[2024-01-24 15:26:04,584] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:04,586] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:04,587] [INFO] DQC Reference Directory: /var/lib/cwl/stg057f8057-bf1c-46c7-a346-e80378bd401c/dqc_reference
[2024-01-24 15:26:07,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:07,023] [INFO] Task started: Prodigal
[2024-01-24 15:26:07,024] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb1112ed-b64c-4f55-a7db-18d11f2ae211/GCF_900604385.1_PRJEB28786_genomic.fna.gz | prodigal -d GCF_900604385.1_PRJEB28786_genomic.fna/cds.fna -a GCF_900604385.1_PRJEB28786_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:25,116] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:25,116] [INFO] Task started: HMMsearch
[2024-01-24 15:26:25,117] [INFO] Running command: hmmsearch --tblout GCF_900604385.1_PRJEB28786_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg057f8057-bf1c-46c7-a346-e80378bd401c/dqc_reference/reference_markers.hmm GCF_900604385.1_PRJEB28786_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:25,402] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:25,404] [INFO] Found 6/6 markers.
[2024-01-24 15:26:25,443] [INFO] Query marker FASTA was written to GCF_900604385.1_PRJEB28786_genomic.fna/markers.fasta
[2024-01-24 15:26:25,444] [INFO] Task started: Blastn
[2024-01-24 15:26:25,444] [INFO] Running command: blastn -query GCF_900604385.1_PRJEB28786_genomic.fna/markers.fasta -db /var/lib/cwl/stg057f8057-bf1c-46c7-a346-e80378bd401c/dqc_reference/reference_markers.fasta -out GCF_900604385.1_PRJEB28786_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:26,072] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:26,077] [INFO] Selected 14 target genomes.
[2024-01-24 15:26:26,077] [INFO] Target genome list was writen to GCF_900604385.1_PRJEB28786_genomic.fna/target_genomes.txt
[2024-01-24 15:26:26,086] [INFO] Task started: fastANI
[2024-01-24 15:26:26,087] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb1112ed-b64c-4f55-a7db-18d11f2ae211/GCF_900604385.1_PRJEB28786_genomic.fna.gz --refList GCF_900604385.1_PRJEB28786_genomic.fna/target_genomes.txt --output GCF_900604385.1_PRJEB28786_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:26:36,916] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:36,917] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg057f8057-bf1c-46c7-a346-e80378bd401c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:26:36,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg057f8057-bf1c-46c7-a346-e80378bd401c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:26:36,928] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:26:36,928] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:26:36,929] [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 megaguti	strain=Marseille-P5997	GCA_900604385.1	2364787	2364787	type	True	100.0	1089	1090	95	conclusive
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	82.9301	563	1090	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	82.7619	560	1090	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	82.7357	570	1090	95	below_threshold
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	82.4003	568	1090	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	82.3718	582	1090	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	82.3527	583	1090	95	below_threshold
Alistipes dispar	strain=5CPEGH6	GCA_006542685.1	2585119	2585119	type	True	82.2098	489	1090	95	below_threshold
Alistipes timonensis	strain=DSM 25383	GCA_900107675.1	1465754	1465754	type	True	81.9203	548	1090	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	81.2516	523	1090	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	80.8884	466	1090	95	below_threshold
Alistipes communis	strain=5CBH24	GCA_006542665.1	2585118	2585118	type	True	80.1147	369	1090	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_025144665.1	1470347	1470347	type	True	77.9108	124	1090	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:26:36,930] [INFO] DFAST Taxonomy check result was written to GCF_900604385.1_PRJEB28786_genomic.fna/tc_result.tsv
[2024-01-24 15:26:36,931] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:26:36,931] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:26:36,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg057f8057-bf1c-46c7-a346-e80378bd401c/dqc_reference/checkm_data
[2024-01-24 15:26:36,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:26:36,973] [INFO] Task started: CheckM
[2024-01-24 15:26:36,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900604385.1_PRJEB28786_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900604385.1_PRJEB28786_genomic.fna/checkm_input GCF_900604385.1_PRJEB28786_genomic.fna/checkm_result
[2024-01-24 15:27:28,663] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:28,664] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:28,687] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:28,688] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:28,689] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900604385.1_PRJEB28786_genomic.fna/markers.fasta)
[2024-01-24 15:27:28,689] [INFO] Task started: Blastn
[2024-01-24 15:27:28,689] [INFO] Running command: blastn -query GCF_900604385.1_PRJEB28786_genomic.fna/markers.fasta -db /var/lib/cwl/stg057f8057-bf1c-46c7-a346-e80378bd401c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900604385.1_PRJEB28786_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:29,822] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:29,828] [INFO] Selected 13 target genomes.
[2024-01-24 15:27:29,828] [INFO] Target genome list was writen to GCF_900604385.1_PRJEB28786_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:29,840] [INFO] Task started: fastANI
[2024-01-24 15:27:29,840] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb1112ed-b64c-4f55-a7db-18d11f2ae211/GCF_900604385.1_PRJEB28786_genomic.fna.gz --refList GCF_900604385.1_PRJEB28786_genomic.fna/target_genomes_gtdb.txt --output GCF_900604385.1_PRJEB28786_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:38,635] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:38,648] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:38,649] [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_900604385.1	s__Alistipes megaguti	100.0	1090	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.62	97.58	0.76	0.76	3	conclusive
GCA_019115745.1	s__Alistipes intestinigallinarum	85.8777	602	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161445.1	s__Alistipes cottocaccae	85.7513	676	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.26	98.26	0.94	0.94	2	-
GCA_900544265.1	s__Alistipes merdavium	83.6374	515	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.60	98.07	0.91	0.88	5	-
GCA_019115605.1	s__Alistipes faecigallinarum	83.4663	463	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000434235.1	s__Alistipes avistercoris	83.3612	540	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.86	98.12	0.90	0.84	7	-
GCA_019118605.1	s__Alistipes faecavium	83.2799	522	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119615.1	s__Alistipes stercoravium	82.826	455	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.09	99.09	0.91	0.91	2	-
GCF_000312145.1	s__Alistipes senegalensis	82.744	562	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.29	97.35	0.84	0.66	10	-
GCF_900083545.1	s__Alistipes provencensis	82.398	568	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	100.00	100.00	1.00	1.00	2	-
GCA_019113885.1	s__Alistipes intestinipullorum	82.3819	439	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541585.1	s__Alistipes sp900541585	82.227	500	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.86	98.76	0.92	0.91	4	-
GCA_900542505.1	s__Alistipes stercorigallinarum	81.9274	445	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.83	98.70	0.90	0.85	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:38,651] [INFO] GTDB search result was written to GCF_900604385.1_PRJEB28786_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:38,652] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:38,658] [INFO] DFAST_QC result json was written to GCF_900604385.1_PRJEB28786_genomic.fna/dqc_result.json
[2024-01-24 15:27:38,658] [INFO] DFAST_QC completed!
[2024-01-24 15:27:38,658] [INFO] Total running time: 0h1m34s