[2024-01-24 12:47:22,095] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:22,097] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:22,097] [INFO] DQC Reference Directory: /var/lib/cwl/stgff0de888-014b-4799-b906-d8e7a83e82da/dqc_reference
[2024-01-24 12:47:23,424] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:23,425] [INFO] Task started: Prodigal
[2024-01-24 12:47:23,426] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc644d17-9fa6-4781-bd34-9485a1c96d6e/GCF_006542685.1_Adis_1.0_genomic.fna.gz | prodigal -d GCF_006542685.1_Adis_1.0_genomic.fna/cds.fna -a GCF_006542685.1_Adis_1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:39,491] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:39,491] [INFO] Task started: HMMsearch
[2024-01-24 12:47:39,491] [INFO] Running command: hmmsearch --tblout GCF_006542685.1_Adis_1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff0de888-014b-4799-b906-d8e7a83e82da/dqc_reference/reference_markers.hmm GCF_006542685.1_Adis_1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:39,729] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:39,730] [INFO] Found 6/6 markers.
[2024-01-24 12:47:39,756] [INFO] Query marker FASTA was written to GCF_006542685.1_Adis_1.0_genomic.fna/markers.fasta
[2024-01-24 12:47:39,757] [INFO] Task started: Blastn
[2024-01-24 12:47:39,757] [INFO] Running command: blastn -query GCF_006542685.1_Adis_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgff0de888-014b-4799-b906-d8e7a83e82da/dqc_reference/reference_markers.fasta -out GCF_006542685.1_Adis_1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:40,443] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:40,447] [INFO] Selected 11 target genomes.
[2024-01-24 12:47:40,448] [INFO] Target genome list was writen to GCF_006542685.1_Adis_1.0_genomic.fna/target_genomes.txt
[2024-01-24 12:47:40,461] [INFO] Task started: fastANI
[2024-01-24 12:47:40,461] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc644d17-9fa6-4781-bd34-9485a1c96d6e/GCF_006542685.1_Adis_1.0_genomic.fna.gz --refList GCF_006542685.1_Adis_1.0_genomic.fna/target_genomes.txt --output GCF_006542685.1_Adis_1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:48,032] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:48,032] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff0de888-014b-4799-b906-d8e7a83e82da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:48,033] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff0de888-014b-4799-b906-d8e7a83e82da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:48,046] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:48,046] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:48,046] [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 dispar	strain=5CPEGH6	GCA_006542685.1	2585119	2585119	type	True	100.0	986	987	95	conclusive
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	83.9595	538	987	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	83.947	530	987	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	83.8477	530	987	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	83.8284	550	987	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	83.8099	551	987	95	below_threshold
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	83.2367	531	987	95	below_threshold
Alistipes timonensis	strain=DSM 25383	GCA_900107675.1	1465754	1465754	type	True	82.7299	519	987	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	81.8729	552	987	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	81.7891	524	987	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_025144995.1	626932	626932	type	True	77.2724	106	987	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:48,048] [INFO] DFAST Taxonomy check result was written to GCF_006542685.1_Adis_1.0_genomic.fna/tc_result.tsv
[2024-01-24 12:47:48,049] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:48,049] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:48,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff0de888-014b-4799-b906-d8e7a83e82da/dqc_reference/checkm_data
[2024-01-24 12:47:48,051] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:48,086] [INFO] Task started: CheckM
[2024-01-24 12:47:48,086] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006542685.1_Adis_1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006542685.1_Adis_1.0_genomic.fna/checkm_input GCF_006542685.1_Adis_1.0_genomic.fna/checkm_result
[2024-01-24 12:48:35,624] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:35,625] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:35,657] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:35,658] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:35,659] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006542685.1_Adis_1.0_genomic.fna/markers.fasta)
[2024-01-24 12:48:35,659] [INFO] Task started: Blastn
[2024-01-24 12:48:35,659] [INFO] Running command: blastn -query GCF_006542685.1_Adis_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgff0de888-014b-4799-b906-d8e7a83e82da/dqc_reference/reference_markers_gtdb.fasta -out GCF_006542685.1_Adis_1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:36,626] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:36,630] [INFO] Selected 12 target genomes.
[2024-01-24 12:48:36,630] [INFO] Target genome list was writen to GCF_006542685.1_Adis_1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:36,642] [INFO] Task started: fastANI
[2024-01-24 12:48:36,642] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc644d17-9fa6-4781-bd34-9485a1c96d6e/GCF_006542685.1_Adis_1.0_genomic.fna.gz --refList GCF_006542685.1_Adis_1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_006542685.1_Adis_1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:44,657] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:44,668] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:44,668] [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_006542685.1	s__Alistipes dispar	100.0	987	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.07	98.96	0.94	0.89	7	conclusive
GCA_019115605.1	s__Alistipes faecigallinarum	84.6943	517	987	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	84.4867	553	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.09	99.09	0.91	0.91	2	-
GCA_000434235.1	s__Alistipes avistercoris	84.1269	541	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.86	98.12	0.90	0.84	7	-
GCF_000312145.1	s__Alistipes senegalensis	83.9333	531	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.29	97.35	0.84	0.66	10	-
GCF_000210575.1	s__Alistipes shahii	83.8099	551	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.59	98.01	0.85	0.77	20	-
GCA_900541585.1	s__Alistipes sp900541585	83.5115	493	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.86	98.76	0.92	0.91	4	-
GCA_900544265.1	s__Alistipes merdavium	83.5016	485	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.60	98.07	0.91	0.88	5	-
GCA_001941065.1	s__Alistipes sp001941065	82.8224	507	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576555.1	s__Alistipes sp910576555	82.7351	450	987	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	82.355	464	987	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	82.3502	484	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.26	98.26	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:44,671] [INFO] GTDB search result was written to GCF_006542685.1_Adis_1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:44,671] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:44,676] [INFO] DFAST_QC result json was written to GCF_006542685.1_Adis_1.0_genomic.fna/dqc_result.json
[2024-01-24 12:48:44,676] [INFO] DFAST_QC completed!
[2024-01-24 12:48:44,676] [INFO] Total running time: 0h1m23s