[2024-01-24 14:14:20,388] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:20,390] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:20,390] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f9d4570-e3ad-497c-813a-fa5134bdc64c/dqc_reference
[2024-01-24 14:14:21,767] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:21,768] [INFO] Task started: Prodigal
[2024-01-24 14:14:21,769] [INFO] Running command: gunzip -c /var/lib/cwl/stg9411bc36-25e9-4f7a-bb3b-7ecd2e8f79d9/GCF_028539255.1_ASM2853925v1_genomic.fna.gz | prodigal -d GCF_028539255.1_ASM2853925v1_genomic.fna/cds.fna -a GCF_028539255.1_ASM2853925v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:29,914] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:29,914] [INFO] Task started: HMMsearch
[2024-01-24 14:14:29,914] [INFO] Running command: hmmsearch --tblout GCF_028539255.1_ASM2853925v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f9d4570-e3ad-497c-813a-fa5134bdc64c/dqc_reference/reference_markers.hmm GCF_028539255.1_ASM2853925v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:30,192] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:30,194] [INFO] Found 6/6 markers.
[2024-01-24 14:14:30,226] [INFO] Query marker FASTA was written to GCF_028539255.1_ASM2853925v1_genomic.fna/markers.fasta
[2024-01-24 14:14:30,226] [INFO] Task started: Blastn
[2024-01-24 14:14:30,226] [INFO] Running command: blastn -query GCF_028539255.1_ASM2853925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f9d4570-e3ad-497c-813a-fa5134bdc64c/dqc_reference/reference_markers.fasta -out GCF_028539255.1_ASM2853925v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:30,862] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:30,866] [INFO] Selected 28 target genomes.
[2024-01-24 14:14:30,866] [INFO] Target genome list was writen to GCF_028539255.1_ASM2853925v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:30,930] [INFO] Task started: fastANI
[2024-01-24 14:14:30,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg9411bc36-25e9-4f7a-bb3b-7ecd2e8f79d9/GCF_028539255.1_ASM2853925v1_genomic.fna.gz --refList GCF_028539255.1_ASM2853925v1_genomic.fna/target_genomes.txt --output GCF_028539255.1_ASM2853925v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:48,495] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:48,495] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f9d4570-e3ad-497c-813a-fa5134bdc64c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:48,496] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f9d4570-e3ad-497c-813a-fa5134bdc64c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:48,509] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:14:48,509] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:48,509] [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
Agathobacter ruminis	strain=JK623	GCA_002735305.1	1712665	1712665	type	True	99.9382	874	915	95	conclusive
Pseudobutyrivibrio ruminis	strain=DSM 9787	GCA_900218035.1	46206	46206	suspected-type	True	78.9921	54	915	95	below_threshold
Eubacterium oxidoreducens	strain=DSM 3217	GCA_900104415.1	1732	1732	type	True	78.5967	62	915	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	77.8735	110	915	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	77.8189	83	915	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	77.5916	82	915	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	77.5642	81	915	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	77.5176	80	915	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:48,516] [INFO] DFAST Taxonomy check result was written to GCF_028539255.1_ASM2853925v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:48,517] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:48,518] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:48,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f9d4570-e3ad-497c-813a-fa5134bdc64c/dqc_reference/checkm_data
[2024-01-24 14:14:48,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:48,566] [INFO] Task started: CheckM
[2024-01-24 14:14:48,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028539255.1_ASM2853925v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028539255.1_ASM2853925v1_genomic.fna/checkm_input GCF_028539255.1_ASM2853925v1_genomic.fna/checkm_result
[2024-01-24 14:15:17,405] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:17,406] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:17,423] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:17,423] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:17,423] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028539255.1_ASM2853925v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:17,424] [INFO] Task started: Blastn
[2024-01-24 14:15:17,424] [INFO] Running command: blastn -query GCF_028539255.1_ASM2853925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f9d4570-e3ad-497c-813a-fa5134bdc64c/dqc_reference/reference_markers_gtdb.fasta -out GCF_028539255.1_ASM2853925v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:18,406] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:18,410] [INFO] Selected 26 target genomes.
[2024-01-24 14:15:18,410] [INFO] Target genome list was writen to GCF_028539255.1_ASM2853925v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:18,430] [INFO] Task started: fastANI
[2024-01-24 14:15:18,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg9411bc36-25e9-4f7a-bb3b-7ecd2e8f79d9/GCF_028539255.1_ASM2853925v1_genomic.fna.gz --refList GCF_028539255.1_ASM2853925v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028539255.1_ASM2853925v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:31,368] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:31,380] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:31,380] [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_002735305.1	s__Agathobacter ruminis	99.9382	874	915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.23	97.94	0.91	0.87	3	conclusive
GCA_015057085.1	s__Agathobacter sp015057085	82.6402	405	915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317585.1	s__Agathobacter sp900317585	78.4915	82	915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.18	95.52	0.87	0.83	5	-
GCF_001406815.1	s__Agathobacter faecis	77.8894	110	915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.10	97.07	0.85	0.62	43	-
GCF_000174195.1	s__Roseburia inulinivorans	77.8708	81	915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	95.90	0.77	0.61	28	-
GCA_004562765.1	s__W0P33-017 sp004562765	77.7082	51	915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__W0P33-017	95.0	97.98	97.98	0.87	0.87	2	-
GCA_017409825.1	s__Agathobacter sp017409825	77.5141	56	915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	96.24	96.24	0.85	0.85	2	-
GCF_001940165.1	s__Roseburia sp001940165	77.4097	88	915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552085.1	s__Agathobacter sp900552085	77.1155	75	915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.03	95.54	0.78	0.69	7	-
GCA_003483745.1	s__Roseburia sp003483745	76.7422	71	915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	97.41	0.84	0.84	3	-
GCA_900550545.1	s__Agathobacter sp900550545	76.7044	101	915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900753715.1	s__Roseburia sp900753715	76.5409	70	915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	99.04	99.04	0.83	0.83	2	-
GCA_910587655.1	s__Agathobacter sp910587655	76.382	66	915	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:31,386] [INFO] GTDB search result was written to GCF_028539255.1_ASM2853925v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:31,387] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:31,391] [INFO] DFAST_QC result json was written to GCF_028539255.1_ASM2853925v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:31,392] [INFO] DFAST_QC completed!
[2024-01-24 14:15:31,392] [INFO] Total running time: 0h1m11s