[2024-01-25 18:47:35,670] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:47:35,671] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:47:35,671] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e5f14bb-3c79-4620-8f99-fa6dec146913/dqc_reference
[2024-01-25 18:47:36,794] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:47:36,795] [INFO] Task started: Prodigal
[2024-01-25 18:47:36,795] [INFO] Running command: gunzip -c /var/lib/cwl/stg56f22b6c-d92c-428f-81c9-2c112da6fcf3/GCF_900636765.1_44503_A02_genomic.fna.gz | prodigal -d GCF_900636765.1_44503_A02_genomic.fna/cds.fna -a GCF_900636765.1_44503_A02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:47:43,563] [INFO] Task succeeded: Prodigal
[2024-01-25 18:47:43,563] [INFO] Task started: HMMsearch
[2024-01-25 18:47:43,563] [INFO] Running command: hmmsearch --tblout GCF_900636765.1_44503_A02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e5f14bb-3c79-4620-8f99-fa6dec146913/dqc_reference/reference_markers.hmm GCF_900636765.1_44503_A02_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:47:43,779] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:47:43,780] [INFO] Found 6/6 markers.
[2024-01-25 18:47:43,803] [INFO] Query marker FASTA was written to GCF_900636765.1_44503_A02_genomic.fna/markers.fasta
[2024-01-25 18:47:43,803] [INFO] Task started: Blastn
[2024-01-25 18:47:43,803] [INFO] Running command: blastn -query GCF_900636765.1_44503_A02_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e5f14bb-3c79-4620-8f99-fa6dec146913/dqc_reference/reference_markers.fasta -out GCF_900636765.1_44503_A02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:44,470] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:44,473] [INFO] Selected 16 target genomes.
[2024-01-25 18:47:44,474] [INFO] Target genome list was writen to GCF_900636765.1_44503_A02_genomic.fna/target_genomes.txt
[2024-01-25 18:47:44,501] [INFO] Task started: fastANI
[2024-01-25 18:47:44,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg56f22b6c-d92c-428f-81c9-2c112da6fcf3/GCF_900636765.1_44503_A02_genomic.fna.gz --refList GCF_900636765.1_44503_A02_genomic.fna/target_genomes.txt --output GCF_900636765.1_44503_A02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:55,504] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:55,504] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e5f14bb-3c79-4620-8f99-fa6dec146913/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:55,505] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e5f14bb-3c79-4620-8f99-fa6dec146913/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:55,515] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:47:55,515] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:47:55,516] [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 canis	strain=NCTC10296	GCA_900636765.1	493	493	type	True	100.0	852	856	95	conclusive
Neisseria canis	strain=ATCC 14687	GCA_002108495.1	493	493	type	True	99.9358	787	856	95	conclusive
Neisseria wadsworthii	strain=9715	GCA_000227765.1	607711	607711	type	True	90.1287	676	856	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	84.5265	379	856	95	below_threshold
Neisseria dumasiana	strain=93087	GCA_002108505.1	1931275	1931275	type	True	84.4171	361	856	95	below_threshold
Neisseria animaloris	strain=DSM 21642	GCA_002108605.1	326522	326522	type	True	83.1774	330	856	95	below_threshold
Neisseria dentiae	strain=DSM 19151	GCA_014055005.1	194197	194197	type	True	80.0962	370	856	95	below_threshold
Neisseria dentiae	strain=DSM 19151	GCA_002108595.1	194197	194197	type	True	79.8337	359	856	95	below_threshold
Uruburuella suis	strain=1258/02	GCA_022870845.1	252130	252130	type	True	79.4604	366	856	95	below_threshold
Uruburuella suis	strain=DSM 17474	GCA_004341385.1	252130	252130	type	True	79.3397	346	856	95	below_threshold
Bergeriella denitrificans	strain=NCTC10295	GCA_900453875.1	494	494	type	True	79.2248	298	856	95	below_threshold
Bergeriella denitrificans	strain=NBRC 102155	GCA_001592185.1	494	494	type	True	79.1258	230	856	95	below_threshold
Neisseria elongata	strain=NCTC10660	GCA_900453895.1	495	495	type	True	79.0625	275	856	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	78.9744	355	856	95	below_threshold
Neisseria elongata subsp. elongata	strain=ATCC 25295	GCA_900113545.1	214482	495	type	True	78.8001	272	856	95	below_threshold
Neisseria meningitidis	strain=PartJ-Nmeningitidis-RM8376	GCA_022869645.1	487	487	type	True	78.7872	242	856	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:55,517] [INFO] DFAST Taxonomy check result was written to GCF_900636765.1_44503_A02_genomic.fna/tc_result.tsv
[2024-01-25 18:47:55,518] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:55,518] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:55,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e5f14bb-3c79-4620-8f99-fa6dec146913/dqc_reference/checkm_data
[2024-01-25 18:47:55,519] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:55,546] [INFO] Task started: CheckM
[2024-01-25 18:47:55,547] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900636765.1_44503_A02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900636765.1_44503_A02_genomic.fna/checkm_input GCF_900636765.1_44503_A02_genomic.fna/checkm_result
[2024-01-25 18:48:19,430] [INFO] Task succeeded: CheckM
[2024-01-25 18:48:19,431] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.10%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:48:19,451] [INFO] ===== Completeness check finished =====
[2024-01-25 18:48:19,451] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:48:19,452] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900636765.1_44503_A02_genomic.fna/markers.fasta)
[2024-01-25 18:48:19,452] [INFO] Task started: Blastn
[2024-01-25 18:48:19,452] [INFO] Running command: blastn -query GCF_900636765.1_44503_A02_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e5f14bb-3c79-4620-8f99-fa6dec146913/dqc_reference/reference_markers_gtdb.fasta -out GCF_900636765.1_44503_A02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:20,606] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:20,609] [INFO] Selected 14 target genomes.
[2024-01-25 18:48:20,609] [INFO] Target genome list was writen to GCF_900636765.1_44503_A02_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:48:20,615] [INFO] Task started: fastANI
[2024-01-25 18:48:20,615] [INFO] Running command: fastANI --query /var/lib/cwl/stg56f22b6c-d92c-428f-81c9-2c112da6fcf3/GCF_900636765.1_44503_A02_genomic.fna.gz --refList GCF_900636765.1_44503_A02_genomic.fna/target_genomes_gtdb.txt --output GCF_900636765.1_44503_A02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:48:29,869] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:29,878] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:48:29,878] [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_900636765.1	s__Neisseria canis	100.0	852	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_000227765.1	s__Neisseria wadsworthii	90.1147	677	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.36	97.06	0.97	0.96	3	-
GCF_001308015.1	s__Neisseria sp001308015	87.4427	672	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002108505.1	s__Neisseria dumasiana	84.3541	363	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.54	97.26	0.91	0.89	4	-
GCF_900187305.1	s__Neisseria zoodegmatis	83.9177	401	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.30	96.60	0.95	0.90	3	-
GCF_900637855.1	s__Neisseria animaloris	83.5168	327	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.11	0.97	0.94	5	-
GCF_014055005.1	s__Neisseria dentiae	80.1036	366	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.99	99.98	1.00	1.00	3	-
GCF_014297595.1	s__Neisseria musculi	79.9165	321	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.59	0.96	0.96	3	-
GCF_004341385.1	s__Neisseria suis	79.3028	348	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.29	97.17	0.93	0.92	3	-
GCF_001592185.1	s__Neisseria denitrificans	79.1088	231	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005886145.1	s__Neisseria sp000090875	78.9312	287	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.69	97.41	0.97	0.94	3	-
GCF_013267835.1	s__Neisseria sp000186165	78.8605	257	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0019	96.64	96.07	0.93	0.88	22	-
GCF_900113545.1	s__Neisseria elongata	78.8111	270	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	96.68	96.06	0.91	0.86	20	-
GCF_008807015.1	s__Neisseria zalophi	78.7369	246	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:48:29,880] [INFO] GTDB search result was written to GCF_900636765.1_44503_A02_genomic.fna/result_gtdb.tsv
[2024-01-25 18:48:29,880] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:48:29,883] [INFO] DFAST_QC result json was written to GCF_900636765.1_44503_A02_genomic.fna/dqc_result.json
[2024-01-25 18:48:29,883] [INFO] DFAST_QC completed!
[2024-01-25 18:48:29,883] [INFO] Total running time: 0h0m54s