[2024-01-24 12:36:24,403] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:24,404] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:24,405] [INFO] DQC Reference Directory: /var/lib/cwl/stg5de54634-ff5e-4b06-93be-2e4c11adfcc6/dqc_reference
[2024-01-24 12:36:25,810] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:25,811] [INFO] Task started: Prodigal
[2024-01-24 12:36:25,811] [INFO] Running command: gunzip -c /var/lib/cwl/stg69944f54-8eae-4000-b4d2-64189d6d4230/GCF_014982715.1_ASM1498271v1_genomic.fna.gz | prodigal -d GCF_014982715.1_ASM1498271v1_genomic.fna/cds.fna -a GCF_014982715.1_ASM1498271v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:42,548] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:42,548] [INFO] Task started: HMMsearch
[2024-01-24 12:36:42,549] [INFO] Running command: hmmsearch --tblout GCF_014982715.1_ASM1498271v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5de54634-ff5e-4b06-93be-2e4c11adfcc6/dqc_reference/reference_markers.hmm GCF_014982715.1_ASM1498271v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:42,811] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:42,813] [INFO] Found 6/6 markers.
[2024-01-24 12:36:42,846] [INFO] Query marker FASTA was written to GCF_014982715.1_ASM1498271v1_genomic.fna/markers.fasta
[2024-01-24 12:36:42,847] [INFO] Task started: Blastn
[2024-01-24 12:36:42,847] [INFO] Running command: blastn -query GCF_014982715.1_ASM1498271v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5de54634-ff5e-4b06-93be-2e4c11adfcc6/dqc_reference/reference_markers.fasta -out GCF_014982715.1_ASM1498271v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:43,488] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:43,492] [INFO] Selected 16 target genomes.
[2024-01-24 12:36:43,493] [INFO] Target genome list was writen to GCF_014982715.1_ASM1498271v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:43,502] [INFO] Task started: fastANI
[2024-01-24 12:36:43,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg69944f54-8eae-4000-b4d2-64189d6d4230/GCF_014982715.1_ASM1498271v1_genomic.fna.gz --refList GCF_014982715.1_ASM1498271v1_genomic.fna/target_genomes.txt --output GCF_014982715.1_ASM1498271v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:52,023] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:52,024] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5de54634-ff5e-4b06-93be-2e4c11adfcc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:52,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5de54634-ff5e-4b06-93be-2e4c11adfcc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:52,040] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:36:52,040] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:36:52,040] [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
Gallalistipes aquisgranensis	strain=DSM 108975	GCA_014982715.1	2779358	2779358	type	True	100.0	994	995	95	conclusive
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	78.797	224	995	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	78.709	213	995	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	78.5972	202	995	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	78.4948	200	995	95	below_threshold
Alistipes dispar	strain=5CPEGH6	GCA_006542685.1	2585119	2585119	type	True	77.9751	179	995	95	below_threshold
Alistipes timonensis	strain=DSM 25383	GCA_900107675.1	1465754	1465754	type	True	77.8624	182	995	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	77.7513	230	995	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_025144665.1	1470347	1470347	type	True	77.7355	199	995	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	77.7281	232	995	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	77.7206	231	995	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_025144995.1	626932	626932	type	True	77.5073	157	995	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_000231275.1	626932	626932	type	True	77.4784	163	995	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	77.2524	178	995	95	below_threshold
Alistipes putredinis	strain=DSM 17216	GCA_000154465.1	28117	28117	type	True	77.0892	131	995	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:52,042] [INFO] DFAST Taxonomy check result was written to GCF_014982715.1_ASM1498271v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:52,043] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:52,043] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:52,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5de54634-ff5e-4b06-93be-2e4c11adfcc6/dqc_reference/checkm_data
[2024-01-24 12:36:52,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:52,079] [INFO] Task started: CheckM
[2024-01-24 12:36:52,079] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014982715.1_ASM1498271v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014982715.1_ASM1498271v1_genomic.fna/checkm_input GCF_014982715.1_ASM1498271v1_genomic.fna/checkm_result
[2024-01-24 12:37:39,013] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:39,014] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:39,031] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:39,031] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:39,031] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014982715.1_ASM1498271v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:39,032] [INFO] Task started: Blastn
[2024-01-24 12:37:39,032] [INFO] Running command: blastn -query GCF_014982715.1_ASM1498271v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5de54634-ff5e-4b06-93be-2e4c11adfcc6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014982715.1_ASM1498271v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:39,929] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:39,933] [INFO] Selected 20 target genomes.
[2024-01-24 12:37:39,933] [INFO] Target genome list was writen to GCF_014982715.1_ASM1498271v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:39,974] [INFO] Task started: fastANI
[2024-01-24 12:37:39,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg69944f54-8eae-4000-b4d2-64189d6d4230/GCF_014982715.1_ASM1498271v1_genomic.fna.gz --refList GCF_014982715.1_ASM1498271v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014982715.1_ASM1498271v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:49,314] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:49,338] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:49,338] [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_014982715.1	s__DSM-108975 sp014982715	100.0	994	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__DSM-108975	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017415005.1	s__RGIG1874 sp017415005	78.258	214	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__RGIG1874	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900290115.1	s__Alistipes excrementigallinarum	78.2248	158	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.90	98.75	0.93	0.91	6	-
GCA_900542505.1	s__Alistipes stercorigallinarum	77.9644	152	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.83	98.70	0.90	0.85	3	-
GCA_019116245.1	s__Tidjanibacter faecipullorum	77.9123	154	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009557455.1	s__Alistipes_A pullistercoris	77.887	170	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	99.39	98.63	0.95	0.90	13	-
GCF_900107675.1	s__Alistipes timonensis	77.8624	182	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.07	98.44	0.92	0.87	7	-
GCA_910583985.1	s__Alistipes_A sp910583985	77.8091	202	995	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_000312145.1	s__Alistipes senegalensis	77.7513	230	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.29	97.35	0.84	0.66	10	-
GCA_910576555.1	s__Alistipes sp910576555	77.7289	162	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118605.1	s__Alistipes faecavium	77.6019	130	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017935625.1	s__RGIG9113 sp017935625	77.5748	193	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__RGIG9113	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544265.1	s__Alistipes merdavium	77.5689	176	995	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	77.5611	168	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.26	98.26	0.94	0.94	2	-
GCA_910577285.1	s__Tidjanibacter sp910577285	77.535	129	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549685.1	s__Alistipes_A sp900549685	77.5105	162	995	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_000231275.1	s__Alistipes_A indistinctus	77.497	162	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	99.29	99.01	0.94	0.90	8	-
GCF_015553985.1	s__Alistipes sp900549305	77.3018	180	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.80	98.50	0.91	0.87	6	-
GCA_905214725.1	s__Alistipes sp905214725	77.0956	123	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900768115.1	s__UBA940 sp900768115	76.7574	76	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__UBA940	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:49,341] [INFO] GTDB search result was written to GCF_014982715.1_ASM1498271v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:49,341] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:49,345] [INFO] DFAST_QC result json was written to GCF_014982715.1_ASM1498271v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:49,346] [INFO] DFAST_QC completed!
[2024-01-24 12:37:49,346] [INFO] Total running time: 0h1m25s