[2024-01-24 10:58:06,480] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:06,482] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:06,482] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7ac9b33-7971-45e2-a34f-15892ba2fe25/dqc_reference
[2024-01-24 10:58:09,633] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:09,634] [INFO] Task started: Prodigal
[2024-01-24 10:58:09,634] [INFO] Running command: gunzip -c /var/lib/cwl/stga4fed296-976e-41e3-8f8c-b989842f4171/GCF_003609595.1_ASM360959v1_genomic.fna.gz | prodigal -d GCF_003609595.1_ASM360959v1_genomic.fna/cds.fna -a GCF_003609595.1_ASM360959v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:13,413] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:13,414] [INFO] Task started: HMMsearch
[2024-01-24 10:58:13,414] [INFO] Running command: hmmsearch --tblout GCF_003609595.1_ASM360959v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7ac9b33-7971-45e2-a34f-15892ba2fe25/dqc_reference/reference_markers.hmm GCF_003609595.1_ASM360959v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:13,809] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:13,811] [INFO] Found 6/6 markers.
[2024-01-24 10:58:13,839] [INFO] Query marker FASTA was written to GCF_003609595.1_ASM360959v1_genomic.fna/markers.fasta
[2024-01-24 10:58:13,840] [INFO] Task started: Blastn
[2024-01-24 10:58:13,840] [INFO] Running command: blastn -query GCF_003609595.1_ASM360959v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7ac9b33-7971-45e2-a34f-15892ba2fe25/dqc_reference/reference_markers.fasta -out GCF_003609595.1_ASM360959v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:17,184] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:17,191] [INFO] Selected 16 target genomes.
[2024-01-24 10:58:17,192] [INFO] Target genome list was writen to GCF_003609595.1_ASM360959v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:17,314] [INFO] Task started: fastANI
[2024-01-24 10:58:17,315] [INFO] Running command: fastANI --query /var/lib/cwl/stga4fed296-976e-41e3-8f8c-b989842f4171/GCF_003609595.1_ASM360959v1_genomic.fna.gz --refList GCF_003609595.1_ASM360959v1_genomic.fna/target_genomes.txt --output GCF_003609595.1_ASM360959v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:25,924] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:25,924] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7ac9b33-7971-45e2-a34f-15892ba2fe25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:25,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7ac9b33-7971-45e2-a34f-15892ba2fe25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:25,939] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:58:25,939] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:25,940] [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
Caminicella sporogenes	strain=AM 1114	GCA_003609595.1	166485	166485	type	True	100.0	803	807	95	conclusive
Caminicella sporogenes	strain=DSM 14501	GCA_900142285.1	166485	166485	type	True	99.9783	796	807	95	conclusive
Paramaledivibacter caminithermalis	strain=DSM 15212	GCA_900142245.1	191027	191027	type	True	77.5594	216	807	95	below_threshold
Maledivibacter halophilus	strain=M1	GCA_900167445.1	36842	36842	type	True	76.6959	198	807	95	below_threshold
Crassaminicella thermophila	strain=SY095	GCA_008152325.1	2599308	2599308	type	True	76.5569	162	807	95	below_threshold
Crassaminicella profunda	strain=Ra1766H	GCA_019884785.1	1286698	1286698	type	True	76.0204	138	807	95	below_threshold
Thermohalobacter berrensis	strain=CTT3	GCA_003609645.1	99594	99594	type	True	75.8843	101	807	95	below_threshold
Abyssisolibacter fermentans	strain=MCWD3	GCA_001559865.1	1766203	1766203	type	True	75.8017	90	807	95	below_threshold
Paraclostridium bifermentans	strain=ATCC 638	GCA_006802875.1	1490	1490	type	True	75.6928	78	807	95	below_threshold
Keratinibaculum paraultunense	strain=DSM 26752	GCA_004343355.1	1278232	1278232	type	True	75.5031	59	807	95	below_threshold
Gottschalkia purinilytica	strain=DSM 1384	GCA_001190785.1	1503	1503	type	True	75.4275	86	807	95	below_threshold
Paraclostridium benzoelyticum	strain=JC272	GCA_001006285.1	1629550	1629550	type	True	75.4251	78	807	95	below_threshold
Paraclostridium dentum	strain=SKVG24	GCA_012922555.1	2662455	2662455	type	True	75.332	90	807	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:25,941] [INFO] DFAST Taxonomy check result was written to GCF_003609595.1_ASM360959v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:25,942] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:25,942] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:25,942] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7ac9b33-7971-45e2-a34f-15892ba2fe25/dqc_reference/checkm_data
[2024-01-24 10:58:25,943] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:25,975] [INFO] Task started: CheckM
[2024-01-24 10:58:25,975] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003609595.1_ASM360959v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003609595.1_ASM360959v1_genomic.fna/checkm_input GCF_003609595.1_ASM360959v1_genomic.fna/checkm_result
[2024-01-24 10:58:46,989] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:46,990] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:47,011] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:47,011] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:47,012] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003609595.1_ASM360959v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:47,013] [INFO] Task started: Blastn
[2024-01-24 10:58:47,013] [INFO] Running command: blastn -query GCF_003609595.1_ASM360959v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7ac9b33-7971-45e2-a34f-15892ba2fe25/dqc_reference/reference_markers_gtdb.fasta -out GCF_003609595.1_ASM360959v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:48,285] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:48,290] [INFO] Selected 18 target genomes.
[2024-01-24 10:58:48,290] [INFO] Target genome list was writen to GCF_003609595.1_ASM360959v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:48,305] [INFO] Task started: fastANI
[2024-01-24 10:58:48,305] [INFO] Running command: fastANI --query /var/lib/cwl/stga4fed296-976e-41e3-8f8c-b989842f4171/GCF_003609595.1_ASM360959v1_genomic.fna.gz --refList GCF_003609595.1_ASM360959v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003609595.1_ASM360959v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:58,119] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:58,131] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:58,131] [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_900142285.1	s__Caminicella sporogenes	99.9783	796	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Caminicellaceae;g__Caminicella	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_900142245.1	s__Paramaledivibacter caminithermalis	77.5461	217	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Caminicellaceae;g__Paramaledivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001316435.1	s__Caloranaerobacter sp001316435	77.5419	104	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Thermohalobacteraceae;g__Caloranaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014236755.1	s__Petromonas tenebris	77.2453	184	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Caminicellaceae;g__Petromonas	95.0	99.79	99.76	0.94	0.93	4	-
GCF_900167445.1	s__Maledivibacter halophilus	76.6978	199	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Caminicellaceae;g__Maledivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008152325.1	s__SY095 sp008152325	76.5419	163	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__SY095	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345705.1	s__Marinisporobacter balticus	76.195	101	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Marinisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003609645.1	s__Thermohalobacter berrensis	75.8844	101	807	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_015686845.1	s__JADPRS01 sp015686845	75.7208	97	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__JADPRS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006802875.1	s__Paraclostridium bifermentans	75.6928	78	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	96.2286	97.64	96.79	0.90	0.86	14	-
GCF_900155565.1	s__Anaerosalibacter_A sp900155565	75.6768	65	807	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	-
GCF_004138215.1	s__Inediibacterium nitritogenes	75.6682	113	807	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_001006285.1	s__Paraclostridium benzoelyticum	75.4251	78	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.4733	N/A	N/A	N/A	N/A	1	-
GCF_001190785.1	s__Gottschalkia_A purinilytica	75.4146	84	807	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	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:58,133] [INFO] GTDB search result was written to GCF_003609595.1_ASM360959v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:58,133] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:58,137] [INFO] DFAST_QC result json was written to GCF_003609595.1_ASM360959v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:58,137] [INFO] DFAST_QC completed!
[2024-01-24 10:58:58,137] [INFO] Total running time: 0h0m52s