[2024-01-24 10:47:22,631] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:22,633] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:22,634] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa04af08-dd4a-4916-9413-5f9523dc46c0/dqc_reference
[2024-01-24 10:47:26,177] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,183] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,183] [INFO] Running command: gunzip -c /var/lib/cwl/stge14de2a0-1122-45bb-a303-45fda2a5f555/GCF_002327085.1_ASM232708v1_genomic.fna.gz | prodigal -d GCF_002327085.1_ASM232708v1_genomic.fna/cds.fna -a GCF_002327085.1_ASM232708v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:34,066] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:34,066] [INFO] Task started: HMMsearch
[2024-01-24 10:47:34,067] [INFO] Running command: hmmsearch --tblout GCF_002327085.1_ASM232708v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa04af08-dd4a-4916-9413-5f9523dc46c0/dqc_reference/reference_markers.hmm GCF_002327085.1_ASM232708v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:34,314] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:34,316] [INFO] Found 6/6 markers.
[2024-01-24 10:47:34,342] [INFO] Query marker FASTA was written to GCF_002327085.1_ASM232708v1_genomic.fna/markers.fasta
[2024-01-24 10:47:34,343] [INFO] Task started: Blastn
[2024-01-24 10:47:34,343] [INFO] Running command: blastn -query GCF_002327085.1_ASM232708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa04af08-dd4a-4916-9413-5f9523dc46c0/dqc_reference/reference_markers.fasta -out GCF_002327085.1_ASM232708v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:35,042] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:35,047] [INFO] Selected 26 target genomes.
[2024-01-24 10:47:35,047] [INFO] Target genome list was writen to GCF_002327085.1_ASM232708v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:35,180] [INFO] Task started: fastANI
[2024-01-24 10:47:35,180] [INFO] Running command: fastANI --query /var/lib/cwl/stge14de2a0-1122-45bb-a303-45fda2a5f555/GCF_002327085.1_ASM232708v1_genomic.fna.gz --refList GCF_002327085.1_ASM232708v1_genomic.fna/target_genomes.txt --output GCF_002327085.1_ASM232708v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:50,207] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:50,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa04af08-dd4a-4916-9413-5f9523dc46c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:50,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa04af08-dd4a-4916-9413-5f9523dc46c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:50,235] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:47:50,235] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:47:50,235] [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
Neisseria iguanae	strain=ATCC 51483	GCA_003013245.1	90242	90242	type	True	84.8582	534	837	95	below_threshold
Neisseria animalis	strain=NCTC10212	GCA_900636515.1	492	492	type	True	80.2368	356	837	95	below_threshold
Neisseria animalis	strain=ATCC 49930	GCA_008806995.1	492	492	type	True	80.0656	373	837	95	below_threshold
Neisseria animalis	strain=DSM 23392	GCA_003795365.1	492	492	type	True	80.0138	353	837	95	below_threshold
Bergeriella denitrificans	strain=NBRC 102155	GCA_001592185.1	494	494	type	True	79.9546	339	837	95	below_threshold
Bergeriella denitrificans	strain=NCTC10295	GCA_900453875.1	494	494	type	True	79.9189	417	837	95	below_threshold
Neisseria flavescens	strain=ATCC 13120	GCA_005221285.1	484	484	type	True	79.8882	352	837	95	below_threshold
Neisseria flavescens	strain=NCTC8263	GCA_900453805.1	484	484	type	True	79.8638	352	837	95	below_threshold
Neisseria sicca	strain=DSM 17713	GCA_014054945.1	490	490	suspected-type	True	79.7024	351	837	95	below_threshold
Neisseria subflava	strain=ATCC 49275	GCA_005221305.1	28449	28449	type	True	79.6094	345	837	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_022749515.1	1056807	1056807	type	True	79.5161	348	837	95	below_threshold
Neisseria dentiae	strain=DSM 19151	GCA_014055005.1	194197	194197	type	True	79.4898	381	837	95	below_threshold
Neisseria sicca	strain=ATCC 29256	GCA_000174655.1	490	490	suspected-type	True	79.4585	347	837	95	below_threshold
Neisseria perflava	strain=CCUG 17915	GCA_023472875.1	33053	33053	suspected-type	True	79.4287	340	837	95	below_threshold
Neisseria dentiae	strain=NCTC13012	GCA_900453685.1	194197	194197	type	True	79.3985	378	837	95	below_threshold
Neisseria meningitidis	strain=PartJ-Nmeningitidis-RM8376	GCA_022869645.1	487	487	type	True	79.3674	300	837	95	below_threshold
Neisseria cinerea	strain=CCUG 2156	GCA_021025975.1	483	483	type	True	79.3517	273	837	95	below_threshold
Neisseria dentiae	strain=DSM 19151	GCA_002108595.1	194197	194197	type	True	79.2195	360	837	95	below_threshold
Neisseria lactamica	strain=NCTC10617	GCA_901482445.1	486	486	type	True	79.1315	314	837	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	79.0254	364	837	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	79.0027	335	837	95	below_threshold
Neisseria lactamica	strain=ATCC 23970	GCA_000173995.1	486	486	type	True	78.9923	286	837	95	below_threshold
Neisseria lactamica	strain=ATCC 23970	GCA_000741965.1	486	486	type	True	78.9911	307	837	95	below_threshold
Neisseria elongata subsp. glycolytica	strain=NCTC11050	GCA_900475815.1	88719	495	type	True	78.8166	261	837	95	below_threshold
Neisseria weaveri	strain=LMG 5135	GCA_000224255.2	28091	28091	type	True	78.7875	273	837	95	below_threshold
Neisseria elongata subsp. glycolytica	strain=ATCC 29315	GCA_000818035.1	88719	495	type	True	78.7663	264	837	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:50,237] [INFO] DFAST Taxonomy check result was written to GCF_002327085.1_ASM232708v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:50,238] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:50,239] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:50,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa04af08-dd4a-4916-9413-5f9523dc46c0/dqc_reference/checkm_data
[2024-01-24 10:47:50,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:50,273] [INFO] Task started: CheckM
[2024-01-24 10:47:50,273] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002327085.1_ASM232708v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002327085.1_ASM232708v1_genomic.fna/checkm_input GCF_002327085.1_ASM232708v1_genomic.fna/checkm_result
[2024-01-24 10:48:18,514] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:18,516] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:18,537] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:18,538] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:18,538] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002327085.1_ASM232708v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:18,539] [INFO] Task started: Blastn
[2024-01-24 10:48:18,539] [INFO] Running command: blastn -query GCF_002327085.1_ASM232708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa04af08-dd4a-4916-9413-5f9523dc46c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_002327085.1_ASM232708v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:19,745] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:19,748] [INFO] Selected 13 target genomes.
[2024-01-24 10:48:19,749] [INFO] Target genome list was writen to GCF_002327085.1_ASM232708v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:19,760] [INFO] Task started: fastANI
[2024-01-24 10:48:19,761] [INFO] Running command: fastANI --query /var/lib/cwl/stge14de2a0-1122-45bb-a303-45fda2a5f555/GCF_002327085.1_ASM232708v1_genomic.fna.gz --refList GCF_002327085.1_ASM232708v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002327085.1_ASM232708v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:28,925] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:28,936] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:28,937] [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_002327085.1	s__Neisseria sp002327085	100.0	833	837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.28	99.27	0.86	0.86	3	conclusive
GCF_009671065.1	s__Neisseria brasiliensis	89.7811	650	837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.38	99.05	0.95	0.90	4	-
GCF_014898075.1	s__Neisseria sp011038745	88.5379	654	837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.25	98.87	0.98	0.97	4	-
GCF_003013245.1	s__Neisseria iguanae	84.8526	535	837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002216145.1	s__Neisseria chenwenguii	80.5921	405	837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.73	99.73	0.96	0.96	2	-
GCF_001592185.1	s__Neisseria denitrificans	79.9977	336	837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013267835.1	s__Neisseria sp000186165	79.7285	364	837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0019	96.64	96.07	0.93	0.88	22	-
GCF_000227275.1	s__Neisseria sp000227275	79.4441	344	837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.3387	97.52	96.71	0.95	0.93	3	-
GCF_014055005.1	s__Neisseria dentiae	79.432	381	837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.99	99.98	1.00	1.00	3	-
GCF_900654165.1	s__Neisseria subflava_C	79.4055	355	837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.6726	97.16	95.72	0.94	0.90	27	-
GCA_000220865.1	s__Neisseria macacae	79.4021	354	837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.509	99.99	99.99	0.98	0.98	2	-
GCF_001618065.1	s__Neisseria flavescens_A	79.2966	355	837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.6469	95.75	95.69	0.92	0.91	4	-
GCF_901482445.1	s__Neisseria lactamica	79.1124	315	837	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.73	97.33	0.93	0.89	36	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:28,938] [INFO] GTDB search result was written to GCF_002327085.1_ASM232708v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:28,939] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:28,948] [INFO] DFAST_QC result json was written to GCF_002327085.1_ASM232708v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:28,948] [INFO] DFAST_QC completed!
[2024-01-24 10:48:28,949] [INFO] Total running time: 0h1m6s