[2024-01-25 18:42:05,709] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:42:05,711] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:42:05,711] [INFO] DQC Reference Directory: /var/lib/cwl/stgbef35a3f-8fa6-4185-bdce-776d756dff21/dqc_reference
[2024-01-25 18:42:06,842] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:42:06,843] [INFO] Task started: Prodigal
[2024-01-25 18:42:06,843] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a98e355-f3b3-45ac-9ca8-c83b83b3d2ba/GCF_016765695.1_ASM1676569v1_genomic.fna.gz | prodigal -d GCF_016765695.1_ASM1676569v1_genomic.fna/cds.fna -a GCF_016765695.1_ASM1676569v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:42:12,462] [INFO] Task succeeded: Prodigal
[2024-01-25 18:42:12,463] [INFO] Task started: HMMsearch
[2024-01-25 18:42:12,463] [INFO] Running command: hmmsearch --tblout GCF_016765695.1_ASM1676569v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbef35a3f-8fa6-4185-bdce-776d756dff21/dqc_reference/reference_markers.hmm GCF_016765695.1_ASM1676569v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:42:12,714] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:42:12,716] [INFO] Found 6/6 markers.
[2024-01-25 18:42:12,753] [INFO] Query marker FASTA was written to GCF_016765695.1_ASM1676569v1_genomic.fna/markers.fasta
[2024-01-25 18:42:12,754] [INFO] Task started: Blastn
[2024-01-25 18:42:12,754] [INFO] Running command: blastn -query GCF_016765695.1_ASM1676569v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbef35a3f-8fa6-4185-bdce-776d756dff21/dqc_reference/reference_markers.fasta -out GCF_016765695.1_ASM1676569v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:13,340] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:13,343] [INFO] Selected 20 target genomes.
[2024-01-25 18:42:13,343] [INFO] Target genome list was writen to GCF_016765695.1_ASM1676569v1_genomic.fna/target_genomes.txt
[2024-01-25 18:42:13,348] [INFO] Task started: fastANI
[2024-01-25 18:42:13,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a98e355-f3b3-45ac-9ca8-c83b83b3d2ba/GCF_016765695.1_ASM1676569v1_genomic.fna.gz --refList GCF_016765695.1_ASM1676569v1_genomic.fna/target_genomes.txt --output GCF_016765695.1_ASM1676569v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:42:22,978] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:22,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbef35a3f-8fa6-4185-bdce-776d756dff21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:42:22,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbef35a3f-8fa6-4185-bdce-776d756dff21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:42:22,996] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:42:22,996] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:42:22,996] [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
Sporosalibacterium faouarense	strain=SOL3f37	GCA_016765695.1	516123	516123	type	True	100.0	1323	1328	95	conclusive
Anaeromonas gelatinilytica	strain=D2Q-14	GCA_016820635.1	2683194	2683194	type	True	76.3637	112	1328	95	below_threshold
Caldisalinibacter kiritimatiensis	strain=L21-TH-D2	GCA_000387765.1	1304284	1304284	type	True	76.3019	118	1328	95	below_threshold
Anaeromonas frigoriresistens	strain=D2Q-11	GCA_016820655.1	2683708	2683708	type	True	76.1854	128	1328	95	below_threshold
Clostridiisalibacter paucivorans	strain=DSM 22131	GCA_000620125.1	408753	408753	type	True	76.0796	83	1328	95	below_threshold
Senegalia massiliensis	strain=SIT17	GCA_900626135.1	1720316	1720316	type	True	75.9016	114	1328	95	below_threshold
Caloranaerobacter ferrireducens	strain=DY22619	GCA_001730685.1	1323370	1323370	type	True	75.7973	98	1328	95	below_threshold
Thermohalobacter berrensis	strain=CTT3	GCA_003609645.1	99594	99594	type	True	75.789	109	1328	95	below_threshold
Gottschalkia purinilytica	strain=DSM 1384	GCA_001190785.1	1503	1503	type	True	75.5883	106	1328	95	below_threshold
Keratinibaculum paraultunense	strain=DSM 26752	GCA_004343355.1	1278232	1278232	type	True	75.1828	55	1328	95	below_threshold
Keratinibaculum paraultunense	strain=KD-1	GCA_016767175.1	1278232	1278232	type	True	75.1605	53	1328	95	below_threshold
Defluviitalea phaphyphila	strain=Alg1	GCA_001466305.1	1473580	1473580	type	True	74.9569	50	1328	95	below_threshold
Clostridium septicum	strain=DSM 7534	GCA_003606265.1	1504	1504	type	True	74.8095	59	1328	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	74.796	61	1328	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:42:22,998] [INFO] DFAST Taxonomy check result was written to GCF_016765695.1_ASM1676569v1_genomic.fna/tc_result.tsv
[2024-01-25 18:42:22,998] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:42:22,999] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:42:22,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbef35a3f-8fa6-4185-bdce-776d756dff21/dqc_reference/checkm_data
[2024-01-25 18:42:23,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:42:23,042] [INFO] Task started: CheckM
[2024-01-25 18:42:23,042] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016765695.1_ASM1676569v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016765695.1_ASM1676569v1_genomic.fna/checkm_input GCF_016765695.1_ASM1676569v1_genomic.fna/checkm_result
[2024-01-25 18:42:44,888] [INFO] Task succeeded: CheckM
[2024-01-25 18:42:44,889] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:42:44,910] [INFO] ===== Completeness check finished =====
[2024-01-25 18:42:44,911] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:42:44,911] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016765695.1_ASM1676569v1_genomic.fna/markers.fasta)
[2024-01-25 18:42:44,911] [INFO] Task started: Blastn
[2024-01-25 18:42:44,911] [INFO] Running command: blastn -query GCF_016765695.1_ASM1676569v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbef35a3f-8fa6-4185-bdce-776d756dff21/dqc_reference/reference_markers_gtdb.fasta -out GCF_016765695.1_ASM1676569v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:45,815] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:45,818] [INFO] Selected 23 target genomes.
[2024-01-25 18:42:45,818] [INFO] Target genome list was writen to GCF_016765695.1_ASM1676569v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:42:46,132] [INFO] Task started: fastANI
[2024-01-25 18:42:46,132] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a98e355-f3b3-45ac-9ca8-c83b83b3d2ba/GCF_016765695.1_ASM1676569v1_genomic.fna.gz --refList GCF_016765695.1_ASM1676569v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016765695.1_ASM1676569v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:57,871] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:57,881] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:42:57,881] [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_016765695.1	s__Sporosalibacterium faouarense	100.0	1323	1328	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__VENL01;g__Sporosalibacterium	95.0	99.35	99.35	0.89	0.89	2	conclusive
GCF_016820635.1	s__Senegalia sp016820635	76.3413	111	1328	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_000387765.1	s__Caldisalinibacter kiritimatiensis	76.2862	119	1328	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Caldisalinibacteraceae;g__Caldisalinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002376545.1	s__Proteiniborus sp002376545	76.2151	87	1328	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Proteiniboraceae;g__Proteiniborus	95.0	99.93	99.93	0.97	0.97	2	-
GCF_016820655.1	s__Senegalia sp016820655	76.199	127	1328	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_000620125.1	s__Clostridiisalibacter paucivorans	76.0796	83	1328	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_001316435.1	s__Caloranaerobacter sp001316435	76.0604	96	1328	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_900626135.1	s__Senegalia massiliensis	75.9016	114	1328	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_001730685.1	s__Caloranaerobacter ferrireducens	75.7973	98	1328	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_003609645.1	s__Thermohalobacter berrensis	75.789	109	1328	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Thermohalobacteraceae;g__Thermohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009911265.1	s__Senegalia massiliensis_A	75.7423	114	1328	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_001190785.1	s__Gottschalkia_A purinilytica	75.5883	106	1328	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Gottschalkiaceae;g__Gottschalkia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009696605.1	s__Anaerosalibacter bizertensis	75.5859	68	1328	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_001282725.1	s__Inediibacterium massiliense	75.2906	66	1328	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Inediibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015668515.1	s__Paraclostridium tenue	75.0933	63	1328	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	98.58	97.73	0.92	0.87	8	-
GCF_001466305.1	s__Defluviitalea phaphyphila	74.9467	51	1328	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Defluviitaleaceae;g__Defluviitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:57,883] [INFO] GTDB search result was written to GCF_016765695.1_ASM1676569v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:57,883] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:57,886] [INFO] DFAST_QC result json was written to GCF_016765695.1_ASM1676569v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:57,887] [INFO] DFAST_QC completed!
[2024-01-25 18:42:57,887] [INFO] Total running time: 0h0m52s