[2024-01-24 13:37:00,148] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:00,151] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:00,151] [INFO] DQC Reference Directory: /var/lib/cwl/stgf161c673-858f-4d21-b5cc-0bf4840486dc/dqc_reference
[2024-01-24 13:37:01,424] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:01,425] [INFO] Task started: Prodigal
[2024-01-24 13:37:01,425] [INFO] Running command: gunzip -c /var/lib/cwl/stg68d5a9d6-4f7f-472c-8a8c-2ba01e624610/GCF_000424105.1_ASM42410v1_genomic.fna.gz | prodigal -d GCF_000424105.1_ASM42410v1_genomic.fna/cds.fna -a GCF_000424105.1_ASM42410v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:06,472] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:06,473] [INFO] Task started: HMMsearch
[2024-01-24 13:37:06,473] [INFO] Running command: hmmsearch --tblout GCF_000424105.1_ASM42410v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf161c673-858f-4d21-b5cc-0bf4840486dc/dqc_reference/reference_markers.hmm GCF_000424105.1_ASM42410v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:06,740] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:06,741] [INFO] Found 6/6 markers.
[2024-01-24 13:37:06,766] [INFO] Query marker FASTA was written to GCF_000424105.1_ASM42410v1_genomic.fna/markers.fasta
[2024-01-24 13:37:06,767] [INFO] Task started: Blastn
[2024-01-24 13:37:06,767] [INFO] Running command: blastn -query GCF_000424105.1_ASM42410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf161c673-858f-4d21-b5cc-0bf4840486dc/dqc_reference/reference_markers.fasta -out GCF_000424105.1_ASM42410v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:07,441] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:07,444] [INFO] Selected 22 target genomes.
[2024-01-24 13:37:07,444] [INFO] Target genome list was writen to GCF_000424105.1_ASM42410v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:07,563] [INFO] Task started: fastANI
[2024-01-24 13:37:07,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg68d5a9d6-4f7f-472c-8a8c-2ba01e624610/GCF_000424105.1_ASM42410v1_genomic.fna.gz --refList GCF_000424105.1_ASM42410v1_genomic.fna/target_genomes.txt --output GCF_000424105.1_ASM42410v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:20,890] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:20,891] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf161c673-858f-4d21-b5cc-0bf4840486dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:20,891] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf161c673-858f-4d21-b5cc-0bf4840486dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:20,899] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:20,899] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:20,899] [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
Lachnospira multipara	strain=ATCC 19207	GCA_000424105.1	28051	28051	type	True	100.0	937	941	95	conclusive
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	78.7882	167	941	95	below_threshold
Lachnobacterium bovis	strain=DSM 14045	GCA_900107245.1	140626	140626	suspected-type	True	78.3088	73	941	95	below_threshold
Eubacterium uniforme	strain=ATCC 35992	GCA_900167115.1	39495	39495	type	True	77.9945	79	941	95	below_threshold
Butyrivibrio hungatei	strain=DSM 14810	GCA_900143205.1	185008	185008	type	True	77.4803	62	941	95	below_threshold
Pseudobutyrivibrio ruminis	strain=DSM 9787	GCA_900218035.1	46206	46206	suspected-type	True	77.4352	76	941	95	below_threshold
Butyrivibrio proteoclasticus	strain=B316	GCA_000145035.1	43305	43305	type	True	77.393	57	941	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:20,901] [INFO] DFAST Taxonomy check result was written to GCF_000424105.1_ASM42410v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:20,901] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:20,901] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:20,902] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf161c673-858f-4d21-b5cc-0bf4840486dc/dqc_reference/checkm_data
[2024-01-24 13:37:20,903] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:20,933] [INFO] Task started: CheckM
[2024-01-24 13:37:20,934] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000424105.1_ASM42410v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000424105.1_ASM42410v1_genomic.fna/checkm_input GCF_000424105.1_ASM42410v1_genomic.fna/checkm_result
[2024-01-24 13:37:43,214] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:43,215] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:43,230] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:43,230] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:43,231] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000424105.1_ASM42410v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:43,231] [INFO] Task started: Blastn
[2024-01-24 13:37:43,231] [INFO] Running command: blastn -query GCF_000424105.1_ASM42410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf161c673-858f-4d21-b5cc-0bf4840486dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000424105.1_ASM42410v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:44,319] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:44,322] [INFO] Selected 15 target genomes.
[2024-01-24 13:37:44,323] [INFO] Target genome list was writen to GCF_000424105.1_ASM42410v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:44,337] [INFO] Task started: fastANI
[2024-01-24 13:37:44,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg68d5a9d6-4f7f-472c-8a8c-2ba01e624610/GCF_000424105.1_ASM42410v1_genomic.fna.gz --refList GCF_000424105.1_ASM42410v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000424105.1_ASM42410v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:51,701] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:51,713] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:51,714] [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_000424105.1	s__Lachnospira multipara	100.0	937	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.5522	98.15	97.62	0.92	0.87	4	conclusive
GCF_900103815.1	s__Lachnospira pectinoschiza_B	95.548	770	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.5522	N/A	N/A	N/A	N/A	1	-
GCF_000702205.1	s__Lachnospira multipara_A	84.9401	556	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.26	97.82	0.94	0.92	3	-
GCF_003464165.1	s__Lachnospira sp003451515	79.1861	151	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	97.95	97.44	0.88	0.84	9	-
GCF_009680455.1	s__Lachnospira eligens_A	78.8733	158	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.6336	97.83	97.23	0.89	0.81	35	-
GCF_000146185.1	s__Lachnospira eligens	78.8052	169	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.6336	96.66	95.71	0.87	0.85	3	-
GCF_003458705.1	s__Lachnospira sp003537285	78.7988	164	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.4867	98.01	96.87	0.87	0.80	8	-
GCA_000436475.1	s__Lachnospira sp000436475	77.8748	126	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	97.97	97.42	0.90	0.86	10	-
GCA_002394205.1	s__Lachnospira sp002394205	77.5536	106	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	99.96	99.94	0.94	0.91	3	-
GCA_017397445.1	s__Lachnospira sp017397445	77.5347	93	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002435585.1	s__Lachnospira sp002435585	77.4899	110	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545725.1	s__Lachnospira sp900545725	77.4513	113	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.88	98.45	0.88	0.87	3	-
GCA_015057605.1	s__SIG291 sp015057605	77.2723	72	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG291	95.0	98.39	98.39	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:51,715] [INFO] GTDB search result was written to GCF_000424105.1_ASM42410v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:51,716] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:51,719] [INFO] DFAST_QC result json was written to GCF_000424105.1_ASM42410v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:51,720] [INFO] DFAST_QC completed!
[2024-01-24 13:37:51,720] [INFO] Total running time: 0h0m52s