[2024-01-25 18:50:20,489] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:50:20,491] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:50:20,491] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e6635e0-d2ee-4b7f-8fd6-cde39e5f90cc/dqc_reference
[2024-01-25 18:50:21,606] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:50:21,607] [INFO] Task started: Prodigal
[2024-01-25 18:50:21,607] [INFO] Running command: gunzip -c /var/lib/cwl/stg34dff4c0-8625-4a19-9f44-9b29da729e7e/GCF_014898075.1_ASM1489807v1_genomic.fna.gz | prodigal -d GCF_014898075.1_ASM1489807v1_genomic.fna/cds.fna -a GCF_014898075.1_ASM1489807v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:50:28,947] [INFO] Task succeeded: Prodigal
[2024-01-25 18:50:28,947] [INFO] Task started: HMMsearch
[2024-01-25 18:50:28,947] [INFO] Running command: hmmsearch --tblout GCF_014898075.1_ASM1489807v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e6635e0-d2ee-4b7f-8fd6-cde39e5f90cc/dqc_reference/reference_markers.hmm GCF_014898075.1_ASM1489807v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:50:29,163] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:50:29,164] [INFO] Found 6/6 markers.
[2024-01-25 18:50:29,186] [INFO] Query marker FASTA was written to GCF_014898075.1_ASM1489807v1_genomic.fna/markers.fasta
[2024-01-25 18:50:29,186] [INFO] Task started: Blastn
[2024-01-25 18:50:29,186] [INFO] Running command: blastn -query GCF_014898075.1_ASM1489807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e6635e0-d2ee-4b7f-8fd6-cde39e5f90cc/dqc_reference/reference_markers.fasta -out GCF_014898075.1_ASM1489807v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:29,901] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:29,904] [INFO] Selected 17 target genomes.
[2024-01-25 18:50:29,904] [INFO] Target genome list was writen to GCF_014898075.1_ASM1489807v1_genomic.fna/target_genomes.txt
[2024-01-25 18:50:29,906] [INFO] Task started: fastANI
[2024-01-25 18:50:29,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg34dff4c0-8625-4a19-9f44-9b29da729e7e/GCF_014898075.1_ASM1489807v1_genomic.fna.gz --refList GCF_014898075.1_ASM1489807v1_genomic.fna/target_genomes.txt --output GCF_014898075.1_ASM1489807v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:50:40,225] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:40,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e6635e0-d2ee-4b7f-8fd6-cde39e5f90cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:50:40,225] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e6635e0-d2ee-4b7f-8fd6-cde39e5f90cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:50:40,236] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:50:40,236] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:50:40,236] [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 iguanae	strain=ATCC 51483	GCA_003013245.1	90242	90242	type	True	85.0917	577	881	95	below_threshold
Bergeriella denitrificans	strain=NBRC 102155	GCA_001592185.1	494	494	type	True	80.3208	358	881	95	below_threshold
Bergeriella denitrificans	strain=NCTC10295	GCA_900453875.1	494	494	type	True	80.3198	465	881	95	below_threshold
Neisseria animalis	strain=NCTC10212	GCA_900636515.1	492	492	type	True	80.2139	416	881	95	below_threshold
Neisseria animalis	strain=ATCC 49930	GCA_008806995.1	492	492	type	True	80.1568	430	881	95	below_threshold
Neisseria flavescens	strain=ATCC 13120	GCA_005221285.1	484	484	type	True	79.98	393	881	95	below_threshold
Neisseria flavescens	strain=NCTC8263	GCA_900453805.1	484	484	type	True	79.8917	405	881	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_022749515.1	1056807	1056807	type	True	79.76	397	881	95	below_threshold
Neisseria sicca	strain=DSM 17713	GCA_014054945.1	490	490	suspected-type	True	79.7501	413	881	95	below_threshold
Neisseria subflava	strain=ATCC 49275	GCA_005221305.1	28449	28449	type	True	79.6928	399	881	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_000813705.1	1056807	1056807	type	True	79.6891	365	881	95	below_threshold
Neisseria sicca	strain=ATCC 29256	GCA_000174655.1	490	490	suspected-type	True	79.5399	402	881	95	below_threshold
Neisseria perflava	strain=CCUG 17915	GCA_023472875.1	33053	33053	suspected-type	True	79.5035	378	881	95	below_threshold
Neisseria meningitidis	strain=PartJ-Nmeningitidis-RM8376	GCA_022869645.1	487	487	type	True	79.2883	347	881	95	below_threshold
Neisseria dentiae	strain=DSM 19151	GCA_002108595.1	194197	194197	type	True	79.0152	386	881	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	78.8909	360	881	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	78.8728	421	881	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:50:40,237] [INFO] DFAST Taxonomy check result was written to GCF_014898075.1_ASM1489807v1_genomic.fna/tc_result.tsv
[2024-01-25 18:50:40,238] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:50:40,238] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:50:40,238] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e6635e0-d2ee-4b7f-8fd6-cde39e5f90cc/dqc_reference/checkm_data
[2024-01-25 18:50:40,239] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:50:40,268] [INFO] Task started: CheckM
[2024-01-25 18:50:40,268] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014898075.1_ASM1489807v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014898075.1_ASM1489807v1_genomic.fna/checkm_input GCF_014898075.1_ASM1489807v1_genomic.fna/checkm_result
[2024-01-25 18:51:05,953] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:05,954] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:06,010] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:06,010] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:06,010] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014898075.1_ASM1489807v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:06,010] [INFO] Task started: Blastn
[2024-01-25 18:51:06,010] [INFO] Running command: blastn -query GCF_014898075.1_ASM1489807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e6635e0-d2ee-4b7f-8fd6-cde39e5f90cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_014898075.1_ASM1489807v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:07,292] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:07,294] [INFO] Selected 12 target genomes.
[2024-01-25 18:51:07,295] [INFO] Target genome list was writen to GCF_014898075.1_ASM1489807v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:07,301] [INFO] Task started: fastANI
[2024-01-25 18:51:07,301] [INFO] Running command: fastANI --query /var/lib/cwl/stg34dff4c0-8625-4a19-9f44-9b29da729e7e/GCF_014898075.1_ASM1489807v1_genomic.fna.gz --refList GCF_014898075.1_ASM1489807v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014898075.1_ASM1489807v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:15,783] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:15,791] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:51:15,791] [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_014898075.1	s__Neisseria sp011038745	100.0	876	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.25	98.87	0.98	0.97	4	conclusive
GCF_009671065.1	s__Neisseria brasiliensis	89.3739	695	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.38	99.05	0.95	0.90	4	-
GCF_002327085.1	s__Neisseria sp002327085	88.5362	648	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.28	99.27	0.86	0.86	3	-
GCF_003013245.1	s__Neisseria iguanae	85.1	577	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592185.1	s__Neisseria denitrificans	80.317	359	881	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	79.7415	461	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.73	99.73	0.96	0.96	2	-
GCF_005221305.1	s__Neisseria subflava	79.6866	397	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.1594	96.50	96.31	0.91	0.87	10	-
GCF_000813705.1	s__Neisseria cerebrosa	79.6462	367	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5429	97.92	97.52	0.91	0.89	5	-
GCF_000952795.1	s__Neisseria sp000952795	79.6041	382	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.4916	98.25	96.69	0.90	0.83	3	-
GCA_001067655.1	s__Neisseria lactamica_B	79.5832	351	881	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	79.5626	369	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5569	97.07	96.76	0.92	0.90	3	-
GCF_001618085.1	s__Neisseria flavescens_C	79.3554	400	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.4709	96.21	96.21	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:51:15,793] [INFO] GTDB search result was written to GCF_014898075.1_ASM1489807v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:15,794] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:15,797] [INFO] DFAST_QC result json was written to GCF_014898075.1_ASM1489807v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:15,797] [INFO] DFAST_QC completed!
[2024-01-25 18:51:15,797] [INFO] Total running time: 0h0m55s