[2024-01-24 14:21:50,785] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:50,787] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:50,787] [INFO] DQC Reference Directory: /var/lib/cwl/stg007f79cc-4c70-4064-b8f3-dfe3c611d683/dqc_reference
[2024-01-24 14:21:52,219] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:52,220] [INFO] Task started: Prodigal
[2024-01-24 14:21:52,220] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf4eb41a-0e79-4d58-bf26-844978feaa6d/GCF_014055005.1_ASM1405500v1_genomic.fna.gz | prodigal -d GCF_014055005.1_ASM1405500v1_genomic.fna/cds.fna -a GCF_014055005.1_ASM1405500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:02,083] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:02,084] [INFO] Task started: HMMsearch
[2024-01-24 14:22:02,084] [INFO] Running command: hmmsearch --tblout GCF_014055005.1_ASM1405500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg007f79cc-4c70-4064-b8f3-dfe3c611d683/dqc_reference/reference_markers.hmm GCF_014055005.1_ASM1405500v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:02,375] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:02,376] [INFO] Found 6/6 markers.
[2024-01-24 14:22:02,403] [INFO] Query marker FASTA was written to GCF_014055005.1_ASM1405500v1_genomic.fna/markers.fasta
[2024-01-24 14:22:02,404] [INFO] Task started: Blastn
[2024-01-24 14:22:02,404] [INFO] Running command: blastn -query GCF_014055005.1_ASM1405500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg007f79cc-4c70-4064-b8f3-dfe3c611d683/dqc_reference/reference_markers.fasta -out GCF_014055005.1_ASM1405500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:03,268] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:03,271] [INFO] Selected 13 target genomes.
[2024-01-24 14:22:03,272] [INFO] Target genome list was writen to GCF_014055005.1_ASM1405500v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:03,281] [INFO] Task started: fastANI
[2024-01-24 14:22:03,281] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf4eb41a-0e79-4d58-bf26-844978feaa6d/GCF_014055005.1_ASM1405500v1_genomic.fna.gz --refList GCF_014055005.1_ASM1405500v1_genomic.fna/target_genomes.txt --output GCF_014055005.1_ASM1405500v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:24,250] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:24,251] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg007f79cc-4c70-4064-b8f3-dfe3c611d683/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:24,251] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg007f79cc-4c70-4064-b8f3-dfe3c611d683/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:24,265] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:22:24,265] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:24,265] [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 dentiae	strain=DSM 19151	GCA_014055005.1	194197	194197	type	True	100.0	916	918	95	conclusive
Neisseria dentiae	strain=NCTC13012	GCA_900453685.1	194197	194197	type	True	99.9998	915	918	95	conclusive
Neisseria dentiae	strain=DSM 19151	GCA_002108595.1	194197	194197	type	True	99.9262	851	918	95	conclusive
Neisseria dumasiana	strain=93087	GCA_002108505.1	1931275	1931275	type	True	82.0066	516	918	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	81.9953	535	918	95	below_threshold
Uruburuella suis	strain=1258/02	GCA_022870845.1	252130	252130	type	True	81.0067	529	918	95	below_threshold
Uruburuella suis	strain=DSM 17474	GCA_004341385.1	252130	252130	type	True	80.8862	508	918	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	80.8171	526	918	95	below_threshold
Kingella potus	strain=NCTC13336	GCA_900451175.1	265175	265175	type	True	80.2166	412	918	95	below_threshold
Kingella potus	strain=3/SID/1128	GCA_022870985.1	265175	265175	type	True	80.1233	411	918	95	below_threshold
Neisseria animalis	strain=ATCC 49930	GCA_008806995.1	492	492	type	True	80.0785	353	918	95	below_threshold
Neisseria animalis	strain=NCTC10212	GCA_900636515.1	492	492	type	True	79.985	352	918	95	below_threshold
Neisseria zalophi	strain=ATCC BAA-2455	GCA_008807015.1	640030	640030	type	True	78.7681	348	918	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:24,267] [INFO] DFAST Taxonomy check result was written to GCF_014055005.1_ASM1405500v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:24,268] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:24,268] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:24,269] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg007f79cc-4c70-4064-b8f3-dfe3c611d683/dqc_reference/checkm_data
[2024-01-24 14:22:24,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:24,304] [INFO] Task started: CheckM
[2024-01-24 14:22:24,305] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014055005.1_ASM1405500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014055005.1_ASM1405500v1_genomic.fna/checkm_input GCF_014055005.1_ASM1405500v1_genomic.fna/checkm_result
[2024-01-24 14:22:55,089] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:55,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:55,109] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:55,109] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:55,110] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014055005.1_ASM1405500v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:55,110] [INFO] Task started: Blastn
[2024-01-24 14:22:55,110] [INFO] Running command: blastn -query GCF_014055005.1_ASM1405500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg007f79cc-4c70-4064-b8f3-dfe3c611d683/dqc_reference/reference_markers_gtdb.fasta -out GCF_014055005.1_ASM1405500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:56,604] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:56,608] [INFO] Selected 14 target genomes.
[2024-01-24 14:22:56,608] [INFO] Target genome list was writen to GCF_014055005.1_ASM1405500v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:56,618] [INFO] Task started: fastANI
[2024-01-24 14:22:56,619] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf4eb41a-0e79-4d58-bf26-844978feaa6d/GCF_014055005.1_ASM1405500v1_genomic.fna.gz --refList GCF_014055005.1_ASM1405500v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014055005.1_ASM1405500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:10,468] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:10,489] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:10,490] [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_014055005.1	s__Neisseria dentiae	100.0	915	918	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.99	99.98	1.00	1.00	3	conclusive
GCF_014297595.1	s__Neisseria musculi	86.8403	654	918	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.59	0.96	0.96	3	-
GCF_900187305.1	s__Neisseria zoodegmatis	82.1732	530	918	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	81.9523	519	918	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	81.4465	450	918	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.11	0.97	0.94	5	-
GCF_001592185.1	s__Neisseria denitrificans	80.9063	355	918	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004341385.1	s__Neisseria suis	80.8862	507	918	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.29	97.17	0.93	0.92	3	-
GCF_900638685.1	s__Neisseria weaveri	80.7368	309	918	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.19	98.86	0.98	0.97	8	-
GCF_002216145.1	s__Neisseria chenwenguii	80.5597	475	918	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.73	99.73	0.96	0.96	2	-
GCF_014055025.1	s__Neisseria bacilliformis	80.3282	423	918	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.33	96.96	0.94	0.89	4	-
GCF_005886145.1	s__Neisseria sp000090875	80.2529	435	918	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.69	97.41	0.97	0.94	3	-
GCF_900636515.1	s__Neisseria animalis	80.0356	350	918	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	99.99	0.99	0.99	3	-
GCF_014054945.1	s__Neisseria sicca	79.4501	411	918	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5569	99.97	99.97	1.00	1.00	2	-
GCF_008807015.1	s__Neisseria zalophi	78.975	344	918	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:10,492] [INFO] GTDB search result was written to GCF_014055005.1_ASM1405500v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:10,493] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:10,497] [INFO] DFAST_QC result json was written to GCF_014055005.1_ASM1405500v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:10,497] [INFO] DFAST_QC completed!
[2024-01-24 14:23:10,497] [INFO] Total running time: 0h1m20s