[2024-01-24 12:36:58,536] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:58,538] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:58,538] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c0d1402-df42-41ac-b7ee-705546209fb7/dqc_reference
[2024-01-24 12:36:59,974] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:59,975] [INFO] Task started: Prodigal
[2024-01-24 12:36:59,975] [INFO] Running command: gunzip -c /var/lib/cwl/stg40cf6a59-fcdc-4044-8425-c9ba6f285d96/GCF_022870845.1_ASM2287084v1_genomic.fna.gz | prodigal -d GCF_022870845.1_ASM2287084v1_genomic.fna/cds.fna -a GCF_022870845.1_ASM2287084v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:11,150] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:11,151] [INFO] Task started: HMMsearch
[2024-01-24 12:37:11,151] [INFO] Running command: hmmsearch --tblout GCF_022870845.1_ASM2287084v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c0d1402-df42-41ac-b7ee-705546209fb7/dqc_reference/reference_markers.hmm GCF_022870845.1_ASM2287084v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:11,434] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:11,436] [INFO] Found 6/6 markers.
[2024-01-24 12:37:11,463] [INFO] Query marker FASTA was written to GCF_022870845.1_ASM2287084v1_genomic.fna/markers.fasta
[2024-01-24 12:37:11,464] [INFO] Task started: Blastn
[2024-01-24 12:37:11,464] [INFO] Running command: blastn -query GCF_022870845.1_ASM2287084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c0d1402-df42-41ac-b7ee-705546209fb7/dqc_reference/reference_markers.fasta -out GCF_022870845.1_ASM2287084v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:12,172] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:12,175] [INFO] Selected 11 target genomes.
[2024-01-24 12:37:12,176] [INFO] Target genome list was writen to GCF_022870845.1_ASM2287084v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:12,180] [INFO] Task started: fastANI
[2024-01-24 12:37:12,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg40cf6a59-fcdc-4044-8425-c9ba6f285d96/GCF_022870845.1_ASM2287084v1_genomic.fna.gz --refList GCF_022870845.1_ASM2287084v1_genomic.fna/target_genomes.txt --output GCF_022870845.1_ASM2287084v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:30,515] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:30,516] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c0d1402-df42-41ac-b7ee-705546209fb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:30,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c0d1402-df42-41ac-b7ee-705546209fb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:30,526] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:37:30,526] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:30,527] [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
Uruburuella suis	strain=1258/02	GCA_022870845.1	252130	252130	type	True	100.0	907	909	95	conclusive
Uruburuella suis	strain=DSM 17474	GCA_004341385.1	252130	252130	type	True	99.9204	843	909	95	conclusive
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	82.9609	670	909	95	below_threshold
Neisseria dentiae	strain=DSM 19151	GCA_014055005.1	194197	194197	type	True	80.9971	540	909	95	below_threshold
Neisseria dentiae	strain=NCTC13012	GCA_900453685.1	194197	194197	type	True	80.9917	533	909	95	below_threshold
Neisseria dentiae	strain=DSM 19151	GCA_002108595.1	194197	194197	type	True	80.9295	516	909	95	below_threshold
Neisseria animaloris	strain=DSM 21642	GCA_002108605.1	326522	326522	type	True	79.4758	371	909	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	79.468	427	909	95	below_threshold
Neisseria elongata subsp. glycolytica	strain=ATCC 29315	GCA_000818035.1	88719	495	type	True	78.7241	317	909	95	below_threshold
Neisseria elongata subsp. glycolytica	strain=NCTC11050	GCA_900475815.1	88719	495	type	True	78.698	321	909	95	below_threshold
Neisseria meningitidis	strain=PartJ-Nmeningitidis-RM8376	GCA_022869645.1	487	487	type	True	78.1974	275	909	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:30,528] [INFO] DFAST Taxonomy check result was written to GCF_022870845.1_ASM2287084v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:30,529] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:30,529] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:30,529] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c0d1402-df42-41ac-b7ee-705546209fb7/dqc_reference/checkm_data
[2024-01-24 12:37:30,531] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:30,568] [INFO] Task started: CheckM
[2024-01-24 12:37:30,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022870845.1_ASM2287084v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022870845.1_ASM2287084v1_genomic.fna/checkm_input GCF_022870845.1_ASM2287084v1_genomic.fna/checkm_result
[2024-01-24 12:38:07,672] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:07,674] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:07,697] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:07,698] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:07,698] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022870845.1_ASM2287084v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:07,699] [INFO] Task started: Blastn
[2024-01-24 12:38:07,699] [INFO] Running command: blastn -query GCF_022870845.1_ASM2287084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c0d1402-df42-41ac-b7ee-705546209fb7/dqc_reference/reference_markers_gtdb.fasta -out GCF_022870845.1_ASM2287084v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:08,739] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:08,744] [INFO] Selected 20 target genomes.
[2024-01-24 12:38:08,744] [INFO] Target genome list was writen to GCF_022870845.1_ASM2287084v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:08,772] [INFO] Task started: fastANI
[2024-01-24 12:38:08,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg40cf6a59-fcdc-4044-8425-c9ba6f285d96/GCF_022870845.1_ASM2287084v1_genomic.fna.gz --refList GCF_022870845.1_ASM2287084v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022870845.1_ASM2287084v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:25,566] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:25,594] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:25,595] [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_004341385.1	s__Neisseria suis	99.9204	843	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.29	97.17	0.93	0.92	3	conclusive
GCF_014055005.1	s__Neisseria dentiae	80.9013	547	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.99	99.98	1.00	1.00	3	-
GCA_016894345.1	s__26B sp016894345	80.3377	473	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__26B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297595.1	s__Neisseria musculi	79.8632	477	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.59	0.96	0.96	3	-
GCF_900637855.1	s__Neisseria animaloris	79.6852	380	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.11	0.97	0.94	5	-
GCF_900187305.1	s__Neisseria zoodegmatis	79.6199	454	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.30	96.60	0.95	0.90	3	-
GCF_900636765.1	s__Neisseria canis	79.582	351	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001592185.1	s__Neisseria denitrificans	79.4999	332	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002216145.1	s__Neisseria chenwenguii	79.1399	407	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.73	99.73	0.96	0.96	2	-
GCF_014898075.1	s__Neisseria sp011038745	78.9713	385	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.25	98.87	0.98	0.97	4	-
GCF_002237445.1	s__Neisseria sp002237445	78.8947	357	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.69	99.69	0.98	0.98	2	-
GCF_001308015.1	s__Neisseria sp001308015	78.7316	330	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900636515.1	s__Neisseria animalis	78.6481	340	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	99.99	0.99	0.99	3	-
GCF_005886145.1	s__Neisseria sp000090875	78.5654	369	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.69	97.41	0.97	0.94	3	-
GCF_000227275.1	s__Neisseria sp000227275	78.3081	326	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.3387	97.52	96.71	0.95	0.93	3	-
GCF_001809325.1	s__Neisseria sp001809325	78.2964	291	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.406	N/A	N/A	N/A	N/A	1	-
GCF_017753665.1	s__Neisseria sicca_D	78.2674	311	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.2415	96.44	95.35	0.92	0.88	6	-
GCF_000260655.1	s__Neisseria sicca_B	78.1444	298	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5569	97.07	96.76	0.92	0.90	3	-
GCF_003044565.1	s__Neisseria sicca_A	78.0138	309	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.01	95.27	0.94	0.92	3	-
GCF_005221305.1	s__Neisseria subflava	77.9699	313	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.1594	96.50	96.31	0.91	0.87	10	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:25,596] [INFO] GTDB search result was written to GCF_022870845.1_ASM2287084v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:25,597] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:25,602] [INFO] DFAST_QC result json was written to GCF_022870845.1_ASM2287084v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:25,603] [INFO] DFAST_QC completed!
[2024-01-24 12:38:25,603] [INFO] Total running time: 0h1m27s