[2024-01-24 15:18:32,619] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:32,621] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:32,622] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe64d378-81b4-4255-b0e8-e9e6125ee1c4/dqc_reference
[2024-01-24 15:18:34,813] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:34,814] [INFO] Task started: Prodigal
[2024-01-24 15:18:34,814] [INFO] Running command: gunzip -c /var/lib/cwl/stg04852ca3-0833-4c72-af18-b044255ecc59/GCF_003609645.1_ASM360964v1_genomic.fna.gz | prodigal -d GCF_003609645.1_ASM360964v1_genomic.fna/cds.fna -a GCF_003609645.1_ASM360964v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:38,753] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:38,753] [INFO] Task started: HMMsearch
[2024-01-24 15:18:38,753] [INFO] Running command: hmmsearch --tblout GCF_003609645.1_ASM360964v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe64d378-81b4-4255-b0e8-e9e6125ee1c4/dqc_reference/reference_markers.hmm GCF_003609645.1_ASM360964v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:39,016] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:39,017] [INFO] Found 6/6 markers.
[2024-01-24 15:18:39,041] [INFO] Query marker FASTA was written to GCF_003609645.1_ASM360964v1_genomic.fna/markers.fasta
[2024-01-24 15:18:39,041] [INFO] Task started: Blastn
[2024-01-24 15:18:39,042] [INFO] Running command: blastn -query GCF_003609645.1_ASM360964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe64d378-81b4-4255-b0e8-e9e6125ee1c4/dqc_reference/reference_markers.fasta -out GCF_003609645.1_ASM360964v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:42,378] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:42,381] [INFO] Selected 13 target genomes.
[2024-01-24 15:18:42,382] [INFO] Target genome list was writen to GCF_003609645.1_ASM360964v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:42,473] [INFO] Task started: fastANI
[2024-01-24 15:18:42,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg04852ca3-0833-4c72-af18-b044255ecc59/GCF_003609645.1_ASM360964v1_genomic.fna.gz --refList GCF_003609645.1_ASM360964v1_genomic.fna/target_genomes.txt --output GCF_003609645.1_ASM360964v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:50,036] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:50,036] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe64d378-81b4-4255-b0e8-e9e6125ee1c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:50,037] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe64d378-81b4-4255-b0e8-e9e6125ee1c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:50,047] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:50,047] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:50,047] [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
Thermohalobacter berrensis	strain=CTT3	GCA_003609645.1	99594	99594	type	True	100.0	900	901	95	conclusive
Caldisalinibacter kiritimatiensis	strain=L21-TH-D2	GCA_000387765.1	1304284	1304284	type	True	77.2655	176	901	95	below_threshold
Caloranaerobacter ferrireducens	strain=DY22619	GCA_001730685.1	1323370	1323370	type	True	76.8466	171	901	95	below_threshold
Anaeromonas gelatinilytica	strain=D2Q-14	GCA_016820635.1	2683194	2683194	type	True	76.0966	111	901	95	below_threshold
Anaeromonas frigoriresistens	strain=D2Q-11	GCA_016820655.1	2683708	2683708	type	True	75.9333	109	901	95	below_threshold
Caminicella sporogenes	strain=AM 1114	GCA_003609595.1	166485	166485	type	True	75.8711	96	901	95	below_threshold
Senegalia massiliensis	strain=SIT17	GCA_900626135.1	1720316	1720316	type	True	75.8089	129	901	95	below_threshold
Clostridiisalibacter paucivorans	strain=DSM 22131	GCA_000620125.1	408753	408753	type	True	75.7707	106	901	95	below_threshold
Proteiniborus ethanoligenes	strain=DSM 21650	GCA_900107485.1	415015	415015	type	True	75.7216	72	901	95	below_threshold
Sporosalibacterium faouarense	strain=SOL3f37	GCA_016765695.1	516123	516123	type	True	75.687	112	901	95	below_threshold
Abyssisolibacter fermentans	strain=MCWD3	GCA_001559865.1	1766203	1766203	type	True	75.6643	98	901	95	below_threshold
Clostridium saudiense	strain=JCC	GCA_000577815.1	1414720	1414720	type	True	74.8033	56	901	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:50,049] [INFO] DFAST Taxonomy check result was written to GCF_003609645.1_ASM360964v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:50,050] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:50,050] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:50,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe64d378-81b4-4255-b0e8-e9e6125ee1c4/dqc_reference/checkm_data
[2024-01-24 15:18:50,051] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:50,078] [INFO] Task started: CheckM
[2024-01-24 15:18:50,079] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003609645.1_ASM360964v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003609645.1_ASM360964v1_genomic.fna/checkm_input GCF_003609645.1_ASM360964v1_genomic.fna/checkm_result
[2024-01-24 15:19:10,815] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:10,816] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:10,843] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:10,844] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:10,844] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003609645.1_ASM360964v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:10,844] [INFO] Task started: Blastn
[2024-01-24 15:19:10,844] [INFO] Running command: blastn -query GCF_003609645.1_ASM360964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe64d378-81b4-4255-b0e8-e9e6125ee1c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_003609645.1_ASM360964v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:11,626] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:11,630] [INFO] Selected 20 target genomes.
[2024-01-24 15:19:11,630] [INFO] Target genome list was writen to GCF_003609645.1_ASM360964v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:11,661] [INFO] Task started: fastANI
[2024-01-24 15:19:11,661] [INFO] Running command: fastANI --query /var/lib/cwl/stg04852ca3-0833-4c72-af18-b044255ecc59/GCF_003609645.1_ASM360964v1_genomic.fna.gz --refList GCF_003609645.1_ASM360964v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003609645.1_ASM360964v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:21,011] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:21,022] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:21,023] [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_003609645.1	s__Thermohalobacter berrensis	100.0	900	901	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Thermohalobacteraceae;g__Thermohalobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000387765.1	s__Caldisalinibacter kiritimatiensis	77.2655	176	901	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Caldisalinibacteraceae;g__Caldisalinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001316435.1	s__Caloranaerobacter sp001316435	76.8946	154	901	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Thermohalobacteraceae;g__Caloranaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001730685.1	s__Caloranaerobacter ferrireducens	76.8596	170	901	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Thermohalobacteraceae;g__Caloranaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155565.1	s__Anaerosalibacter_A sp900155565	76.2634	75	901	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sporanaerobacteraceae;g__Anaerosalibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009711785.1	s__MES13 sp009711785	76.1619	159	901	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__MES13;g__MES13	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820635.1	s__Senegalia sp016820635	76.0966	111	901	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__SIT17;g__Senegalia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009696605.1	s__Anaerosalibacter bizertensis	75.9083	84	901	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sporanaerobacteraceae;g__Anaerosalibacter	95.0	98.53	98.48	0.86	0.84	3	-
GCF_900142285.1	s__Caminicella sporogenes	75.8569	100	901	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Caminicellaceae;g__Caminicella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000620125.1	s__Clostridiisalibacter paucivorans	75.739	107	901	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Clostridiisalibacteraceae;g__Clostridiisalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107485.1	s__Proteiniborus ethanoligenes	75.7216	72	901	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Proteiniboraceae;g__Proteiniborus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765695.1	s__Sporosalibacterium faouarense	75.687	112	901	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__VENL01;g__Sporosalibacterium	95.0	99.35	99.35	0.89	0.89	2	-
GCF_000577815.1	s__Clostridium saudiense	74.8033	56	901	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.39	99.24	0.89	0.87	14	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:21,024] [INFO] GTDB search result was written to GCF_003609645.1_ASM360964v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:21,025] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:21,028] [INFO] DFAST_QC result json was written to GCF_003609645.1_ASM360964v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:21,028] [INFO] DFAST_QC completed!
[2024-01-24 15:19:21,028] [INFO] Total running time: 0h0m48s