[2024-01-24 14:19:00,590] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:00,598] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:00,598] [INFO] DQC Reference Directory: /var/lib/cwl/stg20bf5987-c09e-4c07-a259-335dcfc99a12/dqc_reference
[2024-01-24 14:19:02,006] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:02,007] [INFO] Task started: Prodigal
[2024-01-24 14:19:02,007] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd5d3e86-4cb3-4dca-afbf-f007b331e6e6/GCF_025145645.1_ASM2514564v1_genomic.fna.gz | prodigal -d GCF_025145645.1_ASM2514564v1_genomic.fna/cds.fna -a GCF_025145645.1_ASM2514564v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:24,419] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:24,420] [INFO] Task started: HMMsearch
[2024-01-24 14:19:24,420] [INFO] Running command: hmmsearch --tblout GCF_025145645.1_ASM2514564v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20bf5987-c09e-4c07-a259-335dcfc99a12/dqc_reference/reference_markers.hmm GCF_025145645.1_ASM2514564v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:24,733] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:24,734] [INFO] Found 6/6 markers.
[2024-01-24 14:19:24,771] [INFO] Query marker FASTA was written to GCF_025145645.1_ASM2514564v1_genomic.fna/markers.fasta
[2024-01-24 14:19:24,771] [INFO] Task started: Blastn
[2024-01-24 14:19:24,771] [INFO] Running command: blastn -query GCF_025145645.1_ASM2514564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20bf5987-c09e-4c07-a259-335dcfc99a12/dqc_reference/reference_markers.fasta -out GCF_025145645.1_ASM2514564v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:25,427] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:25,431] [INFO] Selected 9 target genomes.
[2024-01-24 14:19:25,431] [INFO] Target genome list was writen to GCF_025145645.1_ASM2514564v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:25,435] [INFO] Task started: fastANI
[2024-01-24 14:19:25,435] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd5d3e86-4cb3-4dca-afbf-f007b331e6e6/GCF_025145645.1_ASM2514564v1_genomic.fna.gz --refList GCF_025145645.1_ASM2514564v1_genomic.fna/target_genomes.txt --output GCF_025145645.1_ASM2514564v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:33,564] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:33,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20bf5987-c09e-4c07-a259-335dcfc99a12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:33,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20bf5987-c09e-4c07-a259-335dcfc99a12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:33,573] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:19:33,573] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:33,573] [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
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	100.0	1341	1341	95	conclusive
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	99.9967	1341	1341	95	conclusive
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	99.9532	1334	1341	95	conclusive
Alistipes timonensis	strain=DSM 25383	GCA_900107675.1	1465754	1465754	type	True	91.6642	844	1341	95	below_threshold
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	90.1833	842	1341	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	88.3857	751	1341	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	85.2485	717	1341	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	83.5944	622	1341	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_025144665.1	1470347	1470347	type	True	77.7458	161	1341	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:33,575] [INFO] DFAST Taxonomy check result was written to GCF_025145645.1_ASM2514564v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:33,575] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:33,575] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:33,576] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20bf5987-c09e-4c07-a259-335dcfc99a12/dqc_reference/checkm_data
[2024-01-24 14:19:33,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:33,621] [INFO] Task started: CheckM
[2024-01-24 14:19:33,621] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025145645.1_ASM2514564v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025145645.1_ASM2514564v1_genomic.fna/checkm_input GCF_025145645.1_ASM2514564v1_genomic.fna/checkm_result
[2024-01-24 14:20:35,029] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:35,030] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:35,052] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:35,053] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:35,053] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025145645.1_ASM2514564v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:35,053] [INFO] Task started: Blastn
[2024-01-24 14:20:35,054] [INFO] Running command: blastn -query GCF_025145645.1_ASM2514564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20bf5987-c09e-4c07-a259-335dcfc99a12/dqc_reference/reference_markers_gtdb.fasta -out GCF_025145645.1_ASM2514564v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:36,001] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:36,006] [INFO] Selected 6 target genomes.
[2024-01-24 14:20:36,006] [INFO] Target genome list was writen to GCF_025145645.1_ASM2514564v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:36,035] [INFO] Task started: fastANI
[2024-01-24 14:20:36,036] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd5d3e86-4cb3-4dca-afbf-f007b331e6e6/GCF_025145645.1_ASM2514564v1_genomic.fna.gz --refList GCF_025145645.1_ASM2514564v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025145645.1_ASM2514564v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:41,854] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:41,866] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:41,866] [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_000312145.1	s__Alistipes senegalensis	99.9532	1334	1341	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.29	97.35	0.84	0.66	10	conclusive
GCF_900107675.1	s__Alistipes timonensis	91.6642	844	1341	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.07	98.44	0.92	0.87	7	-
GCA_001941065.1	s__Alistipes sp001941065	90.1635	768	1341	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900083545.1	s__Alistipes provencensis	90.1492	844	1341	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000210575.1	s__Alistipes shahii	88.2714	748	1341	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.59	98.01	0.85	0.77	20	-
GCA_900541585.1	s__Alistipes sp900541585	87.0525	665	1341	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.86	98.76	0.92	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:41,868] [INFO] GTDB search result was written to GCF_025145645.1_ASM2514564v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:41,869] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:41,874] [INFO] DFAST_QC result json was written to GCF_025145645.1_ASM2514564v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:41,874] [INFO] DFAST_QC completed!
[2024-01-24 14:20:41,874] [INFO] Total running time: 0h1m41s