[2024-01-24 13:08:58,492] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:08:58,494] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:08:58,494] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c0db874-960b-4f6e-a04e-bd1a44115f6c/dqc_reference
[2024-01-24 13:08:59,700] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:08:59,700] [INFO] Task started: Prodigal
[2024-01-24 13:08:59,701] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3ae393d-de68-4091-80f6-78c4d9934d4f/GCF_003013245.1_ASM301324v1_genomic.fna.gz | prodigal -d GCF_003013245.1_ASM301324v1_genomic.fna/cds.fna -a GCF_003013245.1_ASM301324v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:06,708] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:06,708] [INFO] Task started: HMMsearch
[2024-01-24 13:09:06,708] [INFO] Running command: hmmsearch --tblout GCF_003013245.1_ASM301324v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c0db874-960b-4f6e-a04e-bd1a44115f6c/dqc_reference/reference_markers.hmm GCF_003013245.1_ASM301324v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:06,981] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:06,982] [INFO] Found 6/6 markers.
[2024-01-24 13:09:07,015] [INFO] Query marker FASTA was written to GCF_003013245.1_ASM301324v1_genomic.fna/markers.fasta
[2024-01-24 13:09:07,015] [INFO] Task started: Blastn
[2024-01-24 13:09:07,015] [INFO] Running command: blastn -query GCF_003013245.1_ASM301324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c0db874-960b-4f6e-a04e-bd1a44115f6c/dqc_reference/reference_markers.fasta -out GCF_003013245.1_ASM301324v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:07,709] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:07,714] [INFO] Selected 26 target genomes.
[2024-01-24 13:09:07,714] [INFO] Target genome list was writen to GCF_003013245.1_ASM301324v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:07,880] [INFO] Task started: fastANI
[2024-01-24 13:09:07,880] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3ae393d-de68-4091-80f6-78c4d9934d4f/GCF_003013245.1_ASM301324v1_genomic.fna.gz --refList GCF_003013245.1_ASM301324v1_genomic.fna/target_genomes.txt --output GCF_003013245.1_ASM301324v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:19,895] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:19,895] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c0db874-960b-4f6e-a04e-bd1a44115f6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:19,896] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c0db874-960b-4f6e-a04e-bd1a44115f6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:19,919] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:09:19,919] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:19,920] [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	100.0	766	775	95	conclusive
Bergeriella denitrificans	strain=NBRC 102155	GCA_001592185.1	494	494	type	True	79.5155	292	775	95	below_threshold
Bergeriella denitrificans	strain=NCTC10295	GCA_900453875.1	494	494	type	True	79.4847	362	775	95	below_threshold
Neisseria animalis	strain=ATCC 49930	GCA_008806995.1	492	492	type	True	79.3258	352	775	95	below_threshold
Neisseria animalis	strain=NCTC10212	GCA_900636515.1	492	492	type	True	79.3248	350	775	95	below_threshold
Neisseria perflava	strain=CCUG 17915	GCA_023472875.1	33053	33053	suspected-type	True	79.1341	328	775	95	below_threshold
Neisseria subflava	strain=ATCC 49275	GCA_005221305.1	28449	28449	type	True	79.0858	330	775	95	below_threshold
Neisseria meningitidis	strain=PartJ-Nmeningitidis-RM8376	GCA_022869645.1	487	487	type	True	79.0456	267	775	95	below_threshold
Neisseria cinerea	strain=FDAARGOS_871	GCA_016028715.1	483	483	type	True	78.9411	252	775	95	below_threshold
Neisseria lactamica	strain=NCTC10617	GCA_901482445.1	486	486	type	True	78.8783	263	775	95	below_threshold
Neisseria flavescens	strain=ATCC 13120	GCA_005221285.1	484	484	type	True	78.8735	342	775	95	below_threshold
Neisseria flavescens	strain=NCTC8263	GCA_900453805.1	484	484	type	True	78.8478	350	775	95	below_threshold
Neisseria cinerea	strain=NCTC10294	GCA_900475315.1	483	483	type	True	78.8255	258	775	95	below_threshold
Neisseria lactamica	strain=ATCC 23970	GCA_000741965.1	486	486	type	True	78.8085	266	775	95	below_threshold
Neisseria gonorrhoeae	strain=DSM 9188	GCA_003315235.1	485	485	type	True	78.7323	254	775	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	78.5889	283	775	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	78.5522	300	775	95	below_threshold
Neisseria weaveri	strain=NCTC12742	GCA_900638685.1	28091	28091	type	True	78.5516	248	775	95	below_threshold
Neisseria weaveri	strain=LMG 5135	GCA_000224255.2	28091	28091	type	True	78.4718	245	775	95	below_threshold
Uruburuella suis	strain=DSM 17474	GCA_004341385.1	252130	252130	type	True	78.3278	292	775	95	below_threshold
Neisseria elongata subsp. glycolytica	strain=NCTC11050	GCA_900475815.1	88719	495	type	True	78.3161	236	775	95	below_threshold
Uruburuella suis	strain=1258/02	GCA_022870845.1	252130	252130	type	True	78.3029	289	775	95	below_threshold
Neisseria elongata subsp. glycolytica	strain=ATCC 29315	GCA_000818035.1	88719	495	type	True	78.2797	240	775	95	below_threshold
Neisseria elongata	strain=NCTC10660	GCA_900453895.1	495	495	type	True	78.2462	237	775	95	below_threshold
Neisseria elongata subsp. elongata	strain=ATCC 25295	GCA_900113545.1	214482	495	type	True	78.1117	242	775	95	below_threshold
Neisseria arctica	strain=KH1503	GCA_022870905.1	1470200	1470200	type	True	77.7477	161	775	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:19,921] [INFO] DFAST Taxonomy check result was written to GCF_003013245.1_ASM301324v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:19,922] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:19,922] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:19,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c0db874-960b-4f6e-a04e-bd1a44115f6c/dqc_reference/checkm_data
[2024-01-24 13:09:19,923] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:19,951] [INFO] Task started: CheckM
[2024-01-24 13:09:19,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003013245.1_ASM301324v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003013245.1_ASM301324v1_genomic.fna/checkm_input GCF_003013245.1_ASM301324v1_genomic.fna/checkm_result
[2024-01-24 13:09:46,391] [INFO] Task succeeded: CheckM
[2024-01-24 13:09:46,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:09:46,414] [INFO] ===== Completeness check finished =====
[2024-01-24 13:09:46,414] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:09:46,414] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003013245.1_ASM301324v1_genomic.fna/markers.fasta)
[2024-01-24 13:09:46,415] [INFO] Task started: Blastn
[2024-01-24 13:09:46,415] [INFO] Running command: blastn -query GCF_003013245.1_ASM301324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c0db874-960b-4f6e-a04e-bd1a44115f6c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003013245.1_ASM301324v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:47,623] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:47,626] [INFO] Selected 12 target genomes.
[2024-01-24 13:09:47,626] [INFO] Target genome list was writen to GCF_003013245.1_ASM301324v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:09:47,666] [INFO] Task started: fastANI
[2024-01-24 13:09:47,666] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3ae393d-de68-4091-80f6-78c4d9934d4f/GCF_003013245.1_ASM301324v1_genomic.fna.gz --refList GCF_003013245.1_ASM301324v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003013245.1_ASM301324v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:09:54,830] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:54,847] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:09:54,847] [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_003013245.1	s__Neisseria iguanae	100.0	766	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009671065.1	s__Neisseria brasiliensis	85.2472	577	775	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	84.9266	580	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.25	98.87	0.98	0.97	4	-
GCF_002327085.1	s__Neisseria sp002327085	84.626	541	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.28	99.27	0.86	0.86	3	-
GCF_001592185.1	s__Neisseria denitrificans	79.5461	291	775	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	79.2277	343	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0019	96.64	96.07	0.93	0.88	22	-
GCF_900654165.1	s__Neisseria subflava_C	79.1052	318	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.6726	97.16	95.72	0.94	0.90	27	-
GCF_000227275.1	s__Neisseria sp000227275	79.0878	374	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.3387	97.52	96.71	0.95	0.93	3	-
GCF_002216145.1	s__Neisseria chenwenguii	79.0365	392	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.73	99.73	0.96	0.96	2	-
GCF_001618085.1	s__Neisseria flavescens_C	79.0336	353	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.4709	96.21	96.21	0.92	0.92	2	-
GCF_005886145.1	s__Neisseria sp000090875	78.9473	360	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.69	97.41	0.97	0.94	3	-
GCF_900638685.1	s__Neisseria weaveri	78.6549	241	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.19	98.86	0.98	0.97	8	-
--------------------------------------------------------------------------------
[2024-01-24 13:09:54,849] [INFO] GTDB search result was written to GCF_003013245.1_ASM301324v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:09:54,849] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:09:54,853] [INFO] DFAST_QC result json was written to GCF_003013245.1_ASM301324v1_genomic.fna/dqc_result.json
[2024-01-24 13:09:54,854] [INFO] DFAST_QC completed!
[2024-01-24 13:09:54,854] [INFO] Total running time: 0h0m56s