[2024-01-24 13:55:14,212] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:14,215] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:14,215] [INFO] DQC Reference Directory: /var/lib/cwl/stg510f0baa-59af-41dd-9722-9a3c0b8d1d60/dqc_reference
[2024-01-24 13:55:15,540] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:15,541] [INFO] Task started: Prodigal
[2024-01-24 13:55:15,542] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c8997c9-cef7-492c-9e13-b813c8352bde/GCF_963396185.1_CCUG_4007_T_genomic.fna.gz | prodigal -d GCF_963396185.1_CCUG_4007_T_genomic.fna/cds.fna -a GCF_963396185.1_CCUG_4007_T_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:21,934] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:21,934] [INFO] Task started: HMMsearch
[2024-01-24 13:55:21,934] [INFO] Running command: hmmsearch --tblout GCF_963396185.1_CCUG_4007_T_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg510f0baa-59af-41dd-9722-9a3c0b8d1d60/dqc_reference/reference_markers.hmm GCF_963396185.1_CCUG_4007_T_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:22,248] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:22,250] [INFO] Found 6/6 markers.
[2024-01-24 13:55:22,276] [INFO] Query marker FASTA was written to GCF_963396185.1_CCUG_4007_T_genomic.fna/markers.fasta
[2024-01-24 13:55:22,276] [INFO] Task started: Blastn
[2024-01-24 13:55:22,277] [INFO] Running command: blastn -query GCF_963396185.1_CCUG_4007_T_genomic.fna/markers.fasta -db /var/lib/cwl/stg510f0baa-59af-41dd-9722-9a3c0b8d1d60/dqc_reference/reference_markers.fasta -out GCF_963396185.1_CCUG_4007_T_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:23,052] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:23,055] [INFO] Selected 17 target genomes.
[2024-01-24 13:55:23,055] [INFO] Target genome list was writen to GCF_963396185.1_CCUG_4007_T_genomic.fna/target_genomes.txt
[2024-01-24 13:55:23,082] [INFO] Task started: fastANI
[2024-01-24 13:55:23,082] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c8997c9-cef7-492c-9e13-b813c8352bde/GCF_963396185.1_CCUG_4007_T_genomic.fna.gz --refList GCF_963396185.1_CCUG_4007_T_genomic.fna/target_genomes.txt --output GCF_963396185.1_CCUG_4007_T_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:30,939] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:30,940] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg510f0baa-59af-41dd-9722-9a3c0b8d1d60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:30,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg510f0baa-59af-41dd-9722-9a3c0b8d1d60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:30,953] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:55:30,954] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:30,954] [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 weaveri	strain=NCTC12742	GCA_900638685.1	28091	28091	type	True	99.999	716	717	95	conclusive
Neisseria weaveri	strain=LMG 5135	GCA_000224255.2	28091	28091	type	True	99.9744	694	717	95	conclusive
Neisseria zoodegmatis	strain=NCTC12230	GCA_900187305.1	326523	326523	type	True	85.0815	384	717	95	below_threshold
Neisseria zoodegmatis	strain=DSM 21643	GCA_002108575.1	326523	326523	type	True	84.9297	382	717	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	84.4517	376	717	95	below_threshold
Neisseria canis	strain=ATCC 14687	GCA_002108495.1	493	493	type	True	82.7304	290	717	95	below_threshold
Neisseria wadsworthii	strain=9715	GCA_000227765.1	607711	607711	type	True	82.3109	274	717	95	below_threshold
Neisseria dentiae	strain=DSM 19151	GCA_002108595.1	194197	194197	type	True	80.1929	317	717	95	below_threshold
Bergeriella denitrificans	strain=NBRC 102155	GCA_001592185.1	494	494	type	True	79.2362	241	717	95	below_threshold
Bergeriella denitrificans	strain=NCTC10295	GCA_900453875.1	494	494	type	True	79.2185	297	717	95	below_threshold
Neisseria flavescens	strain=NCTC8263	GCA_900453805.1	484	484	type	True	78.8987	265	717	95	below_threshold
Neisseria cinerea	strain=NCTC10294	GCA_900475315.1	483	483	type	True	78.8737	230	717	95	below_threshold
Neisseria flavescens	strain=ATCC 13120	GCA_005221285.1	484	484	type	True	78.8507	268	717	95	below_threshold
Neisseria cinerea	strain=ATCC 14685	GCA_000173895.1	483	483	type	True	78.6408	231	717	95	below_threshold
Neisseria cinerea	strain=CCUG 2156	GCA_021025975.1	483	483	type	True	78.5813	230	717	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:30,956] [INFO] DFAST Taxonomy check result was written to GCF_963396185.1_CCUG_4007_T_genomic.fna/tc_result.tsv
[2024-01-24 13:55:30,956] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:30,957] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:30,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg510f0baa-59af-41dd-9722-9a3c0b8d1d60/dqc_reference/checkm_data
[2024-01-24 13:55:30,958] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:30,983] [INFO] Task started: CheckM
[2024-01-24 13:55:30,983] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_963396185.1_CCUG_4007_T_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_963396185.1_CCUG_4007_T_genomic.fna/checkm_input GCF_963396185.1_CCUG_4007_T_genomic.fna/checkm_result
[2024-01-24 13:55:56,543] [INFO] Task succeeded: CheckM
[2024-01-24 13:55:56,544] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:55:56,564] [INFO] ===== Completeness check finished =====
[2024-01-24 13:55:56,565] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:55:56,565] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_963396185.1_CCUG_4007_T_genomic.fna/markers.fasta)
[2024-01-24 13:55:56,566] [INFO] Task started: Blastn
[2024-01-24 13:55:56,566] [INFO] Running command: blastn -query GCF_963396185.1_CCUG_4007_T_genomic.fna/markers.fasta -db /var/lib/cwl/stg510f0baa-59af-41dd-9722-9a3c0b8d1d60/dqc_reference/reference_markers_gtdb.fasta -out GCF_963396185.1_CCUG_4007_T_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:57,804] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:57,807] [INFO] Selected 22 target genomes.
[2024-01-24 13:55:57,807] [INFO] Target genome list was writen to GCF_963396185.1_CCUG_4007_T_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:55:57,833] [INFO] Task started: fastANI
[2024-01-24 13:55:57,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c8997c9-cef7-492c-9e13-b813c8352bde/GCF_963396185.1_CCUG_4007_T_genomic.fna.gz --refList GCF_963396185.1_CCUG_4007_T_genomic.fna/target_genomes_gtdb.txt --output GCF_963396185.1_CCUG_4007_T_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:09,302] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:09,324] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:09,324] [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_900638685.1	s__Neisseria weaveri	99.999	716	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.19	98.86	0.98	0.97	8	conclusive
GCF_900187305.1	s__Neisseria zoodegmatis	85.0526	385	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.30	96.60	0.95	0.90	3	-
GCF_002108505.1	s__Neisseria dumasiana	84.3977	373	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.54	97.26	0.91	0.89	4	-
GCF_900637855.1	s__Neisseria animaloris	83.7702	367	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.11	0.97	0.94	5	-
GCF_900636765.1	s__Neisseria canis	82.7062	292	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000227765.1	s__Neisseria wadsworthii	82.3184	274	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.36	97.06	0.97	0.96	3	-
GCF_014055005.1	s__Neisseria dentiae	80.0987	327	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.99	99.98	1.00	1.00	3	-
GCF_900636515.1	s__Neisseria animalis	79.3034	272	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	99.99	0.99	0.99	3	-
GCA_003028315.1	s__Neisseria mucosa	79.2577	263	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5429	96.97	96.70	0.92	0.90	9	-
GCF_002216145.1	s__Neisseria chenwenguii	79.2317	281	717	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	79.2066	243	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000227275.1	s__Neisseria sp000227275	79.1031	273	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.3387	97.52	96.71	0.95	0.93	3	-
GCF_017753665.1	s__Neisseria sicca_D	79.0324	272	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.2415	96.44	95.35	0.92	0.88	6	-
GCF_009671065.1	s__Neisseria brasiliensis	78.9281	323	717	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	78.8952	313	717	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	78.8921	271	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.28	99.27	0.86	0.86	3	-
GCF_005221305.1	s__Neisseria subflava	78.8697	265	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.1594	96.50	96.31	0.91	0.87	10	-
GCF_003044565.1	s__Neisseria sicca_A	78.8576	260	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.01	95.27	0.94	0.92	3	-
GCF_005221285.1	s__Neisseria flavescens	78.8561	266	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.29	96.65	0.97	0.93	6	-
GCF_900475315.1	s__Neisseria cinerea	78.8361	232	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.50	96.82	0.94	0.93	8	-
GCF_008807015.1	s__Neisseria zalophi	78.8094	268	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003045025.1	s__Neisseria subflava_A	78.7691	252	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.3115	96.25	95.58	0.94	0.91	14	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:09,326] [INFO] GTDB search result was written to GCF_963396185.1_CCUG_4007_T_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:09,326] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:09,331] [INFO] DFAST_QC result json was written to GCF_963396185.1_CCUG_4007_T_genomic.fna/dqc_result.json
[2024-01-24 13:56:09,331] [INFO] DFAST_QC completed!
[2024-01-24 13:56:09,331] [INFO] Total running time: 0h0m55s