[2024-01-24 14:22:58,551] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:58,557] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:58,558] [INFO] DQC Reference Directory: /var/lib/cwl/stg18c22c6b-1cce-42e3-ba47-cbe46d5a057b/dqc_reference
[2024-01-24 14:23:01,559] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:01,560] [INFO] Task started: Prodigal
[2024-01-24 14:23:01,560] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9bd1b85-0fe7-41cd-921f-ffc9acc6c544/GCF_002108495.1_ASM210849v1_genomic.fna.gz | prodigal -d GCF_002108495.1_ASM210849v1_genomic.fna/cds.fna -a GCF_002108495.1_ASM210849v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:09,613] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:09,614] [INFO] Task started: HMMsearch
[2024-01-24 14:23:09,614] [INFO] Running command: hmmsearch --tblout GCF_002108495.1_ASM210849v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18c22c6b-1cce-42e3-ba47-cbe46d5a057b/dqc_reference/reference_markers.hmm GCF_002108495.1_ASM210849v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:09,974] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:09,975] [INFO] Found 6/6 markers.
[2024-01-24 14:23:10,008] [INFO] Query marker FASTA was written to GCF_002108495.1_ASM210849v1_genomic.fna/markers.fasta
[2024-01-24 14:23:10,008] [INFO] Task started: Blastn
[2024-01-24 14:23:10,009] [INFO] Running command: blastn -query GCF_002108495.1_ASM210849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18c22c6b-1cce-42e3-ba47-cbe46d5a057b/dqc_reference/reference_markers.fasta -out GCF_002108495.1_ASM210849v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:12,678] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:12,682] [INFO] Selected 16 target genomes.
[2024-01-24 14:23:12,683] [INFO] Target genome list was writen to GCF_002108495.1_ASM210849v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:12,725] [INFO] Task started: fastANI
[2024-01-24 14:23:12,725] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9bd1b85-0fe7-41cd-921f-ffc9acc6c544/GCF_002108495.1_ASM210849v1_genomic.fna.gz --refList GCF_002108495.1_ASM210849v1_genomic.fna/target_genomes.txt --output GCF_002108495.1_ASM210849v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:24,262] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:24,263] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18c22c6b-1cce-42e3-ba47-cbe46d5a057b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:24,263] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18c22c6b-1cce-42e3-ba47-cbe46d5a057b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:24,343] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:23:24,344] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:24,344] [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=ATCC 14687	GCA_002108495.1	493	493	type	True	100.0	789	793	95	conclusive
Neisseria canis	strain=NCTC10296	GCA_900636765.1	493	493	type	True	99.9832	792	793	95	conclusive
Neisseria wadsworthii	strain=9715	GCA_000227765.1	607711	607711	type	True	90.1433	646	793	95	below_threshold
Neisseria dumasiana	strain=93087	GCA_002108505.1	1931275	1931275	type	True	84.3314	349	793	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	84.3154	372	793	95	below_threshold
Neisseria animaloris	strain=DSM 21642	GCA_002108605.1	326522	326522	type	True	83.1428	318	793	95	below_threshold
Neisseria dentiae	strain=DSM 19151	GCA_014055005.1	194197	194197	type	True	79.8924	349	793	95	below_threshold
Neisseria dentiae	strain=DSM 19151	GCA_002108595.1	194197	194197	type	True	79.854	347	793	95	below_threshold
Uruburuella suis	strain=1258/02	GCA_022870845.1	252130	252130	type	True	79.3486	343	793	95	below_threshold
Uruburuella suis	strain=DSM 17474	GCA_004341385.1	252130	252130	type	True	79.2974	332	793	95	below_threshold
Bergeriella denitrificans	strain=NBRC 102155	GCA_001592185.1	494	494	type	True	79.0639	228	793	95	below_threshold
Bergeriella denitrificans	strain=NCTC10295	GCA_900453875.1	494	494	type	True	79.0341	281	793	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	78.8156	350	793	95	below_threshold
Neisseria elongata	strain=NCTC10660	GCA_900453895.1	495	495	type	True	78.7584	262	793	95	below_threshold
Neisseria elongata subsp. elongata	strain=ATCC 25295	GCA_900113545.1	214482	495	type	True	78.702	261	793	95	below_threshold
Neisseria meningitidis	strain=PartJ-Nmeningitidis-RM8376	GCA_022869645.1	487	487	type	True	78.2287	242	793	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:24,346] [INFO] DFAST Taxonomy check result was written to GCF_002108495.1_ASM210849v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:24,347] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:24,347] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:24,347] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18c22c6b-1cce-42e3-ba47-cbe46d5a057b/dqc_reference/checkm_data
[2024-01-24 14:23:24,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:24,392] [INFO] Task started: CheckM
[2024-01-24 14:23:24,393] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002108495.1_ASM210849v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002108495.1_ASM210849v1_genomic.fna/checkm_input GCF_002108495.1_ASM210849v1_genomic.fna/checkm_result
[2024-01-24 14:23:59,037] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:59,040] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.10%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:59,061] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:59,062] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:59,063] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002108495.1_ASM210849v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:59,063] [INFO] Task started: Blastn
[2024-01-24 14:23:59,063] [INFO] Running command: blastn -query GCF_002108495.1_ASM210849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18c22c6b-1cce-42e3-ba47-cbe46d5a057b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002108495.1_ASM210849v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:02,300] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:02,307] [INFO] Selected 14 target genomes.
[2024-01-24 14:24:02,308] [INFO] Target genome list was writen to GCF_002108495.1_ASM210849v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:02,321] [INFO] Task started: fastANI
[2024-01-24 14:24:02,321] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9bd1b85-0fe7-41cd-921f-ffc9acc6c544/GCF_002108495.1_ASM210849v1_genomic.fna.gz --refList GCF_002108495.1_ASM210849v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002108495.1_ASM210849v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:12,856] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:12,931] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:12,931] [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	99.9832	792	793	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	90.112	648	793	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	87.4696	656	793	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	84.2448	352	793	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	83.8266	381	793	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	83.2185	322	793	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	79.9215	346	793	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	79.752	324	793	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	79.2539	334	793	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	79.0738	227	793	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900113545.1	s__Neisseria elongata	78.7392	258	793	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	96.68	96.06	0.91	0.86	20	-
GCF_005886145.1	s__Neisseria sp000090875	78.7308	268	793	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.69	97.41	0.97	0.94	3	-
GCF_008807015.1	s__Neisseria zalophi	78.4783	233	793	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013267835.1	s__Neisseria sp000186165	78.4094	246	793	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0019	96.64	96.07	0.93	0.88	22	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:12,933] [INFO] GTDB search result was written to GCF_002108495.1_ASM210849v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:12,934] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:12,942] [INFO] DFAST_QC result json was written to GCF_002108495.1_ASM210849v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:12,942] [INFO] DFAST_QC completed!
[2024-01-24 14:24:12,942] [INFO] Total running time: 0h1m14s