[2023-06-28 06:39:53,302] [INFO] DFAST_QC pipeline started.
[2023-06-28 06:39:53,305] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 06:39:53,305] [INFO] DQC Reference Directory: /var/lib/cwl/stg13e25bef-6cc3-4ad6-9182-a8cfeb8066ab/dqc_reference
[2023-06-28 06:39:54,594] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 06:39:54,595] [INFO] Task started: Prodigal
[2023-06-28 06:39:54,596] [INFO] Running command: gunzip -c /var/lib/cwl/stg26995ab9-66d9-4d4e-be3c-a99dcdef67e9/GCA_017621675.1_ASM1762167v1_genomic.fna.gz | prodigal -d GCA_017621675.1_ASM1762167v1_genomic.fna/cds.fna -a GCA_017621675.1_ASM1762167v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 06:40:05,990] [INFO] Task succeeded: Prodigal
[2023-06-28 06:40:05,991] [INFO] Task started: HMMsearch
[2023-06-28 06:40:05,991] [INFO] Running command: hmmsearch --tblout GCA_017621675.1_ASM1762167v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13e25bef-6cc3-4ad6-9182-a8cfeb8066ab/dqc_reference/reference_markers.hmm GCA_017621675.1_ASM1762167v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 06:40:06,251] [INFO] Task succeeded: HMMsearch
[2023-06-28 06:40:06,252] [INFO] Found 6/6 markers.
[2023-06-28 06:40:06,277] [INFO] Query marker FASTA was written to GCA_017621675.1_ASM1762167v1_genomic.fna/markers.fasta
[2023-06-28 06:40:06,277] [INFO] Task started: Blastn
[2023-06-28 06:40:06,277] [INFO] Running command: blastn -query GCA_017621675.1_ASM1762167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13e25bef-6cc3-4ad6-9182-a8cfeb8066ab/dqc_reference/reference_markers.fasta -out GCA_017621675.1_ASM1762167v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:40:06,901] [INFO] Task succeeded: Blastn
[2023-06-28 06:40:06,905] [INFO] Selected 23 target genomes.
[2023-06-28 06:40:06,906] [INFO] Target genome list was writen to GCA_017621675.1_ASM1762167v1_genomic.fna/target_genomes.txt
[2023-06-28 06:40:06,907] [INFO] Task started: fastANI
[2023-06-28 06:40:06,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg26995ab9-66d9-4d4e-be3c-a99dcdef67e9/GCA_017621675.1_ASM1762167v1_genomic.fna.gz --refList GCA_017621675.1_ASM1762167v1_genomic.fna/target_genomes.txt --output GCA_017621675.1_ASM1762167v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 06:40:20,736] [INFO] Task succeeded: fastANI
[2023-06-28 06:40:20,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13e25bef-6cc3-4ad6-9182-a8cfeb8066ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 06:40:20,737] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13e25bef-6cc3-4ad6-9182-a8cfeb8066ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 06:40:20,749] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 06:40:20,749] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 06:40:20,749] [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 montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	76.459	58	668	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	76.4013	63	668	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	76.3836	63	668	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	76.266	55	668	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	76.266	55	668	95	below_threshold
Alistipes onderdonkii subsp. vulgaris	strain=3BBH6	GCA_006542645.1	2585117	328813	type	True	76.1863	65	668	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	76.1653	55	668	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	76.1361	60	668	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_000374505.1	328813	328813	type	True	76.11	61	668	95	below_threshold
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	76.0764	57	668	95	below_threshold
Alistipes communis	strain=5CBH24	GCA_006542665.1	2585118	2585118	type	True	75.9223	53	668	95	below_threshold
Alistipes megaguti	strain=Marseille-P5997	GCA_900604385.1	2364787	2364787	type	True	75.8679	70	668	95	below_threshold
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	75.8502	67	668	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 06:40:20,752] [INFO] DFAST Taxonomy check result was written to GCA_017621675.1_ASM1762167v1_genomic.fna/tc_result.tsv
[2023-06-28 06:40:20,753] [INFO] ===== Taxonomy check completed =====
[2023-06-28 06:40:20,753] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 06:40:20,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13e25bef-6cc3-4ad6-9182-a8cfeb8066ab/dqc_reference/checkm_data
[2023-06-28 06:40:20,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 06:40:20,785] [INFO] Task started: CheckM
[2023-06-28 06:40:20,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017621675.1_ASM1762167v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017621675.1_ASM1762167v1_genomic.fna/checkm_input GCA_017621675.1_ASM1762167v1_genomic.fna/checkm_result
[2023-06-28 06:40:57,481] [INFO] Task succeeded: CheckM
[2023-06-28 06:40:57,483] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 06:40:57,504] [INFO] ===== Completeness check finished =====
[2023-06-28 06:40:57,504] [INFO] ===== Start GTDB Search =====
[2023-06-28 06:40:57,504] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017621675.1_ASM1762167v1_genomic.fna/markers.fasta)
[2023-06-28 06:40:57,505] [INFO] Task started: Blastn
[2023-06-28 06:40:57,505] [INFO] Running command: blastn -query GCA_017621675.1_ASM1762167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13e25bef-6cc3-4ad6-9182-a8cfeb8066ab/dqc_reference/reference_markers_gtdb.fasta -out GCA_017621675.1_ASM1762167v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:40:58,317] [INFO] Task succeeded: Blastn
[2023-06-28 06:40:58,323] [INFO] Selected 13 target genomes.
[2023-06-28 06:40:58,323] [INFO] Target genome list was writen to GCA_017621675.1_ASM1762167v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 06:40:58,325] [INFO] Task started: fastANI
[2023-06-28 06:40:58,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg26995ab9-66d9-4d4e-be3c-a99dcdef67e9/GCA_017621675.1_ASM1762167v1_genomic.fna.gz --refList GCA_017621675.1_ASM1762167v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017621675.1_ASM1762167v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 06:41:03,488] [INFO] Task succeeded: fastANI
[2023-06-28 06:41:03,505] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 06:41:03,505] [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_015059845.1	s__Alistipes sp015059845	97.5255	588	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.42	97.01	0.88	0.86	7	conclusive
GCA_017384185.1	s__Alistipes sp017384185	83.9322	305	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017481925.1	s__Alistipes sp017481925	81.5523	388	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	96.75	96.65	0.89	0.83	5	-
GCA_015059925.1	s__Alistipes sp015059925	81.3242	414	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.56	97.45	0.96	0.96	5	-
GCA_017631035.1	s__Alistipes sp017631035	81.1249	247	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017391665.1	s__Alistipes sp017391665	80.887	312	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.61	98.61	0.75	0.75	2	-
GCA_017628595.1	s__Alistipes sp017628595	80.7035	259	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.53	97.53	0.74	0.74	2	-
GCA_015059905.1	s__Alistipes sp015059905	79.9808	345	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	96.97	96.87	0.91	0.89	3	-
GCA_015060015.1	s__Alistipes sp015060015	79.7154	274	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017465605.1	s__Alistipes sp017465605	79.5091	304	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.41	97.24	0.90	0.86	5	-
GCA_017560305.1	s__Alistipes sp017560305	79.3732	299	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015060165.1	s__Alistipes sp015060165	79.1389	292	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.68	97.68	0.91	0.90	3	-
GCA_017631285.1	s__Alistipes sp017631285	79.0224	184	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 06:41:03,536] [INFO] GTDB search result was written to GCA_017621675.1_ASM1762167v1_genomic.fna/result_gtdb.tsv
[2023-06-28 06:41:03,537] [INFO] ===== GTDB Search completed =====
[2023-06-28 06:41:03,543] [INFO] DFAST_QC result json was written to GCA_017621675.1_ASM1762167v1_genomic.fna/dqc_result.json
[2023-06-28 06:41:03,543] [INFO] DFAST_QC completed!
[2023-06-28 06:41:03,544] [INFO] Total running time: 0h1m10s