[2024-01-25 19:04:05,489] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:04:05,491] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:04:05,491] [INFO] DQC Reference Directory: /var/lib/cwl/stga25b54de-11d4-45b5-8065-05076b4dd3b8/dqc_reference
[2024-01-25 19:04:06,668] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:04:06,669] [INFO] Task started: Prodigal
[2024-01-25 19:04:06,669] [INFO] Running command: gunzip -c /var/lib/cwl/stg75e76dc4-8f62-43e3-a3ef-493fe90bd9a3/GCF_900451175.1_50465_B02_genomic.fna.gz | prodigal -d GCF_900451175.1_50465_B02_genomic.fna/cds.fna -a GCF_900451175.1_50465_B02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:04:14,739] [INFO] Task succeeded: Prodigal
[2024-01-25 19:04:14,739] [INFO] Task started: HMMsearch
[2024-01-25 19:04:14,739] [INFO] Running command: hmmsearch --tblout GCF_900451175.1_50465_B02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga25b54de-11d4-45b5-8065-05076b4dd3b8/dqc_reference/reference_markers.hmm GCF_900451175.1_50465_B02_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:04:14,922] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:04:14,923] [INFO] Found 6/6 markers.
[2024-01-25 19:04:14,944] [INFO] Query marker FASTA was written to GCF_900451175.1_50465_B02_genomic.fna/markers.fasta
[2024-01-25 19:04:14,944] [INFO] Task started: Blastn
[2024-01-25 19:04:14,944] [INFO] Running command: blastn -query GCF_900451175.1_50465_B02_genomic.fna/markers.fasta -db /var/lib/cwl/stga25b54de-11d4-45b5-8065-05076b4dd3b8/dqc_reference/reference_markers.fasta -out GCF_900451175.1_50465_B02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:15,557] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:15,560] [INFO] Selected 14 target genomes.
[2024-01-25 19:04:15,560] [INFO] Target genome list was writen to GCF_900451175.1_50465_B02_genomic.fna/target_genomes.txt
[2024-01-25 19:04:15,575] [INFO] Task started: fastANI
[2024-01-25 19:04:15,575] [INFO] Running command: fastANI --query /var/lib/cwl/stg75e76dc4-8f62-43e3-a3ef-493fe90bd9a3/GCF_900451175.1_50465_B02_genomic.fna.gz --refList GCF_900451175.1_50465_B02_genomic.fna/target_genomes.txt --output GCF_900451175.1_50465_B02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:04:27,500] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:27,500] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga25b54de-11d4-45b5-8065-05076b4dd3b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:04:27,500] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga25b54de-11d4-45b5-8065-05076b4dd3b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:04:27,509] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:04:27,509] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:04:27,510] [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
Kingella potus	strain=NCTC13336	GCA_900451175.1	265175	265175	type	True	100.0	817	825	95	conclusive
Kingella potus	strain=3/SID/1128	GCA_022870985.1	265175	265175	type	True	99.8942	804	825	95	conclusive
Neisseria bacilliformis	strain=DSM 23338	GCA_014055025.1	267212	267212	type	True	86.7766	635	825	95	below_threshold
Neisseria bacilliformis	strain=ATCC BAA-1200	GCA_000194925.1	267212	267212	type	True	86.6543	637	825	95	below_threshold
Neisseria elongata	strain=NCTC10660	GCA_900453895.1	495	495	type	True	80.642	458	825	95	below_threshold
Neisseria elongata subsp. elongata	strain=ATCC 25295	GCA_900113545.1	214482	495	type	True	80.5721	446	825	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_022749515.1	1056807	1056807	type	True	79.4225	339	825	95	below_threshold
Neisseria zoodegmatis	strain=NCTC12230	GCA_900187305.1	326523	326523	type	True	79.4091	331	825	95	below_threshold
Neisseria sicca	strain=ATCC 29256	GCA_000174655.1	490	490	suspected-type	True	79.2579	339	825	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	79.1626	323	825	95	below_threshold
Neisseria shayeganii	strain=871	GCA_000226875.1	607712	607712	type	True	79.0249	306	825	95	below_threshold
Neisseria dumasiana	strain=93087	GCA_002108505.1	1931275	1931275	type	True	78.8757	314	825	95	below_threshold
Neisseria weaveri	strain=LMG 5135	GCA_000224255.2	28091	28091	type	True	78.7784	229	825	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	78.6264	345	825	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:04:27,570] [INFO] DFAST Taxonomy check result was written to GCF_900451175.1_50465_B02_genomic.fna/tc_result.tsv
[2024-01-25 19:04:27,571] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:04:27,571] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:04:27,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga25b54de-11d4-45b5-8065-05076b4dd3b8/dqc_reference/checkm_data
[2024-01-25 19:04:27,572] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:04:27,599] [INFO] Task started: CheckM
[2024-01-25 19:04:27,599] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900451175.1_50465_B02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900451175.1_50465_B02_genomic.fna/checkm_input GCF_900451175.1_50465_B02_genomic.fna/checkm_result
[2024-01-25 19:04:53,402] [INFO] Task succeeded: CheckM
[2024-01-25 19:04:53,403] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:04:53,421] [INFO] ===== Completeness check finished =====
[2024-01-25 19:04:53,421] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:04:53,421] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900451175.1_50465_B02_genomic.fna/markers.fasta)
[2024-01-25 19:04:53,421] [INFO] Task started: Blastn
[2024-01-25 19:04:53,421] [INFO] Running command: blastn -query GCF_900451175.1_50465_B02_genomic.fna/markers.fasta -db /var/lib/cwl/stga25b54de-11d4-45b5-8065-05076b4dd3b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_900451175.1_50465_B02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:54,415] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:54,418] [INFO] Selected 17 target genomes.
[2024-01-25 19:04:54,418] [INFO] Target genome list was writen to GCF_900451175.1_50465_B02_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:04:54,446] [INFO] Task started: fastANI
[2024-01-25 19:04:54,446] [INFO] Running command: fastANI --query /var/lib/cwl/stg75e76dc4-8f62-43e3-a3ef-493fe90bd9a3/GCF_900451175.1_50465_B02_genomic.fna.gz --refList GCF_900451175.1_50465_B02_genomic.fna/target_genomes_gtdb.txt --output GCF_900451175.1_50465_B02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:05:06,493] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:06,515] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:05:06,515] [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_900451175.1	s__Neisseria potus	100.0	816	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014055025.1	s__Neisseria bacilliformis	86.7299	638	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.33	96.96	0.94	0.89	4	-
GCF_002237445.1	s__Neisseria sp002237445	84.2079	564	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.69	99.69	0.98	0.98	2	-
GCF_900113545.1	s__Neisseria elongata	80.5798	444	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	96.68	96.06	0.91	0.86	20	-
GCA_905372165.1	s__CAJPNX01 sp905372165	80.1249	318	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__CAJPNX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014055005.1	s__Neisseria dentiae	80.1232	413	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.99	99.98	1.00	1.00	3	-
GCF_005886145.1	s__Neisseria sp000090875	79.9806	380	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.69	97.41	0.97	0.94	3	-
GCF_017753665.1	s__Neisseria sicca_D	79.5492	312	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.2415	96.44	95.35	0.92	0.88	6	-
GCF_001809325.1	s__Neisseria sp001809325	79.4532	324	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.406	N/A	N/A	N/A	N/A	1	-
GCA_000220865.1	s__Neisseria macacae	79.4332	343	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.509	99.99	99.99	0.98	0.98	2	-
GCF_900187305.1	s__Neisseria zoodegmatis	79.3367	342	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.30	96.60	0.95	0.90	3	-
GCF_000227275.1	s__Neisseria sp000227275	79.2441	343	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.3387	97.52	96.71	0.95	0.93	3	-
GCF_900638685.1	s__Neisseria weaveri	79.0445	247	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.19	98.86	0.98	0.97	8	-
GCF_000226875.1	s__Eikenella shayeganii	79.0102	307	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	96.47	96.47	0.85	0.85	2	-
GCF_900637855.1	s__Neisseria animaloris	79.0074	311	825	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	78.7864	323	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.54	97.26	0.91	0.89	4	-
GCF_001308015.1	s__Neisseria sp001308015	78.3801	214	825	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:05:06,516] [INFO] GTDB search result was written to GCF_900451175.1_50465_B02_genomic.fna/result_gtdb.tsv
[2024-01-25 19:05:06,517] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:05:06,521] [INFO] DFAST_QC result json was written to GCF_900451175.1_50465_B02_genomic.fna/dqc_result.json
[2024-01-25 19:05:06,521] [INFO] DFAST_QC completed!
[2024-01-25 19:05:06,521] [INFO] Total running time: 0h1m1s