[2024-01-25 18:58:50,839] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:58:50,841] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:58:50,841] [INFO] DQC Reference Directory: /var/lib/cwl/stg6459c1c6-d4a6-46f2-b296-805747807ed1/dqc_reference
[2024-01-25 18:58:52,048] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:58:52,049] [INFO] Task started: Prodigal
[2024-01-25 18:58:52,049] [INFO] Running command: gunzip -c /var/lib/cwl/stg6cb7edb7-acee-4274-91ee-0f9592f4d42e/GCF_003339815.1_ASM333981v1_genomic.fna.gz | prodigal -d GCF_003339815.1_ASM333981v1_genomic.fna/cds.fna -a GCF_003339815.1_ASM333981v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:59:03,726] [INFO] Task succeeded: Prodigal
[2024-01-25 18:59:03,726] [INFO] Task started: HMMsearch
[2024-01-25 18:59:03,726] [INFO] Running command: hmmsearch --tblout GCF_003339815.1_ASM333981v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6459c1c6-d4a6-46f2-b296-805747807ed1/dqc_reference/reference_markers.hmm GCF_003339815.1_ASM333981v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:59:03,982] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:59:03,983] [INFO] Found 6/6 markers.
[2024-01-25 18:59:04,015] [INFO] Query marker FASTA was written to GCF_003339815.1_ASM333981v1_genomic.fna/markers.fasta
[2024-01-25 18:59:04,015] [INFO] Task started: Blastn
[2024-01-25 18:59:04,015] [INFO] Running command: blastn -query GCF_003339815.1_ASM333981v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6459c1c6-d4a6-46f2-b296-805747807ed1/dqc_reference/reference_markers.fasta -out GCF_003339815.1_ASM333981v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:04,712] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:04,714] [INFO] Selected 8 target genomes.
[2024-01-25 18:59:04,715] [INFO] Target genome list was writen to GCF_003339815.1_ASM333981v1_genomic.fna/target_genomes.txt
[2024-01-25 18:59:04,724] [INFO] Task started: fastANI
[2024-01-25 18:59:04,724] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cb7edb7-acee-4274-91ee-0f9592f4d42e/GCF_003339815.1_ASM333981v1_genomic.fna.gz --refList GCF_003339815.1_ASM333981v1_genomic.fna/target_genomes.txt --output GCF_003339815.1_ASM333981v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:59:12,213] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:12,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6459c1c6-d4a6-46f2-b296-805747807ed1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:59:12,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6459c1c6-d4a6-46f2-b296-805747807ed1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:59:12,220] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:59:12,220] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:59:12,220] [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
Eggerthella sinensis	strain=DSM 16107	GCA_003339815.1	242230	242230	type	True	100.0	1298	1301	95	conclusive
Eggerthella sinensis	strain=DSM 16107	GCA_003725965.1	242230	242230	type	True	99.9336	1209	1301	95	conclusive
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	87.9241	994	1301	95	below_threshold
Eggerthella timonensis	strain=Marseille-P3135	GCA_900184265.1	1871008	1871008	type	True	87.2079	923	1301	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	86.3712	817	1301	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	86.3525	810	1301	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	86.3021	840	1301	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213	GCA_003788975.1	1335613	1335613	type	True	83.6622	655	1301	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:59:12,221] [INFO] DFAST Taxonomy check result was written to GCF_003339815.1_ASM333981v1_genomic.fna/tc_result.tsv
[2024-01-25 18:59:12,222] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:59:12,222] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:59:12,222] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6459c1c6-d4a6-46f2-b296-805747807ed1/dqc_reference/checkm_data
[2024-01-25 18:59:12,223] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:59:12,265] [INFO] Task started: CheckM
[2024-01-25 18:59:12,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003339815.1_ASM333981v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003339815.1_ASM333981v1_genomic.fna/checkm_input GCF_003339815.1_ASM333981v1_genomic.fna/checkm_result
[2024-01-25 18:59:48,157] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:48,158] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:48,170] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:48,170] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:48,171] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003339815.1_ASM333981v1_genomic.fna/markers.fasta)
[2024-01-25 18:59:48,171] [INFO] Task started: Blastn
[2024-01-25 18:59:48,171] [INFO] Running command: blastn -query GCF_003339815.1_ASM333981v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6459c1c6-d4a6-46f2-b296-805747807ed1/dqc_reference/reference_markers_gtdb.fasta -out GCF_003339815.1_ASM333981v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:49,372] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:49,375] [INFO] Selected 7 target genomes.
[2024-01-25 18:59:49,375] [INFO] Target genome list was writen to GCF_003339815.1_ASM333981v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:59:49,382] [INFO] Task started: fastANI
[2024-01-25 18:59:49,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cb7edb7-acee-4274-91ee-0f9592f4d42e/GCF_003339815.1_ASM333981v1_genomic.fna.gz --refList GCF_003339815.1_ASM333981v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003339815.1_ASM333981v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:59:55,678] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:55,683] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:59:55,683] [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_003339815.1	s__Eggerthella sinensis	100.0	1298	1301	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	99.07	98.15	0.94	0.88	3	conclusive
GCF_009834925.2	s__Eggerthella sp014287365	87.9377	993	1301	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	97.74	96.91	0.89	0.85	3	-
GCF_900184265.1	s__Eggerthella timonensis	87.1979	924	1301	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024265.1	s__Eggerthella lenta	86.2981	840	1301	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	98.39	97.51	0.89	0.82	72	-
GCF_902386925.1	s__Arabia massiliensis	84.4485	714	1301	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Arabia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900199375.1	s__Gordonibacter urolithinfaciens	83.6294	677	1301	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.27	97.45	0.89	0.82	14	-
--------------------------------------------------------------------------------
[2024-01-25 18:59:55,684] [INFO] GTDB search result was written to GCF_003339815.1_ASM333981v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:59:55,685] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:59:55,687] [INFO] DFAST_QC result json was written to GCF_003339815.1_ASM333981v1_genomic.fna/dqc_result.json
[2024-01-25 18:59:55,687] [INFO] DFAST_QC completed!
[2024-01-25 18:59:55,687] [INFO] Total running time: 0h1m5s