35,415] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:14:35,415] [INFO] Task started: Prodigal
[2023-06-13 15:14:35,416] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ef1388e-6a2b-47fa-a0e7-7d0b945ae460/GCA_022780205.1_ASM2278020v1_genomic.fna.gz | prodigal -d GCA_022780205.1_ASM2278020v1_genomic.fna/cds.fna -a GCA_022780205.1_ASM2278020v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:14:40,451] [INFO] Task succeeded: Prodigal
[2023-06-13 15:14:40,451] [INFO] Task started: HMMsearch
[2023-06-13 15:14:40,452] [INFO] Running command: hmmsearch --tblout GCA_022780205.1_ASM2278020v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f778afc-1a20-4e52-90e8-af08b3122a86/dqc_reference/reference_markers.hmm GCA_022780205.1_ASM2278020v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:14:40,701] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:14:40,702] [INFO] Found 6/6 markers.
[2023-06-13 15:14:40,732] [INFO] Query marker FASTA was written to GCA_022780205.1_ASM2278020v1_genomic.fna/markers.fasta
[2023-06-13 15:14:40,732] [INFO] Task started: Blastn
[2023-06-13 15:14:40,732] [INFO] Running command: blastn -query GCA_022780205.1_ASM2278020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f778afc-1a20-4e52-90e8-af08b3122a86/dqc_reference/reference_markers.fasta -out GCA_022780205.1_ASM2278020v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:14:41,318] [INFO] Task succeeded: Blastn
[2023-06-13 15:14:41,324] [INFO] Selected 21 target genomes.
[2023-06-13 15:14:41,324] [INFO] Target genome list was writen to GCA_022780205.1_ASM2278020v1_genomic.fna/target_genomes.txt
[2023-06-13 15:14:41,326] [INFO] Task started: fastANI
[2023-06-13 15:14:41,327] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ef1388e-6a2b-47fa-a0e7-7d0b945ae460/GCA_022780205.1_ASM2278020v1_genomic.fna.gz --refList GCA_022780205.1_ASM2278020v1_genomic.fna/target_genomes.txt --output GCA_022780205.1_ASM2278020v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:14:55,953] [INFO] Task succeeded: fastANI
[2023-06-13 15:14:55,954] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f778afc-1a20-4e52-90e8-af08b3122a86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:14:55,955] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f778afc-1a20-4e52-90e8-af08b3122a86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:14:55,969] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 15:14:55,969] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 15:14:55,970] [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 fessum	strain=SNUG30386	GCA_003024715.1	2126740	2126740	type	True	78.4986	194	642	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	77.2006	95	642	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	77.0388	84	642	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	76.9991	68	642	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.9751	84	642	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	76.962	69	642	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	76.9399	93	642	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	76.9361	69	642	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.9082	84	642	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	76.4793	80	642	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 15:14:55,972] [INFO] DFAST Taxonomy check result was written to GCA_022780205.1_ASM2278020v1_genomic.fna/tc_result.tsv
[2023-06-13 15:14:55,972] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:14:55,972] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:14:55,973] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f778afc-1a20-4e52-90e8-af08b3122a86/dqc_reference/checkm_data
[2023-06-13 15:14:55,974] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:14:56,000] [INFO] Task started: CheckM
[2023-06-13 15:14:56,000] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022780205.1_ASM2278020v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022780205.1_ASM2278020v1_genomic.fna/checkm_input GCA_022780205.1_ASM2278020v1_genomic.fna/checkm_result
[2023-06-13 15:15:18,353] [INFO] Task succeeded: CheckM
[2023-06-13 15:15:18,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.34%
Contamintation: 8.80%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-13 15:15:18,380] [INFO] ===== Completeness check finished =====
[2023-06-13 15:15:18,380] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:15:18,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022780205.1_ASM2278020v1_genomic.fna/markers.fasta)
[2023-06-13 15:15:18,381] [INFO] Task started: Blastn
[2023-06-13 15:15:18,381] [INFO] Running command: blastn -query GCA_022780205.1_ASM2278020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f778afc-1a20-4e52-90e8-af08b3122a86/dqc_reference/reference_markers_gtdb.fasta -out GCA_022780205.1_ASM2278020v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:15:19,239] [INFO] Task succeeded: Blastn
[2023-06-13 15:15:19,245] [INFO] Selected 24 target genomes.
[2023-06-13 15:15:19,245] [INFO] Target genome list was writen to GCA_022780205.1_ASM2278020v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:15:19,265] [INFO] Task started: fastANI
[2023-06-13 15:15:19,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ef1388e-6a2b-47fa-a0e7-7d0b945ae460/GCA_022780205.1_ASM2278020v1_genomic.fna.gz --refList GCA_022780205.1_ASM2278020v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022780205.1_ASM2278020v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:15:32,398] [INFO] Task succeeded: fastANI
[2023-06-13 15:15:32,413] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 15:15:32,413] [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_016302185.1	s__Clostridium_Q sp016302185	98.1912	439	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003024715.1	s__Clostridium_Q fessum	78.4986	194	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.33	97.70	0.88	0.81	31	-
GCF_000466485.1	s__Clostridium_Q symbiosum	78.3612	171	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.86	98.57	0.86	0.81	32	-
GCA_900547735.1	s__Clostridium_Q sp900547735	78.2509	168	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900626075.1	s__Clostridium_Q transplantifaecale	78.1505	174	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003480315.1	s__Ventrimonas sp003480315	77.9261	104	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	98.62	98.00	0.91	0.88	5	-
GCA_910575795.1	s__Clostridium_Q sp910575795	77.918	174	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	99.66	99.05	0.95	0.91	4	-
GCA_018223375.1	s__Clostridium_Q sp000435655	77.8996	138	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.36	96.90	0.90	0.85	8	-
GCA_003478355.1	s__UBA3402 sp003478355	77.6707	84	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	97.92	96.21	0.85	0.69	6	-
GCA_009911305.1	s__Clostridium_Q sp009911305	77.6328	176	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.99	98.99	0.91	0.91	2	-
GCA_900538475.1	s__Ventrimonas sp900538475	77.5447	87	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.39	99.20	0.94	0.93	3	-
GCA_014385265.1	s__Copromonas sp000435795	77.2677	81	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	98.24	96.73	0.89	0.84	6	-
GCF_000235505.1	s__Hungatella_A hathewayi_A	77.1488	103	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Hungatella_A	95.0	99.27	96.59	0.97	0.86	6	-
GCA_905215775.1	s__Copromonas sp905215775	77.0864	86	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282095.1	s__Enterocloster sp900538485	77.0441	88	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.11	98.91	0.91	0.88	5	-
GCF_002899675.1	s__CHH4-2 sp002899675	77.0015	77	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CHH4-2	95.0	100.00	100.00	0.98	0.98	2	-
GCA_018715905.1	s__Caccovicinus merdipullorum	76.9776	91	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	98.94	98.69	0.87	0.79	3	-
GCA_900547035.1	s__Enterocloster excrementigallinarum	76.7973	66	642	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.35	98.28	0.80	0.77	6	-
--------------------------------------------------------------------------------
[2023-06-13 15:15:32,415] [INFO] GTDB search result was written to GCA_022780205.1_ASM2278020v1_genomic.fna/result_gtdb.tsv
[2023-06-13 15:15:32,416] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:15:32,420] [INFO] DFAST_QC result json was written to GCA_022780205.1_ASM2278020v1_genomic.fna/dqc_result.json
[2023-06-13 15:15:32,420] [INFO] DFAST_QC completed!
[2023-06-13 15:15:32,420] [INFO] Total running time: 0h0m58s