[2024-01-24 10:47:06,541] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,543] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,543] [INFO] DQC Reference Directory: /var/lib/cwl/stg6621ebe9-3cd6-44b5-b24f-ba9fccb0656d/dqc_reference
[2024-01-24 10:47:12,103] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,104] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,105] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c32f514-3f25-4b8e-9e50-622a3a6c417e/GCF_004345705.1_ASM434570v1_genomic.fna.gz | prodigal -d GCF_004345705.1_ASM434570v1_genomic.fna/cds.fna -a GCF_004345705.1_ASM434570v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:19,060] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:19,061] [INFO] Task started: HMMsearch
[2024-01-24 10:47:19,061] [INFO] Running command: hmmsearch --tblout GCF_004345705.1_ASM434570v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6621ebe9-3cd6-44b5-b24f-ba9fccb0656d/dqc_reference/reference_markers.hmm GCF_004345705.1_ASM434570v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:19,313] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:19,315] [INFO] Found 6/6 markers.
[2024-01-24 10:47:19,344] [INFO] Query marker FASTA was written to GCF_004345705.1_ASM434570v1_genomic.fna/markers.fasta
[2024-01-24 10:47:19,345] [INFO] Task started: Blastn
[2024-01-24 10:47:19,345] [INFO] Running command: blastn -query GCF_004345705.1_ASM434570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6621ebe9-3cd6-44b5-b24f-ba9fccb0656d/dqc_reference/reference_markers.fasta -out GCF_004345705.1_ASM434570v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:19,948] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:19,956] [INFO] Selected 19 target genomes.
[2024-01-24 10:47:19,957] [INFO] Target genome list was writen to GCF_004345705.1_ASM434570v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:20,000] [INFO] Task started: fastANI
[2024-01-24 10:47:20,000] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c32f514-3f25-4b8e-9e50-622a3a6c417e/GCF_004345705.1_ASM434570v1_genomic.fna.gz --refList GCF_004345705.1_ASM434570v1_genomic.fna/target_genomes.txt --output GCF_004345705.1_ASM434570v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:31,906] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:31,906] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6621ebe9-3cd6-44b5-b24f-ba9fccb0656d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:31,906] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6621ebe9-3cd6-44b5-b24f-ba9fccb0656d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:31,917] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:47:31,918] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:47:31,918] [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
Crassaminicella profunda	strain=Ra1766H	GCA_019884785.1	1286698	1286698	type	True	79.8615	623	1252	95	below_threshold
Crassaminicella thermophila	strain=SY095	GCA_008152325.1	2599308	2599308	type	True	79.1759	482	1252	95	below_threshold
Anaerosolibacter carboniphilus	strain=DSM 103526	GCA_014205875.1	1417629	1417629	type	True	77.0747	99	1252	95	below_threshold
Anaeromicrobium sediminis	strain=DY2726D	GCA_002270055.1	1478221	1478221	type	True	76.9758	171	1252	95	below_threshold
Geosporobacter ferrireducens	strain=IRF9	GCA_001750685.1	1424294	1424294	type	True	76.6887	101	1252	95	below_threshold
Maledivibacter halophilus	strain=M1	GCA_900167445.1	36842	36842	type	True	76.1593	101	1252	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_001020205.1	1509	1509	type	True	75.702	76	1252	95	below_threshold
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	75.6737	74	1252	95	below_threshold
Romboutsia hominis	strain=FRIFI	GCA_900002575.1	1507512	1507512	type	True	75.5614	57	1252	95	below_threshold
Paraclostridium benzoelyticum	strain=JC272	GCA_001006285.1	1629550	1629550	type	True	75.3785	51	1252	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	75.161	65	1252	95	below_threshold
[Clostridium] dakarense	strain=FF1	GCA_000499525.1	1301100	1301100	type	True	75.0421	60	1252	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:31,919] [INFO] DFAST Taxonomy check result was written to GCF_004345705.1_ASM434570v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:31,920] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:31,920] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:31,921] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6621ebe9-3cd6-44b5-b24f-ba9fccb0656d/dqc_reference/checkm_data
[2024-01-24 10:47:31,922] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:31,958] [INFO] Task started: CheckM
[2024-01-24 10:47:31,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004345705.1_ASM434570v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004345705.1_ASM434570v1_genomic.fna/checkm_input GCF_004345705.1_ASM434570v1_genomic.fna/checkm_result
[2024-01-24 10:48:00,228] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:00,230] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:00,252] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:00,253] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:00,253] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004345705.1_ASM434570v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:00,253] [INFO] Task started: Blastn
[2024-01-24 10:48:00,253] [INFO] Running command: blastn -query GCF_004345705.1_ASM434570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6621ebe9-3cd6-44b5-b24f-ba9fccb0656d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004345705.1_ASM434570v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:01,137] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:01,140] [INFO] Selected 18 target genomes.
[2024-01-24 10:48:01,140] [INFO] Target genome list was writen to GCF_004345705.1_ASM434570v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:01,242] [INFO] Task started: fastANI
[2024-01-24 10:48:01,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c32f514-3f25-4b8e-9e50-622a3a6c417e/GCF_004345705.1_ASM434570v1_genomic.fna.gz --refList GCF_004345705.1_ASM434570v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004345705.1_ASM434570v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:11,291] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:11,298] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:11,298] [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_004345705.1	s__Marinisporobacter balticus	100.0	1250	1252	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Marinisporobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_019203185.1	s__143-21 sp019203185	79.2475	453	1252	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__143-21	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008152325.1	s__SY095 sp008152325	79.1905	481	1252	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_004138215.1	s__Inediibacterium nitritogenes	77.7784	311	1252	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_015686845.1	s__JADPRS01 sp015686845	77.7329	261	1252	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_001282725.1	s__Inediibacterium massiliense	77.728	340	1252	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_001750685.1	s__Geosporobacter ferrireducens	76.5718	101	1252	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Geosporobacter	95.0	99.59	99.59	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:11,301] [INFO] GTDB search result was written to GCF_004345705.1_ASM434570v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:11,301] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:11,304] [INFO] DFAST_QC result json was written to GCF_004345705.1_ASM434570v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:11,305] [INFO] DFAST_QC completed!
[2024-01-24 10:48:11,305] [INFO] Total running time: 0h1m5s