[2024-01-25 20:23:05,700] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:23:05,702] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:23:05,702] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f5938de-7177-4fcf-8035-38c68639b319/dqc_reference
[2024-01-25 20:23:06,855] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:23:06,855] [INFO] Task started: Prodigal
[2024-01-25 20:23:06,856] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f75ec6f-18ec-48ee-9346-9a548a6cb26f/GCF_003795365.1_ASM379536v1_genomic.fna.gz | prodigal -d GCF_003795365.1_ASM379536v1_genomic.fna/cds.fna -a GCF_003795365.1_ASM379536v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:23:12,873] [INFO] Task succeeded: Prodigal
[2024-01-25 20:23:12,873] [INFO] Task started: HMMsearch
[2024-01-25 20:23:12,873] [INFO] Running command: hmmsearch --tblout GCF_003795365.1_ASM379536v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f5938de-7177-4fcf-8035-38c68639b319/dqc_reference/reference_markers.hmm GCF_003795365.1_ASM379536v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:23:13,123] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:23:13,124] [INFO] Found 6/6 markers.
[2024-01-25 20:23:13,143] [INFO] Query marker FASTA was written to GCF_003795365.1_ASM379536v1_genomic.fna/markers.fasta
[2024-01-25 20:23:13,144] [INFO] Task started: Blastn
[2024-01-25 20:23:13,144] [INFO] Running command: blastn -query GCF_003795365.1_ASM379536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f5938de-7177-4fcf-8035-38c68639b319/dqc_reference/reference_markers.fasta -out GCF_003795365.1_ASM379536v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:13,825] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:13,828] [INFO] Selected 10 target genomes.
[2024-01-25 20:23:13,828] [INFO] Target genome list was writen to GCF_003795365.1_ASM379536v1_genomic.fna/target_genomes.txt
[2024-01-25 20:23:13,833] [INFO] Task started: fastANI
[2024-01-25 20:23:13,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f75ec6f-18ec-48ee-9346-9a548a6cb26f/GCF_003795365.1_ASM379536v1_genomic.fna.gz --refList GCF_003795365.1_ASM379536v1_genomic.fna/target_genomes.txt --output GCF_003795365.1_ASM379536v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:23:21,749] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:21,749] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f5938de-7177-4fcf-8035-38c68639b319/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:23:21,749] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f5938de-7177-4fcf-8035-38c68639b319/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:23:21,758] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:23:21,759] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:23:21,759] [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 animalis	strain=DSM 23392	GCA_003795365.1	492	492	type	True	100.0	706	707	95	conclusive
Neisseria animalis	strain=ATCC 49930	GCA_008806995.1	492	492	type	True	99.9977	706	707	95	conclusive
Neisseria animalis	strain=NCTC10212	GCA_900636515.1	492	492	type	True	99.9937	706	707	95	conclusive
Bergeriella denitrificans	strain=NBRC 102155	GCA_001592185.1	494	494	type	True	84.6379	427	707	95	below_threshold
Bergeriella denitrificans	strain=NCTC10295	GCA_900453875.1	494	494	type	True	84.5569	560	707	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_000813705.1	1056807	1056807	type	True	80.3979	348	707	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_022749515.1	1056807	1056807	type	True	80.3704	361	707	95	below_threshold
Neisseria cinerea	strain=CCUG 2156	GCA_021025975.1	483	483	type	True	79.8094	304	707	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	79.2333	316	707	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	78.8316	331	707	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:23:21,760] [INFO] DFAST Taxonomy check result was written to GCF_003795365.1_ASM379536v1_genomic.fna/tc_result.tsv
[2024-01-25 20:23:21,761] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:23:21,761] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:23:21,761] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f5938de-7177-4fcf-8035-38c68639b319/dqc_reference/checkm_data
[2024-01-25 20:23:21,762] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:23:21,787] [INFO] Task started: CheckM
[2024-01-25 20:23:21,787] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003795365.1_ASM379536v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003795365.1_ASM379536v1_genomic.fna/checkm_input GCF_003795365.1_ASM379536v1_genomic.fna/checkm_result
[2024-01-25 20:23:43,945] [INFO] Task succeeded: CheckM
[2024-01-25 20:23:43,946] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:23:43,961] [INFO] ===== Completeness check finished =====
[2024-01-25 20:23:43,961] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:23:43,961] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003795365.1_ASM379536v1_genomic.fna/markers.fasta)
[2024-01-25 20:23:43,962] [INFO] Task started: Blastn
[2024-01-25 20:23:43,962] [INFO] Running command: blastn -query GCF_003795365.1_ASM379536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f5938de-7177-4fcf-8035-38c68639b319/dqc_reference/reference_markers_gtdb.fasta -out GCF_003795365.1_ASM379536v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:45,003] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:45,005] [INFO] Selected 19 target genomes.
[2024-01-25 20:23:45,006] [INFO] Target genome list was writen to GCF_003795365.1_ASM379536v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:23:45,026] [INFO] Task started: fastANI
[2024-01-25 20:23:45,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f75ec6f-18ec-48ee-9346-9a548a6cb26f/GCF_003795365.1_ASM379536v1_genomic.fna.gz --refList GCF_003795365.1_ASM379536v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003795365.1_ASM379536v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:24:07,335] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:07,347] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:24:07,347] [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_900636515.1	s__Neisseria animalis	99.9937	706	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	99.99	0.99	0.99	3	conclusive
GCF_001592185.1	s__Neisseria denitrificans	84.6892	424	707	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	80.4759	410	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.73	99.73	0.96	0.96	2	-
GCA_001067655.1	s__Neisseria lactamica_B	80.3939	330	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.406	N/A	N/A	N/A	N/A	1	-
GCF_000260655.1	s__Neisseria sicca_B	80.2983	350	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5569	97.07	96.76	0.92	0.90	3	-
GCF_014054945.1	s__Neisseria sicca	80.2935	381	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5569	99.97	99.97	1.00	1.00	2	-
GCA_003028315.1	s__Neisseria mucosa	80.2929	369	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5429	96.97	96.70	0.92	0.90	9	-
GCF_001815675.1	s__Neisseria sp001815675	80.2031	370	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.4201	97.29	97.29	0.90	0.90	2	-
GCF_001809325.1	s__Neisseria sp001809325	80.1962	363	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.406	N/A	N/A	N/A	N/A	1	-
GCF_000227275.1	s__Neisseria sp000227275	80.1711	371	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.3387	97.52	96.71	0.95	0.93	3	-
GCF_005886145.1	s__Neisseria sp000090875	80.1177	372	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.69	97.41	0.97	0.94	3	-
GCF_009671065.1	s__Neisseria brasiliensis	79.9855	414	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.38	99.05	0.95	0.90	4	-
GCF_013267835.1	s__Neisseria sp000186165	79.8781	359	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0019	96.64	96.07	0.93	0.88	22	-
GCF_014055005.1	s__Neisseria dentiae	79.6413	338	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.99	99.98	1.00	1.00	3	-
GCF_900187305.1	s__Neisseria zoodegmatis	79.3581	319	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.30	96.60	0.95	0.90	3	-
GCF_002237445.1	s__Neisseria sp002237445	79.28	278	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.69	99.69	0.98	0.98	2	-
GCF_014055025.1	s__Neisseria bacilliformis	79.2724	272	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.33	96.96	0.94	0.89	4	-
GCF_900637855.1	s__Neisseria animaloris	79.2609	297	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.11	0.97	0.94	5	-
GCF_002108505.1	s__Neisseria dumasiana	79.2503	311	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.54	97.26	0.91	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-25 20:24:07,349] [INFO] GTDB search result was written to GCF_003795365.1_ASM379536v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:24:07,349] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:24:07,352] [INFO] DFAST_QC result json was written to GCF_003795365.1_ASM379536v1_genomic.fna/dqc_result.json
[2024-01-25 20:24:07,352] [INFO] DFAST_QC completed!
[2024-01-25 20:24:07,352] [INFO] Total running time: 0h1m2s