[2023-06-29 00:38:30,746] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:38:30,748] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:38:30,748] [INFO] DQC Reference Directory: /var/lib/cwl/stg21fab109-c3c1-4e1d-ac96-58b665ba6e6b/dqc_reference
[2023-06-29 00:38:32,964] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:38:32,966] [INFO] Task started: Prodigal
[2023-06-29 00:38:32,966] [INFO] Running command: gunzip -c /var/lib/cwl/stg09193b98-6834-4b6b-b558-0647fae09035/GCA_015059965.1_ASM1505996v1_genomic.fna.gz | prodigal -d GCA_015059965.1_ASM1505996v1_genomic.fna/cds.fna -a GCA_015059965.1_ASM1505996v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:38:43,960] [INFO] Task succeeded: Prodigal
[2023-06-29 00:38:43,961] [INFO] Task started: HMMsearch
[2023-06-29 00:38:43,961] [INFO] Running command: hmmsearch --tblout GCA_015059965.1_ASM1505996v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21fab109-c3c1-4e1d-ac96-58b665ba6e6b/dqc_reference/reference_markers.hmm GCA_015059965.1_ASM1505996v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:38:44,211] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:38:44,213] [INFO] Found 6/6 markers.
[2023-06-29 00:38:44,239] [INFO] Query marker FASTA was written to GCA_015059965.1_ASM1505996v1_genomic.fna/markers.fasta
[2023-06-29 00:38:44,239] [INFO] Task started: Blastn
[2023-06-29 00:38:44,239] [INFO] Running command: blastn -query GCA_015059965.1_ASM1505996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21fab109-c3c1-4e1d-ac96-58b665ba6e6b/dqc_reference/reference_markers.fasta -out GCA_015059965.1_ASM1505996v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:38:44,831] [INFO] Task succeeded: Blastn
[2023-06-29 00:38:44,836] [INFO] Selected 16 target genomes.
[2023-06-29 00:38:44,837] [INFO] Target genome list was writen to GCA_015059965.1_ASM1505996v1_genomic.fna/target_genomes.txt
[2023-06-29 00:38:44,841] [INFO] Task started: fastANI
[2023-06-29 00:38:44,842] [INFO] Running command: fastANI --query /var/lib/cwl/stg09193b98-6834-4b6b-b558-0647fae09035/GCA_015059965.1_ASM1505996v1_genomic.fna.gz --refList GCA_015059965.1_ASM1505996v1_genomic.fna/target_genomes.txt --output GCA_015059965.1_ASM1505996v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:38:53,472] [INFO] Task succeeded: fastANI
[2023-06-29 00:38:53,473] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21fab109-c3c1-4e1d-ac96-58b665ba6e6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:38:53,474] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21fab109-c3c1-4e1d-ac96-58b665ba6e6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:38:53,498] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:38:53,499] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 00:38:53,499] [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 megaguti	strain=Marseille-P5997	GCA_900604385.1	2364787	2364787	type	True	78.8553	255	639	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_000374505.1	328813	328813	type	True	78.5413	206	639	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	78.536	207	639	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	78.5069	227	639	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	78.4545	228	639	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	78.4513	227	639	95	below_threshold
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	78.4009	230	639	95	below_threshold
Alistipes dispar	strain=5CPEGH6	GCA_006542685.1	2585119	2585119	type	True	78.3452	230	639	95	below_threshold
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	78.3419	216	639	95	below_threshold
Alistipes onderdonkii subsp. vulgaris	strain=3BBH6	GCA_006542645.1	2585117	328813	type	True	78.3375	204	639	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	78.3053	231	639	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	78.2607	229	639	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	78.1781	211	639	95	below_threshold
Alistipes communis	strain=5CBH24	GCA_006542665.1	2585118	2585118	type	True	77.9651	194	639	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_025144995.1	626932	626932	type	True	76.1002	57	639	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 00:38:53,501] [INFO] DFAST Taxonomy check result was written to GCA_015059965.1_ASM1505996v1_genomic.fna/tc_result.tsv
[2023-06-29 00:38:53,502] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:38:53,502] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:38:53,502] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21fab109-c3c1-4e1d-ac96-58b665ba6e6b/dqc_reference/checkm_data
[2023-06-29 00:38:53,503] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:38:53,530] [INFO] Task started: CheckM
[2023-06-29 00:38:53,530] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015059965.1_ASM1505996v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015059965.1_ASM1505996v1_genomic.fna/checkm_input GCA_015059965.1_ASM1505996v1_genomic.fna/checkm_result
[2023-06-29 00:39:28,299] [INFO] Task succeeded: CheckM
[2023-06-29 00:39:28,301] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:39:28,322] [INFO] ===== Completeness check finished =====
[2023-06-29 00:39:28,322] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:39:28,323] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015059965.1_ASM1505996v1_genomic.fna/markers.fasta)
[2023-06-29 00:39:28,323] [INFO] Task started: Blastn
[2023-06-29 00:39:28,323] [INFO] Running command: blastn -query GCA_015059965.1_ASM1505996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21fab109-c3c1-4e1d-ac96-58b665ba6e6b/dqc_reference/reference_markers_gtdb.fasta -out GCA_015059965.1_ASM1505996v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:39:29,378] [INFO] Task succeeded: Blastn
[2023-06-29 00:39:29,382] [INFO] Selected 16 target genomes.
[2023-06-29 00:39:29,382] [INFO] Target genome list was writen to GCA_015059965.1_ASM1505996v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:39:29,424] [INFO] Task started: fastANI
[2023-06-29 00:39:29,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg09193b98-6834-4b6b-b558-0647fae09035/GCA_015059965.1_ASM1505996v1_genomic.fna.gz --refList GCA_015059965.1_ASM1505996v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015059965.1_ASM1505996v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:39:36,192] [INFO] Task succeeded: fastANI
[2023-06-29 00:39:36,208] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 00:39:36,208] [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_015059965.1	s__Alistipes sp015059965	100.0	639	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_904502075.1	s__Alistipes sp904502075	84.3339	367	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	100.00	100.00	0.98	0.98	2	-
GCA_910577475.1	s__Alistipes sp910577475	79.8486	327	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017624955.1	s__Alistipes sp017624955	79.7192	266	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.00	96.91	0.90	0.90	6	-
GCA_015060045.1	s__Alistipes sp015060045	79.4678	238	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017547175.1	s__Alistipes sp017547175	79.0748	204	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902362705.1	s__Alistipes sp002358415	78.9715	269	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.62	98.83	0.97	0.92	7	-
GCA_017555105.1	s__Alistipes sp017555105	78.9653	235	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017437045.1	s__Alistipes sp017437045	78.8581	220	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.45	97.23	0.95	0.91	4	-
GCA_019115605.1	s__Alistipes faecigallinarum	78.8568	241	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544265.1	s__Alistipes merdavium	78.8547	279	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.60	98.07	0.91	0.88	5	-
GCA_900542505.1	s__Alistipes stercorigallinarum	78.7195	230	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.83	98.70	0.90	0.85	3	-
GCF_000374505.1	s__Alistipes onderdonkii	78.5413	206	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.63	96.86	0.89	0.82	44	-
GCA_019119615.1	s__Alistipes stercoravium	78.4798	241	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.09	99.09	0.91	0.91	2	-
GCA_014796635.1	s__Alistipes sp014796635	78.3805	116	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017936685.1	s__Alistipes sp017936685	77.841	143	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 00:39:36,210] [INFO] GTDB search result was written to GCA_015059965.1_ASM1505996v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:39:36,211] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:39:36,216] [INFO] DFAST_QC result json was written to GCA_015059965.1_ASM1505996v1_genomic.fna/dqc_result.json
[2023-06-29 00:39:36,216] [INFO] DFAST_QC completed!
[2023-06-29 00:39:36,216] [INFO] Total running time: 0h1m5s