[2024-01-24 12:29:36,778] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:36,780] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:36,780] [INFO] DQC Reference Directory: /var/lib/cwl/stg7cf1d8f1-57ad-4ae4-8967-e802b3fb9ddc/dqc_reference
[2024-01-24 12:29:38,102] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:38,103] [INFO] Task started: Prodigal
[2024-01-24 12:29:38,103] [INFO] Running command: gunzip -c /var/lib/cwl/stg6fd8769e-fe76-4391-9da8-cbb2175f0e3d/GCF_014306135.1_ASM1430613v1_genomic.fna.gz | prodigal -d GCF_014306135.1_ASM1430613v1_genomic.fna/cds.fna -a GCF_014306135.1_ASM1430613v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:42,467] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:42,468] [INFO] Task started: HMMsearch
[2024-01-24 12:29:42,468] [INFO] Running command: hmmsearch --tblout GCF_014306135.1_ASM1430613v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7cf1d8f1-57ad-4ae4-8967-e802b3fb9ddc/dqc_reference/reference_markers.hmm GCF_014306135.1_ASM1430613v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:42,731] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:42,732] [INFO] Found 6/6 markers.
[2024-01-24 12:29:42,764] [INFO] Query marker FASTA was written to GCF_014306135.1_ASM1430613v1_genomic.fna/markers.fasta
[2024-01-24 12:29:42,765] [INFO] Task started: Blastn
[2024-01-24 12:29:42,765] [INFO] Running command: blastn -query GCF_014306135.1_ASM1430613v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cf1d8f1-57ad-4ae4-8967-e802b3fb9ddc/dqc_reference/reference_markers.fasta -out GCF_014306135.1_ASM1430613v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:43,352] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:43,355] [INFO] Selected 7 target genomes.
[2024-01-24 12:29:43,356] [INFO] Target genome list was writen to GCF_014306135.1_ASM1430613v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:43,410] [INFO] Task started: fastANI
[2024-01-24 12:29:43,411] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fd8769e-fe76-4391-9da8-cbb2175f0e3d/GCF_014306135.1_ASM1430613v1_genomic.fna.gz --refList GCF_014306135.1_ASM1430613v1_genomic.fna/target_genomes.txt --output GCF_014306135.1_ASM1430613v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:48,553] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:48,553] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7cf1d8f1-57ad-4ae4-8967-e802b3fb9ddc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:48,554] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7cf1d8f1-57ad-4ae4-8967-e802b3fb9ddc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:48,568] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:29:48,569] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:29:48,569] [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
Paeniclostridium sordellii	strain=ATCC9714	GCA_000953675.1	1505	1505	type	True	85.2661	751	993	95	below_threshold
Paraclostridium benzoelyticum	strain=JC272	GCA_001006285.1	1629550	1629550	type	True	83.6485	597	993	95	below_threshold
Paraclostridium bifermentans	strain=ATCC 638	GCA_006802875.1	1490	1490	type	True	83.5655	690	993	95	below_threshold
Paraclostridium dentum	strain=SKVG24	GCA_012922555.1	2662455	2662455	type	True	83.5647	685	993	95	below_threshold
Paraclostridium bifermentans	strain=DSM 14991	GCA_019916025.1	1490	1490	type	True	83.5288	696	993	95	below_threshold
Paraclostridium bifermentans	strain=ATCC 638	GCA_000452245.2	1490	1490	type	True	83.5025	689	993	95	below_threshold
Paraclostridium bifermentans subsp. muricolitidis	strain=PAGU 1678	GCA_019650315.1	2663173	1490	type	True	83.3972	661	993	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:48,571] [INFO] DFAST Taxonomy check result was written to GCF_014306135.1_ASM1430613v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:48,571] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:48,571] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:48,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7cf1d8f1-57ad-4ae4-8967-e802b3fb9ddc/dqc_reference/checkm_data
[2024-01-24 12:29:48,573] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:48,607] [INFO] Task started: CheckM
[2024-01-24 12:29:48,607] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014306135.1_ASM1430613v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014306135.1_ASM1430613v1_genomic.fna/checkm_input GCF_014306135.1_ASM1430613v1_genomic.fna/checkm_result
[2024-01-24 12:30:09,568] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:09,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:09,594] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:09,595] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:09,595] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014306135.1_ASM1430613v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:09,596] [INFO] Task started: Blastn
[2024-01-24 12:30:09,596] [INFO] Running command: blastn -query GCF_014306135.1_ASM1430613v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cf1d8f1-57ad-4ae4-8967-e802b3fb9ddc/dqc_reference/reference_markers_gtdb.fasta -out GCF_014306135.1_ASM1430613v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:10,401] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:10,405] [INFO] Selected 5 target genomes.
[2024-01-24 12:30:10,405] [INFO] Target genome list was writen to GCF_014306135.1_ASM1430613v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:10,412] [INFO] Task started: fastANI
[2024-01-24 12:30:10,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fd8769e-fe76-4391-9da8-cbb2175f0e3d/GCF_014306135.1_ASM1430613v1_genomic.fna.gz --refList GCF_014306135.1_ASM1430613v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014306135.1_ASM1430613v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:14,498] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:14,508] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:14,508] [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_015668515.1	s__Paraclostridium tenue	99.8703	971	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	98.58	97.73	0.92	0.87	8	conclusive
GCF_000953675.1	s__Paraclostridium sordellii	85.2703	752	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	98.12	96.78	0.93	0.89	59	-
GCF_001006285.1	s__Paraclostridium benzoelyticum	83.641	598	993	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_006802875.1	s__Paraclostridium bifermentans	83.5916	688	993	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_000452245.2	s__Paraclostridium bifermentans_A	83.4665	692	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	96.2286	97.39	96.64	0.88	0.81	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:14,510] [INFO] GTDB search result was written to GCF_014306135.1_ASM1430613v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:14,511] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:14,514] [INFO] DFAST_QC result json was written to GCF_014306135.1_ASM1430613v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:14,515] [INFO] DFAST_QC completed!
[2024-01-24 12:30:14,515] [INFO] Total running time: 0h0m38s