[2023-06-28 10:31:02,459] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:31:02,461] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:31:02,462] [INFO] DQC Reference Directory: /var/lib/cwl/stgb813dc08-15b2-42db-b6f0-8d4a1b219c06/dqc_reference
[2023-06-28 10:31:03,675] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:31:03,675] [INFO] Task started: Prodigal
[2023-06-28 10:31:03,676] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc779739-ba61-4f31-ad54-6725672ec8af/GCA_017409425.1_ASM1740942v1_genomic.fna.gz | prodigal -d GCA_017409425.1_ASM1740942v1_genomic.fna/cds.fna -a GCA_017409425.1_ASM1740942v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:31:16,209] [INFO] Task succeeded: Prodigal
[2023-06-28 10:31:16,210] [INFO] Task started: HMMsearch
[2023-06-28 10:31:16,210] [INFO] Running command: hmmsearch --tblout GCA_017409425.1_ASM1740942v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb813dc08-15b2-42db-b6f0-8d4a1b219c06/dqc_reference/reference_markers.hmm GCA_017409425.1_ASM1740942v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:31:16,458] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:31:16,460] [INFO] Found 6/6 markers.
[2023-06-28 10:31:16,486] [INFO] Query marker FASTA was written to GCA_017409425.1_ASM1740942v1_genomic.fna/markers.fasta
[2023-06-28 10:31:16,487] [INFO] Task started: Blastn
[2023-06-28 10:31:16,487] [INFO] Running command: blastn -query GCA_017409425.1_ASM1740942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb813dc08-15b2-42db-b6f0-8d4a1b219c06/dqc_reference/reference_markers.fasta -out GCA_017409425.1_ASM1740942v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:31:17,074] [INFO] Task succeeded: Blastn
[2023-06-28 10:31:17,078] [INFO] Selected 15 target genomes.
[2023-06-28 10:31:17,078] [INFO] Target genome list was writen to GCA_017409425.1_ASM1740942v1_genomic.fna/target_genomes.txt
[2023-06-28 10:31:17,079] [INFO] Task started: fastANI
[2023-06-28 10:31:17,079] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc779739-ba61-4f31-ad54-6725672ec8af/GCA_017409425.1_ASM1740942v1_genomic.fna.gz --refList GCA_017409425.1_ASM1740942v1_genomic.fna/target_genomes.txt --output GCA_017409425.1_ASM1740942v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:31:25,401] [INFO] Task succeeded: fastANI
[2023-06-28 10:31:25,402] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb813dc08-15b2-42db-b6f0-8d4a1b219c06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:31:25,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb813dc08-15b2-42db-b6f0-8d4a1b219c06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:31:25,414] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:31:25,414] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 10:31:25,415] [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 senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	78.9816	258	718	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	78.9317	262	718	95	below_threshold
Alistipes dispar	strain=5CPEGH6	GCA_006542685.1	2585119	2585119	type	True	78.8999	256	718	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	78.8774	269	718	95	below_threshold
Alistipes megaguti	strain=Marseille-P5997	GCA_900604385.1	2364787	2364787	type	True	78.7934	280	718	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	78.787	255	718	95	below_threshold
Alistipes timonensis	strain=DSM 25383	GCA_900107675.1	1465754	1465754	type	True	78.711	258	718	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	78.6604	239	718	95	below_threshold
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	78.6286	272	718	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	78.5813	264	718	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	78.2385	252	718	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_000374505.1	328813	328813	type	True	78.2167	250	718	95	below_threshold
Alistipes onderdonkii subsp. vulgaris	strain=3BBH6	GCA_006542645.1	2585117	328813	type	True	78.1688	244	718	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_025144995.1	626932	626932	type	True	76.3551	55	718	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 10:31:25,417] [INFO] DFAST Taxonomy check result was written to GCA_017409425.1_ASM1740942v1_genomic.fna/tc_result.tsv
[2023-06-28 10:31:25,419] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:31:25,419] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:31:25,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb813dc08-15b2-42db-b6f0-8d4a1b219c06/dqc_reference/checkm_data
[2023-06-28 10:31:25,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:31:25,449] [INFO] Task started: CheckM
[2023-06-28 10:31:25,449] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017409425.1_ASM1740942v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017409425.1_ASM1740942v1_genomic.fna/checkm_input GCA_017409425.1_ASM1740942v1_genomic.fna/checkm_result
[2023-06-28 10:32:04,472] [INFO] Task succeeded: CheckM
[2023-06-28 10:32:04,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 10:32:04,502] [INFO] ===== Completeness check finished =====
[2023-06-28 10:32:04,502] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:32:04,502] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017409425.1_ASM1740942v1_genomic.fna/markers.fasta)
[2023-06-28 10:32:04,503] [INFO] Task started: Blastn
[2023-06-28 10:32:04,503] [INFO] Running command: blastn -query GCA_017409425.1_ASM1740942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb813dc08-15b2-42db-b6f0-8d4a1b219c06/dqc_reference/reference_markers_gtdb.fasta -out GCA_017409425.1_ASM1740942v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:32:05,398] [INFO] Task succeeded: Blastn
[2023-06-28 10:32:05,404] [INFO] Selected 9 target genomes.
[2023-06-28 10:32:05,404] [INFO] Target genome list was writen to GCA_017409425.1_ASM1740942v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:32:05,411] [INFO] Task started: fastANI
[2023-06-28 10:32:05,412] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc779739-ba61-4f31-ad54-6725672ec8af/GCA_017409425.1_ASM1740942v1_genomic.fna.gz --refList GCA_017409425.1_ASM1740942v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017409425.1_ASM1740942v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:32:10,202] [INFO] Task succeeded: fastANI
[2023-06-28 10:32:10,218] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:32:10,218] [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_017624955.1	s__Alistipes sp017624955	96.9535	609	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.00	96.91	0.90	0.90	6	conclusive
GCA_015060045.1	s__Alistipes sp015060045	88.6967	549	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017398045.1	s__Alistipes sp017398045	87.0634	578	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.91	97.91	0.92	0.92	2	-
GCA_017555975.1	s__Alistipes sp017555975	84.7013	400	718	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	83.902	471	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017436185.1	s__Alistipes sp017436185	82.8719	407	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017555105.1	s__Alistipes sp017555105	82.2172	418	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017623115.1	s__Alistipes sp017623115	81.043	391	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.20	98.03	0.95	0.93	4	-
GCA_904502075.1	s__Alistipes sp904502075	79.2899	195	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	100.00	100.00	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-06-28 10:32:10,220] [INFO] GTDB search result was written to GCA_017409425.1_ASM1740942v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:32:10,221] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:32:10,224] [INFO] DFAST_QC result json was written to GCA_017409425.1_ASM1740942v1_genomic.fna/dqc_result.json
[2023-06-28 10:32:10,224] [INFO] DFAST_QC completed!
[2023-06-28 10:32:10,224] [INFO] Total running time: 0h1m8s