[2023-06-18 20:56:05,251] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:56:05,255] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:56:05,255] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa81606c-5dc6-4474-b310-1f91d62cf3e8/dqc_reference
[2023-06-18 20:56:07,102] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:56:07,103] [INFO] Task started: Prodigal
[2023-06-18 20:56:07,103] [INFO] Running command: gunzip -c /var/lib/cwl/stge0780206-faa5-490d-8c21-c939c271b38b/GCA_018376795.1_ASM1837679v1_genomic.fna.gz | prodigal -d GCA_018376795.1_ASM1837679v1_genomic.fna/cds.fna -a GCA_018376795.1_ASM1837679v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:56:19,267] [INFO] Task succeeded: Prodigal
[2023-06-18 20:56:19,267] [INFO] Task started: HMMsearch
[2023-06-18 20:56:19,267] [INFO] Running command: hmmsearch --tblout GCA_018376795.1_ASM1837679v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa81606c-5dc6-4474-b310-1f91d62cf3e8/dqc_reference/reference_markers.hmm GCA_018376795.1_ASM1837679v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:56:19,504] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:56:19,506] [INFO] Found 6/6 markers.
[2023-06-18 20:56:19,533] [INFO] Query marker FASTA was written to GCA_018376795.1_ASM1837679v1_genomic.fna/markers.fasta
[2023-06-18 20:56:19,534] [INFO] Task started: Blastn
[2023-06-18 20:56:19,534] [INFO] Running command: blastn -query GCA_018376795.1_ASM1837679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa81606c-5dc6-4474-b310-1f91d62cf3e8/dqc_reference/reference_markers.fasta -out GCA_018376795.1_ASM1837679v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:56:20,149] [INFO] Task succeeded: Blastn
[2023-06-18 20:56:20,153] [INFO] Selected 15 target genomes.
[2023-06-18 20:56:20,154] [INFO] Target genome list was writen to GCA_018376795.1_ASM1837679v1_genomic.fna/target_genomes.txt
[2023-06-18 20:56:20,155] [INFO] Task started: fastANI
[2023-06-18 20:56:20,156] [INFO] Running command: fastANI --query /var/lib/cwl/stge0780206-faa5-490d-8c21-c939c271b38b/GCA_018376795.1_ASM1837679v1_genomic.fna.gz --refList GCA_018376795.1_ASM1837679v1_genomic.fna/target_genomes.txt --output GCA_018376795.1_ASM1837679v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:56:27,772] [INFO] Task succeeded: fastANI
[2023-06-18 20:56:27,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa81606c-5dc6-4474-b310-1f91d62cf3e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:56:27,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa81606c-5dc6-4474-b310-1f91d62cf3e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:56:27,786] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 20:56:27,786] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 20:56:27,786] [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 shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	77.9454	168	723	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	77.9379	163	723	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	77.6373	205	723	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	77.6063	202	723	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	77.5485	205	723	95	below_threshold
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	77.536	193	723	95	below_threshold
Alistipes communis	strain=5CBH24	GCA_006542665.1	2585118	2585118	type	True	77.3819	196	723	95	below_threshold
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	77.3686	186	723	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	77.3382	169	723	95	below_threshold
Alistipes onderdonkii subsp. vulgaris	strain=3BBH6	GCA_006542645.1	2585117	328813	type	True	77.1171	155	723	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	77.0373	153	723	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_000374505.1	328813	328813	type	True	76.9897	158	723	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_000231275.1	626932	626932	type	True	76.0324	50	723	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 20:56:27,788] [INFO] DFAST Taxonomy check result was written to GCA_018376795.1_ASM1837679v1_genomic.fna/tc_result.tsv
[2023-06-18 20:56:27,789] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:56:27,789] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:56:27,789] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa81606c-5dc6-4474-b310-1f91d62cf3e8/dqc_reference/checkm_data
[2023-06-18 20:56:27,790] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:56:27,819] [INFO] Task started: CheckM
[2023-06-18 20:56:27,819] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018376795.1_ASM1837679v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018376795.1_ASM1837679v1_genomic.fna/checkm_input GCA_018376795.1_ASM1837679v1_genomic.fna/checkm_result
[2023-06-18 20:57:04,252] [INFO] Task succeeded: CheckM
[2023-06-18 20:57:04,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 20:57:04,274] [INFO] ===== Completeness check finished =====
[2023-06-18 20:57:04,274] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:57:04,275] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018376795.1_ASM1837679v1_genomic.fna/markers.fasta)
[2023-06-18 20:57:04,275] [INFO] Task started: Blastn
[2023-06-18 20:57:04,275] [INFO] Running command: blastn -query GCA_018376795.1_ASM1837679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa81606c-5dc6-4474-b310-1f91d62cf3e8/dqc_reference/reference_markers_gtdb.fasta -out GCA_018376795.1_ASM1837679v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:57:05,114] [INFO] Task succeeded: Blastn
[2023-06-18 20:57:05,119] [INFO] Selected 17 target genomes.
[2023-06-18 20:57:05,120] [INFO] Target genome list was writen to GCA_018376795.1_ASM1837679v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:57:05,126] [INFO] Task started: fastANI
[2023-06-18 20:57:05,126] [INFO] Running command: fastANI --query /var/lib/cwl/stge0780206-faa5-490d-8c21-c939c271b38b/GCA_018376795.1_ASM1837679v1_genomic.fna.gz --refList GCA_018376795.1_ASM1837679v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018376795.1_ASM1837679v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:57:12,854] [INFO] Task succeeded: fastANI
[2023-06-18 20:57:12,874] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 20:57:12,874] [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_905213895.1	s__Alistipes sp900548155	96.9479	648	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.70	96.93	0.90	0.83	5	conclusive
GCA_900761235.1	s__Alistipes sp900761235	93.953	515	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017410165.1	s__Alistipes sp017410165	78.3584	233	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000210575.1	s__Alistipes shahii	77.9454	168	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.59	98.01	0.85	0.77	20	-
GCA_017936685.1	s__Alistipes sp017936685	77.8937	177	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017483225.1	s__Alistipes sp017483225	77.8418	167	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910574205.1	s__Alistipes sp002362235	77.7965	174	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.85	98.52	0.94	0.92	5	-
GCF_000312145.1	s__Alistipes senegalensis	77.6373	205	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.29	97.35	0.84	0.66	10	-
GCF_900021155.1	s__Alistipes excrementavium	77.5867	154	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.37	98.83	0.93	0.90	7	-
GCF_000265365.1	s__Alistipes finegoldii	77.536	193	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.50	97.54	0.87	0.79	15	-
GCA_902388705.1	s__Alistipes sp902388705	77.5127	188	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.98	97.96	0.93	0.92	3	-
GCA_900542505.1	s__Alistipes stercorigallinarum	77.4322	179	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.83	98.70	0.90	0.85	3	-
GCA_017504485.1	s__Alistipes sp017504485	77.424	139	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900083545.1	s__Alistipes provencensis	77.3686	186	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	100.00	100.00	1.00	1.00	2	-
GCA_910576555.1	s__Alistipes sp910576555	77.3335	177	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577475.1	s__Alistipes sp910577475	77.329	159	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550375.1	s__Alistipes sp900550375	76.9723	141	723	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-18 20:57:12,877] [INFO] GTDB search result was written to GCA_018376795.1_ASM1837679v1_genomic.fna/result_gtdb.tsv
[2023-06-18 20:57:12,877] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:57:12,881] [INFO] DFAST_QC result json was written to GCA_018376795.1_ASM1837679v1_genomic.fna/dqc_result.json
[2023-06-18 20:57:12,881] [INFO] DFAST_QC completed!
[2023-06-18 20:57:12,881] [INFO] Total running time: 0h1m8s