[2024-01-25 18:58:05,616] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:58:05,618] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:58:05,618] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd529704-be4b-4d0e-ba1c-7ed2c74c7efe/dqc_reference
[2024-01-25 18:58:06,791] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:58:06,792] [INFO] Task started: Prodigal
[2024-01-25 18:58:06,792] [INFO] Running command: gunzip -c /var/lib/cwl/stg30c70c75-c25b-4294-9fe1-917f81cd4549/GCF_000392375.2_ASM39237v2_genomic.fna.gz | prodigal -d GCF_000392375.2_ASM39237v2_genomic.fna/cds.fna -a GCF_000392375.2_ASM39237v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:58:11,273] [INFO] Task succeeded: Prodigal
[2024-01-25 18:58:11,273] [INFO] Task started: HMMsearch
[2024-01-25 18:58:11,273] [INFO] Running command: hmmsearch --tblout GCF_000392375.2_ASM39237v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd529704-be4b-4d0e-ba1c-7ed2c74c7efe/dqc_reference/reference_markers.hmm GCF_000392375.2_ASM39237v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:58:11,495] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:58:11,496] [INFO] Found 6/6 markers.
[2024-01-25 18:58:11,522] [INFO] Query marker FASTA was written to GCF_000392375.2_ASM39237v2_genomic.fna/markers.fasta
[2024-01-25 18:58:11,523] [INFO] Task started: Blastn
[2024-01-25 18:58:11,523] [INFO] Running command: blastn -query GCF_000392375.2_ASM39237v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd529704-be4b-4d0e-ba1c-7ed2c74c7efe/dqc_reference/reference_markers.fasta -out GCF_000392375.2_ASM39237v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:12,080] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:12,084] [INFO] Selected 16 target genomes.
[2024-01-25 18:58:12,084] [INFO] Target genome list was writen to GCF_000392375.2_ASM39237v2_genomic.fna/target_genomes.txt
[2024-01-25 18:58:12,095] [INFO] Task started: fastANI
[2024-01-25 18:58:12,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg30c70c75-c25b-4294-9fe1-917f81cd4549/GCF_000392375.2_ASM39237v2_genomic.fna.gz --refList GCF_000392375.2_ASM39237v2_genomic.fna/target_genomes.txt --output GCF_000392375.2_ASM39237v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:58:22,519] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:22,519] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd529704-be4b-4d0e-ba1c-7ed2c74c7efe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:58:22,520] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd529704-be4b-4d0e-ba1c-7ed2c74c7efe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:58:22,529] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:58:22,530] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:58:22,530] [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 tyrobutyricum	strain=DSM 2637	GCA_000392375.2	1519	1519	type	True	100.0	920	928	95	conclusive
Clostridium tyrobutyricum	strain=DSM 2637	GCA_000429805.1	1519	1519	type	True	99.991	926	928	95	conclusive
Clostridium tyrobutyricum	strain=ATCC 25755	GCA_000359585.1	1519	1519	type	True	99.9874	924	928	95	conclusive
Clostridium algifaecis	strain=DSM 28783	GCA_017874415.1	1472040	1472040	type	True	79.2114	398	928	95	below_threshold
Clostridium autoethanogenum	strain=DSM 10061	GCA_000484505.2	84023	84023	suspected-type	True	77.5476	262	928	95	below_threshold
Clostridium scatologenes	strain=ATCC 25775	GCA_000968375.1	1548	1548	type	True	77.4852	218	928	95	below_threshold
Clostridium kluyveri	strain=DSM 555	GCA_000016505.1	1534	1534	type	True	77.3924	238	928	95	below_threshold
Clostridium kluyveri	strain=NBRC 12016	GCA_000010265.1	1534	1534	type	True	77.3794	240	928	95	below_threshold
Clostridium drakei	strain=SL1	GCA_003096175.1	332101	332101	type	True	77.3471	199	928	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	76.9718	185	928	95	below_threshold
Clostridium arbusti	strain=SL206	GCA_000246895.2	1137848	1137848	type	True	76.7611	115	928	95	below_threshold
Clostridium botulinum	strain=ATCC 25763	GCA_001276985.1	1491	1491	type	True	76.1562	123	928	95	below_threshold
Clostridium botulinum	strain=ATCC 25763	GCA_011017965.1	1491	1491	type	True	76.119	123	928	95	below_threshold
Clostridium swellfunianum	strain=CICC 10730	GCA_023656515.1	1367462	1367462	type	True	76.0909	69	928	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	75.5578	84	928	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	75.5303	55	928	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:58:22,532] [INFO] DFAST Taxonomy check result was written to GCF_000392375.2_ASM39237v2_genomic.fna/tc_result.tsv
[2024-01-25 18:58:22,533] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:58:22,533] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:58:22,533] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd529704-be4b-4d0e-ba1c-7ed2c74c7efe/dqc_reference/checkm_data
[2024-01-25 18:58:22,534] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:58:22,564] [INFO] Task started: CheckM
[2024-01-25 18:58:22,564] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000392375.2_ASM39237v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000392375.2_ASM39237v2_genomic.fna/checkm_input GCF_000392375.2_ASM39237v2_genomic.fna/checkm_result
[2024-01-25 18:58:41,376] [INFO] Task succeeded: CheckM
[2024-01-25 18:58:41,377] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:58:41,394] [INFO] ===== Completeness check finished =====
[2024-01-25 18:58:41,394] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:58:41,394] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000392375.2_ASM39237v2_genomic.fna/markers.fasta)
[2024-01-25 18:58:41,395] [INFO] Task started: Blastn
[2024-01-25 18:58:41,395] [INFO] Running command: blastn -query GCF_000392375.2_ASM39237v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd529704-be4b-4d0e-ba1c-7ed2c74c7efe/dqc_reference/reference_markers_gtdb.fasta -out GCF_000392375.2_ASM39237v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:42,216] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:42,220] [INFO] Selected 17 target genomes.
[2024-01-25 18:58:42,220] [INFO] Target genome list was writen to GCF_000392375.2_ASM39237v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:58:42,232] [INFO] Task started: fastANI
[2024-01-25 18:58:42,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg30c70c75-c25b-4294-9fe1-917f81cd4549/GCF_000392375.2_ASM39237v2_genomic.fna.gz --refList GCF_000392375.2_ASM39237v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000392375.2_ASM39237v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:58:53,720] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:53,730] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:58:53,731] [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_000359585.1	s__Clostridium_B tyrobutyricum	99.9874	924	928	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	99.17	95.02	0.91	0.82	32	conclusive
GCF_017874415.1	s__Clostridium_B algifaecis	79.2112	398	928	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_014050525.1	s__Clostridium_B sp014050525	78.623	327	928	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_000143685.1	s__Clostridium_B ljungdahlii	77.9638	281	928	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	98.76	97.79	0.92	0.88	9	-
GCF_004006395.2	s__Clostridium_B sp004006395	77.7343	253	928	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_000968375.1	s__Clostridium_AM scatologenes	77.5005	217	928	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	96.092	N/A	N/A	N/A	N/A	1	-
GCF_001636845.1	s__Clostridium_B ljungdahlii_A	77.4062	241	928	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_000016505.1	s__Clostridium_B kluyveri	77.3924	238	928	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	97.52	95.05	0.91	0.81	3	-
GCF_001675165.1	s__Clostridium_B ragsdalei	77.3373	247	928	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	98.18	98.18	0.88	0.88	2	-
GCF_000633595.2	s__Clostridium_AM drakei	77.2379	198	928	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	96.092	100.00	100.00	1.00	1.00	2	-
GCF_001038625.1	s__Clostridium_AM carboxidivorans	77.2016	218	928	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	99.97	99.96	1.00	0.99	3	-
GCF_012926525.1	s__Clostridium_AM sp012926525	76.9582	186	928	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002006355.1	s__Clostridium_S felsineum	76.6806	125	928	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_S	95.0	98.29	98.24	0.88	0.87	4	-
GCF_002029235.1	s__Clostridium_AE oryzae	76.6139	66	928	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AE	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001276985.1	s__Clostridium_F botulinum	76.1701	122	928	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_018918325.1	s__Clostridium sp018918325	75.9973	64	928	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_001735765.2	s__Clostridium taeniosporum	75.9913	81	928	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 18:58:53,732] [INFO] GTDB search result was written to GCF_000392375.2_ASM39237v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:58:53,732] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:58:53,736] [INFO] DFAST_QC result json was written to GCF_000392375.2_ASM39237v2_genomic.fna/dqc_result.json
[2024-01-25 18:58:53,736] [INFO] DFAST_QC completed!
[2024-01-25 18:58:53,736] [INFO] Total running time: 0h0m48s