[2024-01-24 10:57:19,732] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:19,735] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:19,735] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3508b50-3e2d-4f01-8082-d93703d9709c/dqc_reference
[2024-01-24 10:57:22,297] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:22,298] [INFO] Task started: Prodigal
[2024-01-24 10:57:22,299] [INFO] Running command: gunzip -c /var/lib/cwl/stg3549b87a-294d-4beb-986a-11978be6267a/GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna.gz | prodigal -d GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna/cds.fna -a GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:33,435] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:33,436] [INFO] Task started: HMMsearch
[2024-01-24 10:57:33,436] [INFO] Running command: hmmsearch --tblout GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3508b50-3e2d-4f01-8082-d93703d9709c/dqc_reference/reference_markers.hmm GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:33,665] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:33,666] [INFO] Found 6/6 markers.
[2024-01-24 10:57:33,686] [INFO] Query marker FASTA was written to GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna/markers.fasta
[2024-01-24 10:57:33,686] [INFO] Task started: Blastn
[2024-01-24 10:57:33,686] [INFO] Running command: blastn -query GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3508b50-3e2d-4f01-8082-d93703d9709c/dqc_reference/reference_markers.fasta -out GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:34,297] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:34,303] [INFO] Selected 14 target genomes.
[2024-01-24 10:57:34,303] [INFO] Target genome list was writen to GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna/target_genomes.txt
[2024-01-24 10:57:34,433] [INFO] Task started: fastANI
[2024-01-24 10:57:34,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg3549b87a-294d-4beb-986a-11978be6267a/GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna.gz --refList GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna/target_genomes.txt --output GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:42,916] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:42,917] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3508b50-3e2d-4f01-8082-d93703d9709c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:42,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3508b50-3e2d-4f01-8082-d93703d9709c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:42,933] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:57:42,933] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:57:42,933] [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_000312145.1	1288121	1288121	type	True	81.1598	399	641	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	81.1192	391	641	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	81.0401	411	641	95	below_threshold
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	80.8854	386	641	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	80.8497	398	641	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	80.8197	409	641	95	below_threshold
Alistipes dispar	strain=5CPEGH6	GCA_006542685.1	2585119	2585119	type	True	80.7284	379	641	95	below_threshold
Alistipes timonensis	strain=DSM 25383	GCA_900107675.1	1465754	1465754	type	True	80.5043	384	641	95	below_threshold
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	80.4527	374	641	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	80.2525	360	641	95	below_threshold
Alistipes onderdonkii subsp. vulgaris	strain=3BBH6	GCA_006542645.1	2585117	328813	type	True	80.0402	375	641	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	80.0317	382	641	95	below_threshold
Alistipes communis	strain=5CBH24	GCA_006542665.1	2585118	2585118	type	True	78.9616	305	641	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_025144665.1	1470347	1470347	type	True	76.8979	105	641	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:42,938] [INFO] DFAST Taxonomy check result was written to GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna/tc_result.tsv
[2024-01-24 10:57:42,940] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:42,940] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:42,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3508b50-3e2d-4f01-8082-d93703d9709c/dqc_reference/checkm_data
[2024-01-24 10:57:42,941] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:42,967] [INFO] Task started: CheckM
[2024-01-24 10:57:42,968] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna/checkm_input GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna/checkm_result
[2024-01-24 10:58:16,475] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:16,477] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:16,501] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:16,501] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:16,502] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna/markers.fasta)
[2024-01-24 10:58:16,502] [INFO] Task started: Blastn
[2024-01-24 10:58:16,502] [INFO] Running command: blastn -query GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3508b50-3e2d-4f01-8082-d93703d9709c/dqc_reference/reference_markers_gtdb.fasta -out GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:17,432] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:17,435] [INFO] Selected 12 target genomes.
[2024-01-24 10:58:17,435] [INFO] Target genome list was writen to GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:17,486] [INFO] Task started: fastANI
[2024-01-24 10:58:17,487] [INFO] Running command: fastANI --query /var/lib/cwl/stg3549b87a-294d-4beb-986a-11978be6267a/GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna.gz --refList GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna/target_genomes_gtdb.txt --output GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:23,756] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:23,772] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:23,772] [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
GCA_002428825.1	s__Alistipes sp002428825	98.4182	569	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.47	98.29	0.93	0.91	4	conclusive
GCA_014796635.1	s__Alistipes sp014796635	84.8778	286	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575495.1	s__Alistipes sp910575495	84.5193	477	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.23	98.47	0.95	0.90	3	-
GCA_910580175.1	s__Alistipes sp910580175	83.1113	451	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553175.1	s__Alistipes sp900553175	82.1495	284	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312145.1	s__Alistipes senegalensis	81.1636	398	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.29	97.35	0.84	0.66	10	-
GCF_006542685.1	s__Alistipes dispar	80.7284	379	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.07	98.96	0.94	0.89	7	-
GCA_900542505.1	s__Alistipes stercorigallinarum	80.5356	338	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.83	98.70	0.90	0.85	3	-
GCF_000265365.1	s__Alistipes finegoldii	80.4527	374	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.50	97.54	0.87	0.79	15	-
GCF_002161445.1	s__Alistipes cottocaccae	80.2503	353	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.26	98.26	0.94	0.94	2	-
GCA_019115745.1	s__Alistipes intestinigallinarum	79.788	306	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006542665.1	s__Alistipes communis	78.9471	306	641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.74	98.62	0.92	0.87	10	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:23,773] [INFO] GTDB search result was written to GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:23,774] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:23,777] [INFO] DFAST_QC result json was written to GCF_943193205.1_Alistipes_sp_nov_DSM112343_genomic.fna/dqc_result.json
[2024-01-24 10:58:23,778] [INFO] DFAST_QC completed!
[2024-01-24 10:58:23,778] [INFO] Total running time: 0h1m4s