[2024-01-24 13:19:25,486] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:25,488] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:25,488] [INFO] DQC Reference Directory: /var/lib/cwl/stga27d0092-8ab5-43af-9397-af92542322ca/dqc_reference
[2024-01-24 13:19:26,663] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:26,664] [INFO] Task started: Prodigal
[2024-01-24 13:19:26,664] [INFO] Running command: gunzip -c /var/lib/cwl/stg27779fb9-c73e-4bde-b32f-6c83be85ed60/GCF_020908015.1_ASM2090801v1_genomic.fna.gz | prodigal -d GCF_020908015.1_ASM2090801v1_genomic.fna/cds.fna -a GCF_020908015.1_ASM2090801v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:34,045] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:34,045] [INFO] Task started: HMMsearch
[2024-01-24 13:19:34,046] [INFO] Running command: hmmsearch --tblout GCF_020908015.1_ASM2090801v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga27d0092-8ab5-43af-9397-af92542322ca/dqc_reference/reference_markers.hmm GCF_020908015.1_ASM2090801v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:34,351] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:34,352] [INFO] Found 6/6 markers.
[2024-01-24 13:19:34,389] [INFO] Query marker FASTA was written to GCF_020908015.1_ASM2090801v1_genomic.fna/markers.fasta
[2024-01-24 13:19:34,390] [INFO] Task started: Blastn
[2024-01-24 13:19:34,390] [INFO] Running command: blastn -query GCF_020908015.1_ASM2090801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga27d0092-8ab5-43af-9397-af92542322ca/dqc_reference/reference_markers.fasta -out GCF_020908015.1_ASM2090801v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:34,966] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:34,970] [INFO] Selected 18 target genomes.
[2024-01-24 13:19:34,970] [INFO] Target genome list was writen to GCF_020908015.1_ASM2090801v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:34,980] [INFO] Task started: fastANI
[2024-01-24 13:19:34,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg27779fb9-c73e-4bde-b32f-6c83be85ed60/GCF_020908015.1_ASM2090801v1_genomic.fna.gz --refList GCF_020908015.1_ASM2090801v1_genomic.fna/target_genomes.txt --output GCF_020908015.1_ASM2090801v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:47,065] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:47,066] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga27d0092-8ab5-43af-9397-af92542322ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:47,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga27d0092-8ab5-43af-9397-af92542322ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:47,085] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:47,085] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:47,085] [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 luticellarii	strain=DSM 29923	GCA_002995845.1	1691940	1691940	type	True	84.2087	781	1258	95	below_threshold
Clostridium kluyveri	strain=DSM 555	GCA_000016505.1	1534	1534	type	True	79.1421	324	1258	95	below_threshold
Clostridium kluyveri	strain=NBRC 12016	GCA_000010265.1	1534	1534	type	True	79.1201	326	1258	95	below_threshold
Clostridium autoethanogenum	strain=JA1-1	GCA_002189005.1	84023	84023	suspected-type	True	78.5187	379	1258	95	below_threshold
Clostridium autoethanogenum	strain=DSM 10061	GCA_000484505.2	84023	84023	suspected-type	True	78.4589	386	1258	95	below_threshold
Clostridium autoethanogenum	strain=DSM 10061	GCA_000427255.1	84023	84023	suspected-type	True	78.4555	371	1258	95	below_threshold
Clostridium ljungdahlii	strain=DSM 13528	GCA_000143685.1	1538	1538	suspected-type	True	78.4508	382	1258	95	below_threshold
Clostridium fermenticellae	strain=JN500901	GCA_003600355.1	2068654	2068654	type	True	77.9073	170	1258	95	below_threshold
Clostridium scatologenes	strain=ATCC 25775	GCA_000968375.1	1548	1548	type	True	77.2993	238	1258	95	below_threshold
Clostridium algifaecis	strain=DSM 28783	GCA_017874415.1	1472040	1472040	type	True	77.1264	215	1258	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	76.9995	202	1258	95	below_threshold
Clostridium aciditolerans	strain=DSM 17425	GCA_016316925.1	339861	339861	type	True	76.8349	173	1258	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	76.57	170	1258	95	below_threshold
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	76.2597	102	1258	95	below_threshold
Clostridium arbusti	strain=SL206	GCA_000246895.2	1137848	1137848	type	True	76.2494	89	1258	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:47,087] [INFO] DFAST Taxonomy check result was written to GCF_020908015.1_ASM2090801v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:47,088] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:47,088] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:47,088] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga27d0092-8ab5-43af-9397-af92542322ca/dqc_reference/checkm_data
[2024-01-24 13:19:47,089] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:47,128] [INFO] Task started: CheckM
[2024-01-24 13:19:47,128] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020908015.1_ASM2090801v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020908015.1_ASM2090801v1_genomic.fna/checkm_input GCF_020908015.1_ASM2090801v1_genomic.fna/checkm_result
[2024-01-24 13:20:14,995] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:14,997] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:15,016] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:15,016] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:15,017] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020908015.1_ASM2090801v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:15,017] [INFO] Task started: Blastn
[2024-01-24 13:20:15,017] [INFO] Running command: blastn -query GCF_020908015.1_ASM2090801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga27d0092-8ab5-43af-9397-af92542322ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_020908015.1_ASM2090801v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:15,770] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:15,774] [INFO] Selected 15 target genomes.
[2024-01-24 13:20:15,774] [INFO] Target genome list was writen to GCF_020908015.1_ASM2090801v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:15,811] [INFO] Task started: fastANI
[2024-01-24 13:20:15,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg27779fb9-c73e-4bde-b32f-6c83be85ed60/GCF_020908015.1_ASM2090801v1_genomic.fna.gz --refList GCF_020908015.1_ASM2090801v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020908015.1_ASM2090801v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:26,523] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:26,538] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:26,538] [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_902809985.1	s__Clostridium_B sp902809985	99.1049	1137	1258	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	99.08	99.06	0.93	0.92	3	conclusive
GCF_002995845.1	s__Clostridium_B luticellarii	84.2173	780	1258	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	-
GCA_903789665.1	s__Clostridium_B sp003497125	82.1358	708	1258	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	99.52	99.48	0.90	0.85	3	-
GCF_000016505.1	s__Clostridium_B kluyveri	79.1321	325	1258	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_000143685.1	s__Clostridium_B ljungdahlii	78.4184	386	1258	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_001636845.1	s__Clostridium_B ljungdahlii_A	78.358	390	1258	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_001675165.1	s__Clostridium_B ragsdalei	78.271	388	1258	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_004006395.2	s__Clostridium_B sp004006395	78.2675	417	1258	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	77.2761	240	1258	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_017874415.1	s__Clostridium_B algifaecis	77.1264	215	1258	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_000633595.2	s__Clostridium_AM drakei	77.0003	240	1258	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_016316925.1	s__Clostridium_AM aciditolerans	76.8233	176	1258	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_000389635.1	s__Clostridium_I pasteurianum_A	76.4881	102	1258	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 13:20:26,540] [INFO] GTDB search result was written to GCF_020908015.1_ASM2090801v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:26,540] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:26,544] [INFO] DFAST_QC result json was written to GCF_020908015.1_ASM2090801v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:26,544] [INFO] DFAST_QC completed!
[2024-01-24 13:20:26,544] [INFO] Total running time: 0h1m1s