[2024-01-24 15:18:51,880] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:51,883] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:51,883] [INFO] DQC Reference Directory: /var/lib/cwl/stg7cccce98-d43d-4a78-aaa3-67d92fa6a9bf/dqc_reference
[2024-01-24 15:18:54,596] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:54,598] [INFO] Task started: Prodigal
[2024-01-24 15:18:54,598] [INFO] Running command: gunzip -c /var/lib/cwl/stg58dab104-3426-429a-9c09-255ed9e9b14e/GCF_002216145.1_ASM221614v1_genomic.fna.gz | prodigal -d GCF_002216145.1_ASM221614v1_genomic.fna/cds.fna -a GCF_002216145.1_ASM221614v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:02,234] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:02,235] [INFO] Task started: HMMsearch
[2024-01-24 15:19:02,235] [INFO] Running command: hmmsearch --tblout GCF_002216145.1_ASM221614v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7cccce98-d43d-4a78-aaa3-67d92fa6a9bf/dqc_reference/reference_markers.hmm GCF_002216145.1_ASM221614v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:02,475] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:02,476] [INFO] Found 6/6 markers.
[2024-01-24 15:19:02,500] [INFO] Query marker FASTA was written to GCF_002216145.1_ASM221614v1_genomic.fna/markers.fasta
[2024-01-24 15:19:02,500] [INFO] Task started: Blastn
[2024-01-24 15:19:02,500] [INFO] Running command: blastn -query GCF_002216145.1_ASM221614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cccce98-d43d-4a78-aaa3-67d92fa6a9bf/dqc_reference/reference_markers.fasta -out GCF_002216145.1_ASM221614v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:03,418] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:03,421] [INFO] Selected 26 target genomes.
[2024-01-24 15:19:03,421] [INFO] Target genome list was writen to GCF_002216145.1_ASM221614v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:03,459] [INFO] Task started: fastANI
[2024-01-24 15:19:03,459] [INFO] Running command: fastANI --query /var/lib/cwl/stg58dab104-3426-429a-9c09-255ed9e9b14e/GCF_002216145.1_ASM221614v1_genomic.fna.gz --refList GCF_002216145.1_ASM221614v1_genomic.fna/target_genomes.txt --output GCF_002216145.1_ASM221614v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:20,536] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:20,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7cccce98-d43d-4a78-aaa3-67d92fa6a9bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:20,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7cccce98-d43d-4a78-aaa3-67d92fa6a9bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:20,556] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:19:20,556] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:19:20,557] [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
Bergeriella denitrificans	strain=NCTC10295	GCA_900453875.1	494	494	type	True	81.4124	490	832	95	below_threshold
Bergeriella denitrificans	strain=NBRC 102155	GCA_001592185.1	494	494	type	True	81.3912	384	832	95	below_threshold
Neisseria sicca	strain=DSM 17713	GCA_014054945.1	490	490	suspected-type	True	80.6565	479	832	95	below_threshold
Neisseria animalis	strain=NCTC10212	GCA_900636515.1	492	492	type	True	80.5688	430	832	95	below_threshold
Neisseria animalis	strain=ATCC 49930	GCA_008806995.1	492	492	type	True	80.5526	431	832	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_022749515.1	1056807	1056807	type	True	80.5385	475	832	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_000813705.1	1056807	1056807	type	True	80.5107	433	832	95	below_threshold
Neisseria sicca	strain=ATCC 29256	GCA_000174655.1	490	490	suspected-type	True	80.4669	477	832	95	below_threshold
Neisseria meningitidis	strain=PartJ-Nmeningitidis-RM8376	GCA_022869645.1	487	487	type	True	80.4036	374	832	95	below_threshold
Neisseria dentiae	strain=DSM 19151	GCA_002108595.1	194197	194197	type	True	80.3743	460	832	95	below_threshold
Neisseria animalis	strain=DSM 23392	GCA_003795365.1	492	492	type	True	80.3393	419	832	95	below_threshold
Neisseria dentiae	strain=DSM 19151	GCA_014055005.1	194197	194197	type	True	80.331	487	832	95	below_threshold
Neisseria meningitidis	strain=NCTC10025	GCA_900638555.1	487	487	type	True	80.2924	383	832	95	below_threshold
Neisseria dentiae	strain=NCTC13012	GCA_900453685.1	194197	194197	type	True	80.2794	485	832	95	below_threshold
Neisseria bacilliformis	strain=DSM 23338	GCA_014055025.1	267212	267212	type	True	80.2302	410	832	95	below_threshold
Neisseria elongata subsp. glycolytica	strain=NCTC11050	GCA_900475815.1	88719	495	type	True	79.9612	362	832	95	below_threshold
Neisseria gonorrhoeae	strain=DSM 9188	GCA_003315235.1	485	485	type	True	79.9319	370	832	95	below_threshold
Neisseria bacilliformis	strain=ATCC BAA-1200	GCA_000194925.1	267212	267212	type	True	79.9265	400	832	95	below_threshold
Neisseria elongata	strain=NCTC10660	GCA_900453895.1	495	495	type	True	79.784	373	832	95	below_threshold
Neisseria cinerea	strain=CCUG 2156	GCA_021025975.1	483	483	type	True	79.6877	336	832	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	79.6142	388	832	95	below_threshold
Kingella potus	strain=NCTC13336	GCA_900451175.1	265175	265175	type	True	79.6127	400	832	95	below_threshold
Kingella potus	strain=3/SID/1128	GCA_022870985.1	265175	265175	type	True	79.4609	404	832	95	below_threshold
Neisseria perflava	strain=CCUG 17915	GCA_023472875.1	33053	33053	suspected-type	True	79.234	386	832	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	78.9969	423	832	95	below_threshold
Neisseria shayeganii	strain=871	GCA_000226875.1	607712	607712	type	True	78.7161	290	832	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:20,558] [INFO] DFAST Taxonomy check result was written to GCF_002216145.1_ASM221614v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:20,559] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:20,559] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:20,559] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7cccce98-d43d-4a78-aaa3-67d92fa6a9bf/dqc_reference/checkm_data
[2024-01-24 15:19:20,560] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:20,588] [INFO] Task started: CheckM
[2024-01-24 15:19:20,588] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002216145.1_ASM221614v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002216145.1_ASM221614v1_genomic.fna/checkm_input GCF_002216145.1_ASM221614v1_genomic.fna/checkm_result
[2024-01-24 15:19:47,433] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:47,434] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:47,453] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:47,454] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:47,454] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002216145.1_ASM221614v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:47,454] [INFO] Task started: Blastn
[2024-01-24 15:19:47,455] [INFO] Running command: blastn -query GCF_002216145.1_ASM221614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cccce98-d43d-4a78-aaa3-67d92fa6a9bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_002216145.1_ASM221614v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:49,134] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:49,141] [INFO] Selected 20 target genomes.
[2024-01-24 15:19:49,141] [INFO] Target genome list was writen to GCF_002216145.1_ASM221614v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:49,157] [INFO] Task started: fastANI
[2024-01-24 15:19:49,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg58dab104-3426-429a-9c09-255ed9e9b14e/GCF_002216145.1_ASM221614v1_genomic.fna.gz --refList GCF_002216145.1_ASM221614v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002216145.1_ASM221614v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:02,159] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:02,179] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:02,180] [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_002216145.1	s__Neisseria chenwenguii	100.0	829	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.73	99.73	0.96	0.96	2	conclusive
GCF_001592185.1	s__Neisseria denitrificans	81.3506	387	832	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	80.9254	497	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.69	97.41	0.97	0.94	3	-
GCF_900636515.1	s__Neisseria animalis	80.5643	427	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	99.99	0.99	0.99	3	-
GCF_000227275.1	s__Neisseria sp000227275	80.4301	487	832	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	80.4112	451	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.406	N/A	N/A	N/A	N/A	1	-
GCF_014055005.1	s__Neisseria dentiae	80.4105	478	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.99	99.98	1.00	1.00	3	-
GCA_000220865.1	s__Neisseria macacae	80.3788	471	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.509	99.99	99.99	0.98	0.98	2	-
GCF_900638555.1	s__Neisseria meningitidis	80.3189	381	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0389	97.78	97.16	0.95	0.86	2138	-
GCF_000260655.1	s__Neisseria sicca_B	80.3182	453	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5569	97.07	96.76	0.92	0.90	3	-
GCF_014055025.1	s__Neisseria bacilliformis	80.2012	407	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.33	96.96	0.94	0.89	4	-
GCF_003044565.1	s__Neisseria sicca_A	80.1694	461	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.01	95.27	0.94	0.92	3	-
GCF_003315235.1	s__Neisseria gonorrhoeae	79.9997	365	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0389	99.56	98.98	0.97	0.89	796	-
GCF_002237445.1	s__Neisseria sp002237445	79.896	404	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.69	99.69	0.98	0.98	2	-
GCF_014898075.1	s__Neisseria sp011038745	79.8034	466	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.25	98.87	0.98	0.97	4	-
GCF_900113545.1	s__Neisseria elongata	79.6919	362	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	96.68	96.06	0.91	0.86	20	-
GCF_900451175.1	s__Neisseria potus	79.668	399	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990355.1	s__Eikenella corrodens_B	79.1212	295	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001648475.1	s__Eikenella halliae	79.0293	287	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905372165.1	s__CAJPNX01 sp905372165	78.5424	279	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__CAJPNX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:02,181] [INFO] GTDB search result was written to GCF_002216145.1_ASM221614v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:02,182] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:02,186] [INFO] DFAST_QC result json was written to GCF_002216145.1_ASM221614v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:02,187] [INFO] DFAST_QC completed!
[2024-01-24 15:20:02,187] [INFO] Total running time: 0h1m10s