[2024-01-24 13:36:31,028] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:31,030] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:31,031] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f9c197e-e571-46e9-9fe6-e535a9241572/dqc_reference
[2024-01-24 13:36:32,410] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:32,410] [INFO] Task started: Prodigal
[2024-01-24 13:36:32,411] [INFO] Running command: gunzip -c /var/lib/cwl/stg8dcfd13d-761e-4297-a034-a8bc4409c205/GCF_001440545.1_ASM144054v1_genomic.fna.gz | prodigal -d GCF_001440545.1_ASM144054v1_genomic.fna/cds.fna -a GCF_001440545.1_ASM144054v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:36,815] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:36,816] [INFO] Task started: HMMsearch
[2024-01-24 13:36:36,816] [INFO] Running command: hmmsearch --tblout GCF_001440545.1_ASM144054v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f9c197e-e571-46e9-9fe6-e535a9241572/dqc_reference/reference_markers.hmm GCF_001440545.1_ASM144054v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:37,078] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:37,080] [INFO] Found 6/6 markers.
[2024-01-24 13:36:37,106] [INFO] Query marker FASTA was written to GCF_001440545.1_ASM144054v1_genomic.fna/markers.fasta
[2024-01-24 13:36:37,106] [INFO] Task started: Blastn
[2024-01-24 13:36:37,107] [INFO] Running command: blastn -query GCF_001440545.1_ASM144054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f9c197e-e571-46e9-9fe6-e535a9241572/dqc_reference/reference_markers.fasta -out GCF_001440545.1_ASM144054v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:37,682] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:37,686] [INFO] Selected 13 target genomes.
[2024-01-24 13:36:37,686] [INFO] Target genome list was writen to GCF_001440545.1_ASM144054v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:37,727] [INFO] Task started: fastANI
[2024-01-24 13:36:37,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg8dcfd13d-761e-4297-a034-a8bc4409c205/GCF_001440545.1_ASM144054v1_genomic.fna.gz --refList GCF_001440545.1_ASM144054v1_genomic.fna/target_genomes.txt --output GCF_001440545.1_ASM144054v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:36:44,806] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:44,806] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f9c197e-e571-46e9-9fe6-e535a9241572/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:36:44,807] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f9c197e-e571-46e9-9fe6-e535a9241572/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:36:44,813] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:36:44,813] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:36:44,813] [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
Caloramator mitchellensis	strain=VF08	GCA_001440545.1	908809	908809	type	True	100.0	782	784	95	conclusive
Caloramator australicus	strain=RC3	GCA_000297115.1	515264	515264	type	True	78.3237	287	784	95	below_threshold
Caloramator fervidus	strain=DSM 5463	GCA_900108045.1	29344	29344	type	True	77.4669	200	784	95	below_threshold
Fonticella tunisiensis	strain=DSM 24455	GCA_004364155.1	1096341	1096341	type	True	77.1756	76	784	95	below_threshold
Clostridium punense	strain=DSM 28650	GCA_017874425.1	1054297	1054297	type	True	75.7267	51	784	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:36:44,815] [INFO] DFAST Taxonomy check result was written to GCF_001440545.1_ASM144054v1_genomic.fna/tc_result.tsv
[2024-01-24 13:36:44,816] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:36:44,816] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:36:44,816] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f9c197e-e571-46e9-9fe6-e535a9241572/dqc_reference/checkm_data
[2024-01-24 13:36:44,819] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:36:44,849] [INFO] Task started: CheckM
[2024-01-24 13:36:44,849] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001440545.1_ASM144054v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001440545.1_ASM144054v1_genomic.fna/checkm_input GCF_001440545.1_ASM144054v1_genomic.fna/checkm_result
[2024-01-24 13:37:05,508] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:05,509] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:05,529] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:05,530] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:05,530] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001440545.1_ASM144054v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:05,531] [INFO] Task started: Blastn
[2024-01-24 13:37:05,531] [INFO] Running command: blastn -query GCF_001440545.1_ASM144054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f9c197e-e571-46e9-9fe6-e535a9241572/dqc_reference/reference_markers_gtdb.fasta -out GCF_001440545.1_ASM144054v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:06,318] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:06,322] [INFO] Selected 13 target genomes.
[2024-01-24 13:37:06,322] [INFO] Target genome list was writen to GCF_001440545.1_ASM144054v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:06,376] [INFO] Task started: fastANI
[2024-01-24 13:37:06,376] [INFO] Running command: fastANI --query /var/lib/cwl/stg8dcfd13d-761e-4297-a034-a8bc4409c205/GCF_001440545.1_ASM144054v1_genomic.fna.gz --refList GCF_001440545.1_ASM144054v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001440545.1_ASM144054v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:12,802] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:12,810] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:12,811] [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_001440545.1	s__Caloramator mitchellensis	100.0	782	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000297115.1	s__Caloramator australicus	78.2977	289	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129265.1	s__Caloramator_A proteoclasticus	77.5247	130	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator_A	95.0	98.54	98.54	0.90	0.90	2	-
GCF_900108045.1	s__Caloramator fervidus	77.452	201	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430995.1	s__Thermobrachium celere	77.3657	144	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Thermobrachium	95.0	98.16	98.16	0.91	0.91	2	-
GCF_004364155.1	s__Fonticella tunisiensis	77.1491	75	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Fonticella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006016075.1	s__Caloramator_B sp006016075	76.9144	126	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874425.1	s__Clostridium_J punense	75.7267	51	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	99.96	99.96	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:12,812] [INFO] GTDB search result was written to GCF_001440545.1_ASM144054v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:12,813] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:12,815] [INFO] DFAST_QC result json was written to GCF_001440545.1_ASM144054v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:12,816] [INFO] DFAST_QC completed!
[2024-01-24 13:37:12,816] [INFO] Total running time: 0h0m42s