[2024-01-25 17:50:50,888] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:50:50,890] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:50:50,890] [INFO] DQC Reference Directory: /var/lib/cwl/stga86cb2d6-0d6d-4aa7-81e8-bf265a357a54/dqc_reference
[2024-01-25 17:50:52,044] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:50:52,044] [INFO] Task started: Prodigal
[2024-01-25 17:50:52,044] [INFO] Running command: gunzip -c /var/lib/cwl/stgd55a94b1-9b7f-479e-a47b-1d135f51fad7/GCF_017873955.1_ASM1787395v1_genomic.fna.gz | prodigal -d GCF_017873955.1_ASM1787395v1_genomic.fna/cds.fna -a GCF_017873955.1_ASM1787395v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:50:57,386] [INFO] Task succeeded: Prodigal
[2024-01-25 17:50:57,386] [INFO] Task started: HMMsearch
[2024-01-25 17:50:57,386] [INFO] Running command: hmmsearch --tblout GCF_017873955.1_ASM1787395v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga86cb2d6-0d6d-4aa7-81e8-bf265a357a54/dqc_reference/reference_markers.hmm GCF_017873955.1_ASM1787395v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:50:57,608] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:50:57,609] [INFO] Found 6/6 markers.
[2024-01-25 17:50:57,637] [INFO] Query marker FASTA was written to GCF_017873955.1_ASM1787395v1_genomic.fna/markers.fasta
[2024-01-25 17:50:57,638] [INFO] Task started: Blastn
[2024-01-25 17:50:57,638] [INFO] Running command: blastn -query GCF_017873955.1_ASM1787395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga86cb2d6-0d6d-4aa7-81e8-bf265a357a54/dqc_reference/reference_markers.fasta -out GCF_017873955.1_ASM1787395v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:58,170] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:58,172] [INFO] Selected 21 target genomes.
[2024-01-25 17:50:58,173] [INFO] Target genome list was writen to GCF_017873955.1_ASM1787395v1_genomic.fna/target_genomes.txt
[2024-01-25 17:50:58,183] [INFO] Task started: fastANI
[2024-01-25 17:50:58,183] [INFO] Running command: fastANI --query /var/lib/cwl/stgd55a94b1-9b7f-479e-a47b-1d135f51fad7/GCF_017873955.1_ASM1787395v1_genomic.fna.gz --refList GCF_017873955.1_ASM1787395v1_genomic.fna/target_genomes.txt --output GCF_017873955.1_ASM1787395v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:10,139] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:10,140] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga86cb2d6-0d6d-4aa7-81e8-bf265a357a54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:10,140] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga86cb2d6-0d6d-4aa7-81e8-bf265a357a54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:10,150] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:51:10,150] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:51:10,150] [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
Sedimentibacter acidaminivorans	strain=DSM 24004	GCA_017873955.1	913099	913099	type	True	100.0	1159	1159	95	conclusive
Sedimentibacter saalensis	strain=DSM 13558	GCA_007830175.1	130788	130788	type	True	77.2585	202	1159	95	below_threshold
Sedimentibacter hydroxybenzoicus	strain=DSM 7310	GCA_013403245.1	29345	29345	type	True	76.8454	150	1159	95	below_threshold
Proteiniborus ethanoligenes	strain=DSM 21650	GCA_900107485.1	415015	415015	type	True	75.5479	55	1159	95	below_threshold
Sporosalibacterium faouarense	strain=SOL3f37	GCA_016765695.1	516123	516123	type	True	75.4313	60	1159	95	below_threshold
Clostridiisalibacter paucivorans	strain=DSM 22131	GCA_000620125.1	408753	408753	type	True	75.3596	51	1159	95	below_threshold
Terrisporobacter mayombei	strain=DSM 6539	GCA_020748465.1	1541	1541	type	True	75.2071	62	1159	95	below_threshold
Paraclostridium benzoelyticum	strain=JC272	GCA_001006285.1	1629550	1629550	type	True	75.152	52	1159	95	below_threshold
Paraclostridium bifermentans	strain=DSM 14991	GCA_019916025.1	1490	1490	type	True	75.0525	72	1159	95	below_threshold
Paraclostridium bifermentans	strain=ATCC 638	GCA_000452245.2	1490	1490	type	True	75.0367	73	1159	95	below_threshold
Paeniclostridium sordellii	strain=ATCC9714	GCA_000953675.1	1505	1505	type	True	74.9652	70	1159	95	below_threshold
Terrisporobacter glycolicus	strain=ATCC 14880	GCA_000373865.1	36841	36841	suspected-type	True	74.9401	72	1159	95	below_threshold
Terrisporobacter glycolicus	strain=DSM 1288	GCA_000439105.1	36841	36841	suspected-type	True	74.9215	70	1159	95	below_threshold
Clostridium massiliodielmoense	strain=MT26	GCA_900176615.1	1776385	1776385	type	True	74.9189	54	1159	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	74.8534	83	1159	95	below_threshold
Clostridium prolinivorans	strain=PYR-10	GCA_004011155.1	2769420	2769420	type	True	74.852	67	1159	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:10,151] [INFO] DFAST Taxonomy check result was written to GCF_017873955.1_ASM1787395v1_genomic.fna/tc_result.tsv
[2024-01-25 17:51:10,152] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:10,152] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:10,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga86cb2d6-0d6d-4aa7-81e8-bf265a357a54/dqc_reference/checkm_data
[2024-01-25 17:51:10,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:10,189] [INFO] Task started: CheckM
[2024-01-25 17:51:10,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873955.1_ASM1787395v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873955.1_ASM1787395v1_genomic.fna/checkm_input GCF_017873955.1_ASM1787395v1_genomic.fna/checkm_result
[2024-01-25 17:51:31,982] [INFO] Task succeeded: CheckM
[2024-01-25 17:51:31,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:51:31,999] [INFO] ===== Completeness check finished =====
[2024-01-25 17:51:31,999] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:51:32,000] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873955.1_ASM1787395v1_genomic.fna/markers.fasta)
[2024-01-25 17:51:32,000] [INFO] Task started: Blastn
[2024-01-25 17:51:32,000] [INFO] Running command: blastn -query GCF_017873955.1_ASM1787395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga86cb2d6-0d6d-4aa7-81e8-bf265a357a54/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873955.1_ASM1787395v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:32,823] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:32,827] [INFO] Selected 24 target genomes.
[2024-01-25 17:51:32,827] [INFO] Target genome list was writen to GCF_017873955.1_ASM1787395v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:51:32,851] [INFO] Task started: fastANI
[2024-01-25 17:51:32,851] [INFO] Running command: fastANI --query /var/lib/cwl/stgd55a94b1-9b7f-479e-a47b-1d135f51fad7/GCF_017873955.1_ASM1787395v1_genomic.fna.gz --refList GCF_017873955.1_ASM1787395v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873955.1_ASM1787395v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:51:46,979] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:46,991] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:51:46,991] [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_017873955.1	s__Sedimentibacter acidaminivorans	100.0	1159	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002435835.1	s__Sedimentibacter sp002435835	77.5396	331	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422545.1	s__Sedimentibacter sp002422545	77.2739	182	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830175.1	s__Sedimentibacter saalensis	77.2308	202	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002331025.1	s__Sedimentibacter sp002331025	76.885	156	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	97.64	97.63	0.83	0.82	3	-
GCF_013403245.1	s__Sedimentibacter hydroxybenzoicus	76.8309	151	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002479485.1	s__UBA1535 sp002479485	76.7599	117	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__UBA1535	95.0	98.88	98.88	0.91	0.91	2	-
GCA_002332905.1	s__UBA1535 sp002332905	76.4007	96	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__UBA1535	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012518555.1	s__Sedimentibacter sp012518555	76.3043	125	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352195.1	s__UBA1535 sp017352195	76.1021	128	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__UBA1535	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002396645.1	s__UBA1535 sp002396645	76.0121	83	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__UBA1535	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908435.1	s__Alkaliphilus_B halophilus	75.4364	53	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Alkaliphilus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765695.1	s__Sporosalibacterium faouarense	75.4313	60	1159	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_000452245.2	s__Paraclostridium bifermentans_A	75.03	74	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	96.2286	97.39	96.64	0.88	0.81	7	-
GCF_900114105.1	s__Terrisporobacter glycolicus_A	75.0148	69	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	98.29	98.07	0.91	0.91	3	-
GCF_001299635.1	s__Clostridioides difficile_A	75.0028	69	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridioides	95.0	98.74	95.22	0.93	0.91	9	-
GCF_900176615.1	s__Clostridium_H massiliodielmoense	74.9189	54	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	98.64	96.44	0.92	0.87	5	-
GCF_000439105.1	s__Terrisporobacter glycolicus	74.9162	71	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	99.67	99.35	0.98	0.96	3	-
GCA_017934475.1	s__UMGS1663 sp017934475	74.8038	50	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1663	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:51:46,992] [INFO] GTDB search result was written to GCF_017873955.1_ASM1787395v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:51:46,993] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:51:46,997] [INFO] DFAST_QC result json was written to GCF_017873955.1_ASM1787395v1_genomic.fna/dqc_result.json
[2024-01-25 17:51:46,998] [INFO] DFAST_QC completed!
[2024-01-25 17:51:46,998] [INFO] Total running time: 0h0m56s