[2024-01-25 19:46:20,602] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:46:20,603] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:46:20,603] [INFO] DQC Reference Directory: /var/lib/cwl/stgc595bdaa-05fd-4ec2-887d-8214342425a7/dqc_reference
[2024-01-25 19:46:21,742] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:46:21,743] [INFO] Task started: Prodigal
[2024-01-25 19:46:21,743] [INFO] Running command: gunzip -c /var/lib/cwl/stgece11e61-652a-4929-bb01-8697a6f11079/GCF_023547005.1_ASM2354700v1_genomic.fna.gz | prodigal -d GCF_023547005.1_ASM2354700v1_genomic.fna/cds.fna -a GCF_023547005.1_ASM2354700v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:46:28,061] [INFO] Task succeeded: Prodigal
[2024-01-25 19:46:28,061] [INFO] Task started: HMMsearch
[2024-01-25 19:46:28,061] [INFO] Running command: hmmsearch --tblout GCF_023547005.1_ASM2354700v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc595bdaa-05fd-4ec2-887d-8214342425a7/dqc_reference/reference_markers.hmm GCF_023547005.1_ASM2354700v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:46:28,264] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:46:28,265] [INFO] Found 6/6 markers.
[2024-01-25 19:46:28,285] [INFO] Query marker FASTA was written to GCF_023547005.1_ASM2354700v1_genomic.fna/markers.fasta
[2024-01-25 19:46:28,285] [INFO] Task started: Blastn
[2024-01-25 19:46:28,285] [INFO] Running command: blastn -query GCF_023547005.1_ASM2354700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc595bdaa-05fd-4ec2-887d-8214342425a7/dqc_reference/reference_markers.fasta -out GCF_023547005.1_ASM2354700v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:28,931] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:28,935] [INFO] Selected 13 target genomes.
[2024-01-25 19:46:28,935] [INFO] Target genome list was writen to GCF_023547005.1_ASM2354700v1_genomic.fna/target_genomes.txt
[2024-01-25 19:46:28,942] [INFO] Task started: fastANI
[2024-01-25 19:46:28,942] [INFO] Running command: fastANI --query /var/lib/cwl/stgece11e61-652a-4929-bb01-8697a6f11079/GCF_023547005.1_ASM2354700v1_genomic.fna.gz --refList GCF_023547005.1_ASM2354700v1_genomic.fna/target_genomes.txt --output GCF_023547005.1_ASM2354700v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:35,415] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:35,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc595bdaa-05fd-4ec2-887d-8214342425a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:35,416] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc595bdaa-05fd-4ec2-887d-8214342425a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:35,428] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:46:35,429] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:46:35,429] [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
Conchiformibius steedae	strain=DSM 2580	GCA_023547005.1	153493	153493	type	True	100.0	698	699	95	conclusive
Conchiformibius steedae	strain=DSM 2580	GCA_014054725.1	153493	153493	type	True	99.9942	698	699	95	conclusive
Conchiformibius steedae	strain=DSM 2580	GCA_000620925.1	153493	153493	type	True	99.9604	682	699	95	conclusive
Conchiformibius kuhniae	strain=17694	GCA_022871025.1	211502	211502	type	True	82.0546	491	699	95	below_threshold
Conchiformibius kuhniae	strain=DSM 17694	GCA_000428785.1	211502	211502	type	True	81.8869	486	699	95	below_threshold
Alysiella crassa	strain=NCTC10283	GCA_900445245.1	153491	153491	type	True	78.7937	264	699	95	below_threshold
Alysiella crassa	strain=S6	GCA_022871045.1	153491	153491	type	True	78.7805	265	699	95	below_threshold
Alysiella crassa	strain=DSM 2578	GCA_000745955.1	153491	153491	type	True	78.5405	257	699	95	below_threshold
Kingella bonacorsii	strain=Marseille-Q4569	GCA_016623605.1	2796361	2796361	type	True	78.5126	226	699	95	below_threshold
Neisseria meningitidis	strain=PartJ-Nmeningitidis-RM8376	GCA_022869645.1	487	487	type	True	78.36	166	699	95	below_threshold
Kingella kingae	strain=4177/66	GCA_022871005.1	504	504	type	True	78.1067	214	699	95	below_threshold
Neisseria arctica	strain=KH1503	GCA_022870905.1	1470200	1470200	type	True	77.979	112	699	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	77.8798	197	699	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:35,433] [INFO] DFAST Taxonomy check result was written to GCF_023547005.1_ASM2354700v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:35,434] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:35,434] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:35,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc595bdaa-05fd-4ec2-887d-8214342425a7/dqc_reference/checkm_data
[2024-01-25 19:46:35,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:35,458] [INFO] Task started: CheckM
[2024-01-25 19:46:35,458] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023547005.1_ASM2354700v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023547005.1_ASM2354700v1_genomic.fna/checkm_input GCF_023547005.1_ASM2354700v1_genomic.fna/checkm_result
[2024-01-25 19:46:58,570] [INFO] Task succeeded: CheckM
[2024-01-25 19:46:58,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:46:58,599] [INFO] ===== Completeness check finished =====
[2024-01-25 19:46:58,599] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:46:58,599] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023547005.1_ASM2354700v1_genomic.fna/markers.fasta)
[2024-01-25 19:46:58,600] [INFO] Task started: Blastn
[2024-01-25 19:46:58,600] [INFO] Running command: blastn -query GCF_023547005.1_ASM2354700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc595bdaa-05fd-4ec2-887d-8214342425a7/dqc_reference/reference_markers_gtdb.fasta -out GCF_023547005.1_ASM2354700v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:59,714] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:59,717] [INFO] Selected 18 target genomes.
[2024-01-25 19:46:59,717] [INFO] Target genome list was writen to GCF_023547005.1_ASM2354700v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:46:59,745] [INFO] Task started: fastANI
[2024-01-25 19:46:59,745] [INFO] Running command: fastANI --query /var/lib/cwl/stgece11e61-652a-4929-bb01-8697a6f11079/GCF_023547005.1_ASM2354700v1_genomic.fna.gz --refList GCF_023547005.1_ASM2354700v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023547005.1_ASM2354700v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:47:08,184] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:08,195] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:47:08,195] [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_014054725.1	s__Conchiformibius steedae	99.9944	696	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Conchiformibius	95.0	98.09	96.18	0.94	0.87	3	conclusive
GCF_000428785.1	s__Conchiformibius kuhniae	81.8747	486	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Conchiformibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014054525.1	s__Alysiella filiformis	78.6192	290	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000745955.1	s__Alysiella crassa	78.503	260	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.94	99.94	0.99	0.99	2	-
GCF_900187305.1	s__Neisseria zoodegmatis	78.3323	200	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.30	96.60	0.95	0.90	3	-
GCF_014055005.1	s__Neisseria dentiae	78.3183	197	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.99	99.98	1.00	1.00	3	-
GCF_900636765.1	s__Neisseria canis	78.2075	177	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014054985.1	s__Kingella_B oralis	78.1897	223	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_B	95.0	98.22	96.45	0.95	0.91	3	-
GCF_900638685.1	s__Neisseria weaveri	78.1425	161	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.19	98.86	0.98	0.97	8	-
GCF_013267835.1	s__Neisseria sp000186165	78.0478	160	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0019	96.64	96.07	0.93	0.88	22	-
GCF_003351665.1	s__Neisseria perflava	78.0413	155	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.6726	97.77	96.48	0.96	0.95	5	-
GCF_014297595.1	s__Neisseria musculi	78.0326	175	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.59	0.96	0.96	3	-
GCF_000190695.1	s__Kingella_A denitrificans	77.9703	206	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_A	95.0	98.63	96.04	0.97	0.93	4	-
GCF_900113545.1	s__Neisseria elongata	77.7872	153	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	96.68	96.06	0.91	0.86	20	-
GCF_001618085.1	s__Neisseria flavescens_C	77.5431	143	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.4709	96.21	96.21	0.92	0.92	2	-
GCF_001648355.1	s__Eikenella longinqua	77.5135	136	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003044645.1	s__Neisseria subflava_B	77.4551	147	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.654	N/A	N/A	N/A	N/A	1	-
GCA_905372165.1	s__CAJPNX01 sp905372165	77.0523	166	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__CAJPNX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:47:08,197] [INFO] GTDB search result was written to GCF_023547005.1_ASM2354700v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:47:08,197] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:47:08,201] [INFO] DFAST_QC result json was written to GCF_023547005.1_ASM2354700v1_genomic.fna/dqc_result.json
[2024-01-25 19:47:08,201] [INFO] DFAST_QC completed!
[2024-01-25 19:47:08,201] [INFO] Total running time: 0h0m48s