[2024-01-24 13:25:31,120] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:31,122] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:31,123] [INFO] DQC Reference Directory: /var/lib/cwl/stg90c11052-fd40-4c99-af31-e6358efafaa9/dqc_reference
[2024-01-24 13:25:32,512] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:32,513] [INFO] Task started: Prodigal
[2024-01-24 13:25:32,513] [INFO] Running command: gunzip -c /var/lib/cwl/stgb151280d-d01e-403a-aed8-fa71ed0e81ec/GCF_025144665.1_ASM2514466v1_genomic.fna.gz | prodigal -d GCF_025144665.1_ASM2514466v1_genomic.fna/cds.fna -a GCF_025144665.1_ASM2514466v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:46,723] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:46,724] [INFO] Task started: HMMsearch
[2024-01-24 13:25:46,724] [INFO] Running command: hmmsearch --tblout GCF_025144665.1_ASM2514466v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90c11052-fd40-4c99-af31-e6358efafaa9/dqc_reference/reference_markers.hmm GCF_025144665.1_ASM2514466v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:47,013] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:47,015] [INFO] Found 6/6 markers.
[2024-01-24 13:25:47,038] [INFO] Query marker FASTA was written to GCF_025144665.1_ASM2514466v1_genomic.fna/markers.fasta
[2024-01-24 13:25:47,039] [INFO] Task started: Blastn
[2024-01-24 13:25:47,039] [INFO] Running command: blastn -query GCF_025144665.1_ASM2514466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90c11052-fd40-4c99-af31-e6358efafaa9/dqc_reference/reference_markers.fasta -out GCF_025144665.1_ASM2514466v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:47,803] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:47,806] [INFO] Selected 12 target genomes.
[2024-01-24 13:25:47,806] [INFO] Target genome list was writen to GCF_025144665.1_ASM2514466v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:47,812] [INFO] Task started: fastANI
[2024-01-24 13:25:47,812] [INFO] Running command: fastANI --query /var/lib/cwl/stgb151280d-d01e-403a-aed8-fa71ed0e81ec/GCF_025144665.1_ASM2514466v1_genomic.fna.gz --refList GCF_025144665.1_ASM2514466v1_genomic.fna/target_genomes.txt --output GCF_025144665.1_ASM2514466v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:55,064] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:55,065] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90c11052-fd40-4c99-af31-e6358efafaa9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:55,066] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90c11052-fd40-4c99-af31-e6358efafaa9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:55,081] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:25:55,082] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:55,082] [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 ihumii	strain=AP11	GCA_025144665.1	1470347	1470347	type	True	100.0	921	926	95	conclusive
Alistipes ihumii	strain=AP11	GCA_000321205.1	1470347	1470347	type	True	99.9886	897	926	95	conclusive
Alistipes indistinctus	strain=YIT 12060	GCA_025144995.1	626932	626932	type	True	78.2947	231	926	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_000231275.1	626932	626932	type	True	78.0622	243	926	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	77.9898	148	926	95	below_threshold
Alistipes dispar	strain=5CPEGH6	GCA_006542685.1	2585119	2585119	type	True	77.9421	147	926	95	below_threshold
Alistipes communis	strain=5CBH24	GCA_006542665.1	2585118	2585118	type	True	77.8433	156	926	95	below_threshold
Gallalistipes aquisgranensis	strain=DSM 108975	GCA_014982715.1	2779358	2779358	type	True	77.5771	209	926	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	77.5393	155	926	95	below_threshold
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	77.4909	145	926	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	77.4693	150	926	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:55,083] [INFO] DFAST Taxonomy check result was written to GCF_025144665.1_ASM2514466v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:55,084] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:55,084] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:55,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90c11052-fd40-4c99-af31-e6358efafaa9/dqc_reference/checkm_data
[2024-01-24 13:25:55,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:55,115] [INFO] Task started: CheckM
[2024-01-24 13:25:55,115] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025144665.1_ASM2514466v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025144665.1_ASM2514466v1_genomic.fna/checkm_input GCF_025144665.1_ASM2514466v1_genomic.fna/checkm_result
[2024-01-24 13:26:36,412] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:36,413] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:36,440] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:36,441] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:36,441] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025144665.1_ASM2514466v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:36,442] [INFO] Task started: Blastn
[2024-01-24 13:26:36,442] [INFO] Running command: blastn -query GCF_025144665.1_ASM2514466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90c11052-fd40-4c99-af31-e6358efafaa9/dqc_reference/reference_markers_gtdb.fasta -out GCF_025144665.1_ASM2514466v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:37,362] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:37,366] [INFO] Selected 10 target genomes.
[2024-01-24 13:26:37,366] [INFO] Target genome list was writen to GCF_025144665.1_ASM2514466v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:37,380] [INFO] Task started: fastANI
[2024-01-24 13:26:37,380] [INFO] Running command: fastANI --query /var/lib/cwl/stgb151280d-d01e-403a-aed8-fa71ed0e81ec/GCF_025144665.1_ASM2514466v1_genomic.fna.gz --refList GCF_025144665.1_ASM2514466v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025144665.1_ASM2514466v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:42,394] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:42,411] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:42,412] [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_000321205.1	s__Alistipes_A ihumii	99.9886	897	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	99.03	98.23	0.96	0.93	6	conclusive
GCA_910583985.1	s__Alistipes_A sp910583985	79.5052	387	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549685.1	s__Alistipes_A sp900549685	78.8912	327	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009557455.1	s__Alistipes_A pullistercoris	78.8845	348	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	99.39	98.63	0.95	0.90	13	-
GCA_017415005.1	s__RGIG1874 sp017415005	78.1585	225	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__RGIG1874	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000231275.1	s__Alistipes_A indistinctus	78.062	243	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	99.29	99.01	0.94	0.90	8	-
GCA_900544265.1	s__Alistipes merdavium	77.4948	137	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.60	98.07	0.91	0.88	5	-
GCF_000210575.1	s__Alistipes shahii	77.4693	150	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.59	98.01	0.85	0.77	20	-
GCA_017935625.1	s__RGIG9113 sp017935625	76.9009	122	926	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__RGIG9113	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:42,414] [INFO] GTDB search result was written to GCF_025144665.1_ASM2514466v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:42,414] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:42,418] [INFO] DFAST_QC result json was written to GCF_025144665.1_ASM2514466v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:42,418] [INFO] DFAST_QC completed!
[2024-01-24 13:26:42,418] [INFO] Total running time: 0h1m11s