[2024-01-24 12:13:29,042] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:29,046] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:29,047] [INFO] DQC Reference Directory: /var/lib/cwl/stgcab87eea-b9a3-41a5-b645-001c81cc86e0/dqc_reference
[2024-01-24 12:13:30,457] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:30,458] [INFO] Task started: Prodigal
[2024-01-24 12:13:30,458] [INFO] Running command: gunzip -c /var/lib/cwl/stg735726b3-7dde-4152-ace5-d183e09b9c1b/GCF_025147765.1_ASM2514776v1_genomic.fna.gz | prodigal -d GCF_025147765.1_ASM2514776v1_genomic.fna/cds.fna -a GCF_025147765.1_ASM2514776v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:39,541] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:39,542] [INFO] Task started: HMMsearch
[2024-01-24 12:13:39,542] [INFO] Running command: hmmsearch --tblout GCF_025147765.1_ASM2514776v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcab87eea-b9a3-41a5-b645-001c81cc86e0/dqc_reference/reference_markers.hmm GCF_025147765.1_ASM2514776v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:39,824] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:39,825] [INFO] Found 6/6 markers.
[2024-01-24 12:13:39,868] [INFO] Query marker FASTA was written to GCF_025147765.1_ASM2514776v1_genomic.fna/markers.fasta
[2024-01-24 12:13:39,868] [INFO] Task started: Blastn
[2024-01-24 12:13:39,868] [INFO] Running command: blastn -query GCF_025147765.1_ASM2514776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcab87eea-b9a3-41a5-b645-001c81cc86e0/dqc_reference/reference_markers.fasta -out GCF_025147765.1_ASM2514776v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:40,583] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:40,586] [INFO] Selected 12 target genomes.
[2024-01-24 12:13:40,586] [INFO] Target genome list was writen to GCF_025147765.1_ASM2514776v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:40,592] [INFO] Task started: fastANI
[2024-01-24 12:13:40,592] [INFO] Running command: fastANI --query /var/lib/cwl/stg735726b3-7dde-4152-ace5-d183e09b9c1b/GCF_025147765.1_ASM2514776v1_genomic.fna.gz --refList GCF_025147765.1_ASM2514776v1_genomic.fna/target_genomes.txt --output GCF_025147765.1_ASM2514776v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:51,303] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:51,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcab87eea-b9a3-41a5-b645-001c81cc86e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:51,304] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcab87eea-b9a3-41a5-b645-001c81cc86e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:51,315] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:13:51,315] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:51,315] [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
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	100.0	1216	1216	95	conclusive
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	99.9569	1180	1216	95	conclusive
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	84.6414	719	1216	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	83.359	404	1216	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	82.9096	395	1216	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	81.6842	391	1216	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	81.6333	177	1216	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	81.4763	372	1216	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	81.2967	196	1216	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	81.2642	176	1216	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	79.8818	333	1216	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	77.3376	88	1216	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:51,317] [INFO] DFAST Taxonomy check result was written to GCF_025147765.1_ASM2514776v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:51,318] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:51,318] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:51,318] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcab87eea-b9a3-41a5-b645-001c81cc86e0/dqc_reference/checkm_data
[2024-01-24 12:13:51,319] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:51,403] [INFO] Task started: CheckM
[2024-01-24 12:13:51,404] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025147765.1_ASM2514776v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025147765.1_ASM2514776v1_genomic.fna/checkm_input GCF_025147765.1_ASM2514776v1_genomic.fna/checkm_result
[2024-01-24 12:14:24,356] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:24,358] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:24,379] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:24,380] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:24,380] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025147765.1_ASM2514776v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:24,381] [INFO] Task started: Blastn
[2024-01-24 12:14:24,381] [INFO] Running command: blastn -query GCF_025147765.1_ASM2514776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcab87eea-b9a3-41a5-b645-001c81cc86e0/dqc_reference/reference_markers_gtdb.fasta -out GCF_025147765.1_ASM2514776v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:25,469] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:25,473] [INFO] Selected 7 target genomes.
[2024-01-24 12:14:25,473] [INFO] Target genome list was writen to GCF_025147765.1_ASM2514776v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:25,479] [INFO] Task started: fastANI
[2024-01-24 12:14:25,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg735726b3-7dde-4152-ace5-d183e09b9c1b/GCF_025147765.1_ASM2514776v1_genomic.fna.gz --refList GCF_025147765.1_ASM2514776v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025147765.1_ASM2514776v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:31,421] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:31,428] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:31,429] [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_000153905.1	s__Blautia_A obeum	99.9569	1180	1216	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.25	97.20	0.82	0.75	45	conclusive
GCF_018918125.1	s__Blautia_A sp018918125	85.2165	694	1216	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000210015.1	s__Blautia_A obeum_B	84.9501	728	1216	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.64	98.44	0.85	0.84	7	-
GCF_900120195.1	s__Blautia_A sp900120195	84.6457	722	1216	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.52	98.42	0.85	0.83	5	-
GCA_900066355.1	s__Blautia_A sp900066355	84.5327	709	1216	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.38	98.38	0.93	0.93	2	-
GCF_003461245.1	s__Blautia_A sp000436615	84.297	666	1216	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.75	98.36	0.88	0.81	8	-
GCA_900551715.1	s__Blautia_A sp900551715	81.275	411	1216	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:31,439] [INFO] GTDB search result was written to GCF_025147765.1_ASM2514776v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:31,439] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:31,447] [INFO] DFAST_QC result json was written to GCF_025147765.1_ASM2514776v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:31,448] [INFO] DFAST_QC completed!
[2024-01-24 12:14:31,448] [INFO] Total running time: 0h1m2s