[2024-01-25 18:56:50,603] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:56:50,611] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:56:50,611] [INFO] DQC Reference Directory: /var/lib/cwl/stg72664422-202c-4ad7-ac06-fd2a46135854/dqc_reference
[2024-01-25 18:56:51,866] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:56:51,866] [INFO] Task started: Prodigal
[2024-01-25 18:56:51,866] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e7c0820-df1b-48a2-8859-dafbd90a5d86/GCF_000601455.1_Fervidicella_assembly_genomic.fna.gz | prodigal -d GCF_000601455.1_Fervidicella_assembly_genomic.fna/cds.fna -a GCF_000601455.1_Fervidicella_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:56:56,031] [INFO] Task succeeded: Prodigal
[2024-01-25 18:56:56,031] [INFO] Task started: HMMsearch
[2024-01-25 18:56:56,031] [INFO] Running command: hmmsearch --tblout GCF_000601455.1_Fervidicella_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72664422-202c-4ad7-ac06-fd2a46135854/dqc_reference/reference_markers.hmm GCF_000601455.1_Fervidicella_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:56:56,290] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:56:56,291] [INFO] Found 6/6 markers.
[2024-01-25 18:56:56,319] [INFO] Query marker FASTA was written to GCF_000601455.1_Fervidicella_assembly_genomic.fna/markers.fasta
[2024-01-25 18:56:56,320] [INFO] Task started: Blastn
[2024-01-25 18:56:56,320] [INFO] Running command: blastn -query GCF_000601455.1_Fervidicella_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg72664422-202c-4ad7-ac06-fd2a46135854/dqc_reference/reference_markers.fasta -out GCF_000601455.1_Fervidicella_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:56,862] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:56,866] [INFO] Selected 14 target genomes.
[2024-01-25 18:56:56,866] [INFO] Target genome list was writen to GCF_000601455.1_Fervidicella_assembly_genomic.fna/target_genomes.txt
[2024-01-25 18:56:56,883] [INFO] Task started: fastANI
[2024-01-25 18:56:56,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e7c0820-df1b-48a2-8859-dafbd90a5d86/GCF_000601455.1_Fervidicella_assembly_genomic.fna.gz --refList GCF_000601455.1_Fervidicella_assembly_genomic.fna/target_genomes.txt --output GCF_000601455.1_Fervidicella_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:57:05,006] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:05,006] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72664422-202c-4ad7-ac06-fd2a46135854/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:57:05,007] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72664422-202c-4ad7-ac06-fd2a46135854/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:57:05,015] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:57:05,015] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:57:05,015] [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
Fervidicella metallireducens	strain=AeB	GCA_000601455.1	655338	655338	type	True	100.0	876	880	95	conclusive
Clostridium prolinivorans	strain=PYR-10	GCA_004011155.1	2769420	2769420	type	True	80.3481	86	880	95	below_threshold
Clostridium homopropionicum	strain=DSM 5847	GCA_001263795.1	36844	36844	type	True	77.0402	60	880	95	below_threshold
Clostridium homopropionicum	strain=DSM 5847	GCA_900113195.1	36844	36844	type	True	76.9611	60	880	95	below_threshold
Caloramator fervidus	strain=DSM 5463	GCA_900108045.1	29344	29344	type	True	76.8309	93	880	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	76.108	53	880	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	75.8267	57	880	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	75.7825	66	880	95	below_threshold
Clostridium aciditolerans	strain=DSM 17425	GCA_016316925.1	339861	339861	type	True	75.7582	58	880	95	below_threshold
Clostridium pascui	strain=DSM 10365	GCA_016908015.1	46609	46609	type	True	75.5869	62	880	95	below_threshold
Clostridium acetireducens	strain=DSM 10703	GCA_001758365.1	76489	76489	type	True	75.3611	54	880	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:57:05,017] [INFO] DFAST Taxonomy check result was written to GCF_000601455.1_Fervidicella_assembly_genomic.fna/tc_result.tsv
[2024-01-25 18:57:05,017] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:57:05,017] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:57:05,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72664422-202c-4ad7-ac06-fd2a46135854/dqc_reference/checkm_data
[2024-01-25 18:57:05,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:57:05,050] [INFO] Task started: CheckM
[2024-01-25 18:57:05,050] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000601455.1_Fervidicella_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000601455.1_Fervidicella_assembly_genomic.fna/checkm_input GCF_000601455.1_Fervidicella_assembly_genomic.fna/checkm_result
[2024-01-25 18:57:23,604] [INFO] Task succeeded: CheckM
[2024-01-25 18:57:23,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:57:23,622] [INFO] ===== Completeness check finished =====
[2024-01-25 18:57:23,623] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:57:23,623] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000601455.1_Fervidicella_assembly_genomic.fna/markers.fasta)
[2024-01-25 18:57:23,623] [INFO] Task started: Blastn
[2024-01-25 18:57:23,623] [INFO] Running command: blastn -query GCF_000601455.1_Fervidicella_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg72664422-202c-4ad7-ac06-fd2a46135854/dqc_reference/reference_markers_gtdb.fasta -out GCF_000601455.1_Fervidicella_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:24,377] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:24,382] [INFO] Selected 19 target genomes.
[2024-01-25 18:57:24,382] [INFO] Target genome list was writen to GCF_000601455.1_Fervidicella_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:57:24,407] [INFO] Task started: fastANI
[2024-01-25 18:57:24,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e7c0820-df1b-48a2-8859-dafbd90a5d86/GCF_000601455.1_Fervidicella_assembly_genomic.fna.gz --refList GCF_000601455.1_Fervidicella_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_000601455.1_Fervidicella_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:57:35,577] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:35,589] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:57:35,589] [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_000601455.1	s__Fervidicella metallireducens	100.0	876	880	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Fervidicella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900167505.1	s__F0540 sp900167505	79.7073	80	880	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__F0540	95.0	98.87	98.87	0.90	0.90	2	-
GCF_900129265.1	s__Caloramator_A proteoclasticus	77.8917	144	880	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator_A	95.0	98.54	98.54	0.90	0.90	2	-
GCF_006016075.1	s__Caloramator_B sp006016075	77.069	114	880	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_001263795.1	s__Clostridium_H homopropionicum	77.0402	60	880	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900108045.1	s__Caloramator fervidus	76.8326	93	880	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002400085.1	s__UBA4839 sp002400085	76.4451	58	880	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__UBA4839	95.0	99.41	99.11	0.85	0.82	15	-
GCF_019207025.1	s__Clostridium_AM sp019207025	75.7624	67	880	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_016316925.1	s__Clostridium_AM aciditolerans	75.7582	58	880	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_900185645.1	s__Clostridium_AK sp900185645	75.6305	64	880	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AK	95.0	96.24	95.22	0.84	0.82	3	-
GCF_016765615.1	s__Clostridium_T sp016765615	75.6181	63	880	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_T	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001758365.1	s__Clostridium_C acetireducens	75.3611	54	880	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:57:35,591] [INFO] GTDB search result was written to GCF_000601455.1_Fervidicella_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 18:57:35,593] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:57:35,596] [INFO] DFAST_QC result json was written to GCF_000601455.1_Fervidicella_assembly_genomic.fna/dqc_result.json
[2024-01-25 18:57:35,596] [INFO] DFAST_QC completed!
[2024-01-25 18:57:35,596] [INFO] Total running time: 0h0m45s