[2024-01-24 15:09:55,814] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:09:55,816] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:09:55,816] [INFO] DQC Reference Directory: /var/lib/cwl/stg74eabd5c-50db-4a24-aec6-b862523cf4bf/dqc_reference
[2024-01-24 15:09:58,163] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:09:58,164] [INFO] Task started: Prodigal
[2024-01-24 15:09:58,164] [INFO] Running command: gunzip -c /var/lib/cwl/stg606804ec-92cb-4790-a90e-78f65b8c919e/GCF_018918345.1_ASM1891834v1_genomic.fna.gz | prodigal -d GCF_018918345.1_ASM1891834v1_genomic.fna/cds.fna -a GCF_018918345.1_ASM1891834v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:07,174] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:07,175] [INFO] Task started: HMMsearch
[2024-01-24 15:10:07,175] [INFO] Running command: hmmsearch --tblout GCF_018918345.1_ASM1891834v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74eabd5c-50db-4a24-aec6-b862523cf4bf/dqc_reference/reference_markers.hmm GCF_018918345.1_ASM1891834v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:07,485] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:07,486] [INFO] Found 6/6 markers.
[2024-01-24 15:10:07,520] [INFO] Query marker FASTA was written to GCF_018918345.1_ASM1891834v1_genomic.fna/markers.fasta
[2024-01-24 15:10:07,520] [INFO] Task started: Blastn
[2024-01-24 15:10:07,520] [INFO] Running command: blastn -query GCF_018918345.1_ASM1891834v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74eabd5c-50db-4a24-aec6-b862523cf4bf/dqc_reference/reference_markers.fasta -out GCF_018918345.1_ASM1891834v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:08,315] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:08,318] [INFO] Selected 19 target genomes.
[2024-01-24 15:10:08,319] [INFO] Target genome list was writen to GCF_018918345.1_ASM1891834v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:08,337] [INFO] Task started: fastANI
[2024-01-24 15:10:08,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg606804ec-92cb-4790-a90e-78f65b8c919e/GCF_018918345.1_ASM1891834v1_genomic.fna.gz --refList GCF_018918345.1_ASM1891834v1_genomic.fna/target_genomes.txt --output GCF_018918345.1_ASM1891834v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:19,905] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:19,905] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74eabd5c-50db-4a24-aec6-b862523cf4bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:19,906] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74eabd5c-50db-4a24-aec6-b862523cf4bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:19,915] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:19,915] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:19,915] [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
Butyricicoccus intestinisimiae	strain=MSJd-7	GCA_018918345.1	2841509	2841509	type	True	100.0	894	894	95	conclusive
Butyricicoccus porcorum	strain=BB10	GCA_002157465.1	1945634	1945634	type	True	79.9219	343	894	95	below_threshold
Butyricicoccus pullicaecorum	strain=DSM 23266	GCA_900167005.1	501571	501571	type	True	78.8176	90	894	95	below_threshold
Butyricicoccus faecihominis	strain=JCM 31056	GCA_014648015.1	1712515	1712515	type	True	78.6587	139	894	95	below_threshold
Agathobaculum desmolans	strain=ATCC 43058	GCA_000701665.1	39484	39484	type	True	77.3152	80	894	95	below_threshold
Intestinibacillus massiliensis	strain=type strain: Marseille-P3216	GCA_900155735.1	1871029	1871029	type	True	76.9067	80	894	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:19,917] [INFO] DFAST Taxonomy check result was written to GCF_018918345.1_ASM1891834v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:19,917] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:19,918] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:19,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74eabd5c-50db-4a24-aec6-b862523cf4bf/dqc_reference/checkm_data
[2024-01-24 15:10:19,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:19,946] [INFO] Task started: CheckM
[2024-01-24 15:10:19,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018918345.1_ASM1891834v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018918345.1_ASM1891834v1_genomic.fna/checkm_input GCF_018918345.1_ASM1891834v1_genomic.fna/checkm_result
[2024-01-24 15:10:50,882] [INFO] Task succeeded: CheckM
[2024-01-24 15:10:50,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:10:50,903] [INFO] ===== Completeness check finished =====
[2024-01-24 15:10:50,904] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:10:50,904] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018918345.1_ASM1891834v1_genomic.fna/markers.fasta)
[2024-01-24 15:10:50,905] [INFO] Task started: Blastn
[2024-01-24 15:10:50,905] [INFO] Running command: blastn -query GCF_018918345.1_ASM1891834v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74eabd5c-50db-4a24-aec6-b862523cf4bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_018918345.1_ASM1891834v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:52,024] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:52,034] [INFO] Selected 10 target genomes.
[2024-01-24 15:10:52,035] [INFO] Target genome list was writen to GCF_018918345.1_ASM1891834v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:10:52,044] [INFO] Task started: fastANI
[2024-01-24 15:10:52,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg606804ec-92cb-4790-a90e-78f65b8c919e/GCF_018918345.1_ASM1891834v1_genomic.fna.gz --refList GCF_018918345.1_ASM1891834v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018918345.1_ASM1891834v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:10:56,652] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:56,665] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:10:56,665] [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_018918345.1	s__Butyricicoccus_A sp002395695	100.0	894	894	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A	95.0	98.08	98.03	0.91	0.78	6	conclusive
GCA_004555915.1	s__Butyricicoccus_A sp004555915	80.3999	353	894	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A	95.0	99.18	99.18	0.98	0.98	2	-
GCF_002157465.1	s__Butyricicoccus_A porcorum	79.9176	344	894	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A	95.0	99.36	99.36	0.89	0.89	2	-
GCA_002449635.1	s__Butyricicoccus_A sp002449635	79.161	222	894	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A	95.0	99.64	99.40	0.85	0.80	8	-
GCA_019112985.1	s__Butyricicoccus_A stercorigallinarum	79.0944	268	894	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016293155.1	s__JAEDEU01 sp016293155	79.0024	188	894	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__JAEDEU01	95.0	98.88	98.88	0.85	0.85	2	-
GCA_003096535.1	s__Agathobaculum butyriciproducens	78.4053	151	894	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	96.66	95.68	0.85	0.79	34	-
GCA_900544475.1	s__Agathobaculum sp900544475	77.6979	94	894	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	97.90	97.82	0.89	0.86	3	-
GCF_900625105.1	s__Agathobaculum sp900625105	77.2696	113	894	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:10:56,667] [INFO] GTDB search result was written to GCF_018918345.1_ASM1891834v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:10:56,668] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:10:56,674] [INFO] DFAST_QC result json was written to GCF_018918345.1_ASM1891834v1_genomic.fna/dqc_result.json
[2024-01-24 15:10:56,674] [INFO] DFAST_QC completed!
[2024-01-24 15:10:56,674] [INFO] Total running time: 0h1m1s