[2024-01-24 14:14:16,179] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:16,180] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:16,181] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a783b28-9ae9-4e59-9117-d70af642e2d9/dqc_reference
[2024-01-24 14:14:17,391] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:17,392] [INFO] Task started: Prodigal
[2024-01-24 14:14:17,392] [INFO] Running command: gunzip -c /var/lib/cwl/stgede49472-bb24-49dc-a574-56e449e8789f/GCF_006542665.1_Acom_1.0_genomic.fna.gz | prodigal -d GCF_006542665.1_Acom_1.0_genomic.fna/cds.fna -a GCF_006542665.1_Acom_1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:35,346] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:35,346] [INFO] Task started: HMMsearch
[2024-01-24 14:14:35,347] [INFO] Running command: hmmsearch --tblout GCF_006542665.1_Acom_1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a783b28-9ae9-4e59-9117-d70af642e2d9/dqc_reference/reference_markers.hmm GCF_006542665.1_Acom_1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:35,631] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:35,632] [INFO] Found 6/6 markers.
[2024-01-24 14:14:35,684] [INFO] Query marker FASTA was written to GCF_006542665.1_Acom_1.0_genomic.fna/markers.fasta
[2024-01-24 14:14:35,693] [INFO] Task started: Blastn
[2024-01-24 14:14:35,693] [INFO] Running command: blastn -query GCF_006542665.1_Acom_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a783b28-9ae9-4e59-9117-d70af642e2d9/dqc_reference/reference_markers.fasta -out GCF_006542665.1_Acom_1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:36,366] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:36,370] [INFO] Selected 14 target genomes.
[2024-01-24 14:14:36,370] [INFO] Target genome list was writen to GCF_006542665.1_Acom_1.0_genomic.fna/target_genomes.txt
[2024-01-24 14:14:36,385] [INFO] Task started: fastANI
[2024-01-24 14:14:36,385] [INFO] Running command: fastANI --query /var/lib/cwl/stgede49472-bb24-49dc-a574-56e449e8789f/GCF_006542665.1_Acom_1.0_genomic.fna.gz --refList GCF_006542665.1_Acom_1.0_genomic.fna/target_genomes.txt --output GCF_006542665.1_Acom_1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:46,090] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:46,090] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a783b28-9ae9-4e59-9117-d70af642e2d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:46,091] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a783b28-9ae9-4e59-9117-d70af642e2d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:46,103] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:14:46,103] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:46,103] [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 communis	strain=5CBH24	GCA_006542665.1	2585118	2585118	type	True	100.0	1100	1100	95	conclusive
Alistipes dispar	strain=5CPEGH6	GCA_006542685.1	2585119	2585119	type	True	81.4847	445	1100	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	81.26	460	1100	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	81.2319	458	1100	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	81.163	466	1100	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	81.1242	451	1100	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	80.9732	472	1100	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_000374505.1	328813	328813	type	True	80.7443	426	1100	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	80.7101	429	1100	95	below_threshold
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	80.1121	441	1100	95	below_threshold
Alistipes onderdonkii subsp. vulgaris	strain=3BBH6	GCA_006542645.1	2585117	328813	type	True	79.9436	411	1100	95	below_threshold
Alistipes megaguti	strain=Marseille-P5997	GCA_900604385.1	2364787	2364787	type	True	79.9107	377	1100	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	79.5642	418	1100	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_025144665.1	1470347	1470347	type	True	77.916	154	1100	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:46,105] [INFO] DFAST Taxonomy check result was written to GCF_006542665.1_Acom_1.0_genomic.fna/tc_result.tsv
[2024-01-24 14:14:46,106] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:46,106] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:46,106] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a783b28-9ae9-4e59-9117-d70af642e2d9/dqc_reference/checkm_data
[2024-01-24 14:14:46,107] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:46,143] [INFO] Task started: CheckM
[2024-01-24 14:14:46,143] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006542665.1_Acom_1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006542665.1_Acom_1.0_genomic.fna/checkm_input GCF_006542665.1_Acom_1.0_genomic.fna/checkm_result
[2024-01-24 14:15:35,838] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:35,839] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:35,857] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:35,857] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:35,857] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006542665.1_Acom_1.0_genomic.fna/markers.fasta)
[2024-01-24 14:15:35,858] [INFO] Task started: Blastn
[2024-01-24 14:15:35,858] [INFO] Running command: blastn -query GCF_006542665.1_Acom_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a783b28-9ae9-4e59-9117-d70af642e2d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_006542665.1_Acom_1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:36,931] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:36,934] [INFO] Selected 14 target genomes.
[2024-01-24 14:15:36,935] [INFO] Target genome list was writen to GCF_006542665.1_Acom_1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:36,962] [INFO] Task started: fastANI
[2024-01-24 14:15:36,962] [INFO] Running command: fastANI --query /var/lib/cwl/stgede49472-bb24-49dc-a574-56e449e8789f/GCF_006542665.1_Acom_1.0_genomic.fna.gz --refList GCF_006542665.1_Acom_1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_006542665.1_Acom_1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:45,667] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:45,679] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:45,679] [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_006542665.1	s__Alistipes communis	100.0	1100	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.74	98.62	0.92	0.87	10	conclusive
GCA_900550375.1	s__Alistipes sp900550375	87.5084	563	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900552955.1	s__Alistipes sp900552955	86.7985	435	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214725.1	s__Alistipes sp905214725	86.2939	621	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900021155.1	s__Alistipes excrementavium	81.5344	399	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.37	98.83	0.93	0.90	7	-
GCF_006542685.1	s__Alistipes dispar	81.4725	446	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.07	98.96	0.94	0.89	7	-
GCA_902362705.1	s__Alistipes sp002358415	80.51	356	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.62	98.83	0.97	0.92	7	-
GCA_900544265.1	s__Alistipes merdavium	80.3166	360	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.60	98.07	0.91	0.88	5	-
GCF_002161445.1	s__Alistipes cottocaccae	80.1946	364	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.26	98.26	0.94	0.94	2	-
GCF_900290115.1	s__Alistipes excrementigallinarum	80.1264	363	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.90	98.75	0.93	0.91	6	-
GCF_000265365.1	s__Alistipes finegoldii	80.1118	440	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.50	97.54	0.87	0.79	15	-
GCA_900541585.1	s__Alistipes sp900541585	80.0836	402	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.86	98.76	0.92	0.91	4	-
GCA_019118605.1	s__Alistipes faecavium	79.5978	342	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113885.1	s__Alistipes intestinipullorum	78.8323	292	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:45,680] [INFO] GTDB search result was written to GCF_006542665.1_Acom_1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:45,681] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:45,684] [INFO] DFAST_QC result json was written to GCF_006542665.1_Acom_1.0_genomic.fna/dqc_result.json
[2024-01-24 14:15:45,684] [INFO] DFAST_QC completed!
[2024-01-24 14:15:45,685] [INFO] Total running time: 0h1m30s