[2024-01-25 18:59:50,828] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:59:50,829] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:59:50,829] [INFO] DQC Reference Directory: /var/lib/cwl/stg5caaee22-a3b7-44d0-a6cd-b82e1304aa56/dqc_reference
[2024-01-25 18:59:51,961] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:59:51,962] [INFO] Task started: Prodigal
[2024-01-25 18:59:51,962] [INFO] Running command: gunzip -c /var/lib/cwl/stg486aa7fa-b5f7-430a-b18c-687ff8145590/GCF_024834045.1_ASM2483404v1_genomic.fna.gz | prodigal -d GCF_024834045.1_ASM2483404v1_genomic.fna/cds.fna -a GCF_024834045.1_ASM2483404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:59:57,317] [INFO] Task succeeded: Prodigal
[2024-01-25 18:59:57,318] [INFO] Task started: HMMsearch
[2024-01-25 18:59:57,318] [INFO] Running command: hmmsearch --tblout GCF_024834045.1_ASM2483404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5caaee22-a3b7-44d0-a6cd-b82e1304aa56/dqc_reference/reference_markers.hmm GCF_024834045.1_ASM2483404v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:59:57,536] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:59:57,537] [INFO] Found 6/6 markers.
[2024-01-25 18:59:57,560] [INFO] Query marker FASTA was written to GCF_024834045.1_ASM2483404v1_genomic.fna/markers.fasta
[2024-01-25 18:59:57,560] [INFO] Task started: Blastn
[2024-01-25 18:59:57,561] [INFO] Running command: blastn -query GCF_024834045.1_ASM2483404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5caaee22-a3b7-44d0-a6cd-b82e1304aa56/dqc_reference/reference_markers.fasta -out GCF_024834045.1_ASM2483404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:58,222] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:58,225] [INFO] Selected 16 target genomes.
[2024-01-25 18:59:58,225] [INFO] Target genome list was writen to GCF_024834045.1_ASM2483404v1_genomic.fna/target_genomes.txt
[2024-01-25 18:59:58,241] [INFO] Task started: fastANI
[2024-01-25 18:59:58,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg486aa7fa-b5f7-430a-b18c-687ff8145590/GCF_024834045.1_ASM2483404v1_genomic.fna.gz --refList GCF_024834045.1_ASM2483404v1_genomic.fna/target_genomes.txt --output GCF_024834045.1_ASM2483404v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:00:05,737] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:05,738] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5caaee22-a3b7-44d0-a6cd-b82e1304aa56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:00:05,738] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5caaee22-a3b7-44d0-a6cd-b82e1304aa56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:00:05,748] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:00:05,748] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:00:05,748] [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 zalophi	strain=ATCC BAA-2455	GCA_008807015.1	640030	640030	type	True	90.9457	641	760	95	below_threshold
Neisseria zoodegmatis	strain=NCTC12230	GCA_900187305.1	326523	326523	type	True	79.7061	385	760	95	below_threshold
Neisseria zoodegmatis	strain=DSM 21643	GCA_002108575.1	326523	326523	type	True	79.589	391	760	95	below_threshold
Neisseria dumasiana	strain=93087	GCA_002108505.1	1931275	1931275	type	True	79.391	392	760	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	79.3645	404	760	95	below_threshold
Neisseria animaloris	strain=DSM 21642	GCA_002108605.1	326522	326522	type	True	79.2986	338	760	95	below_threshold
Neisseria animaloris	strain=NCTC12228	GCA_900637855.1	326522	326522	type	True	79.2692	335	760	95	below_threshold
Neisseria weaveri	strain=NCTC12742	GCA_900638685.1	28091	28091	type	True	78.8674	275	760	95	below_threshold
Neisseria weaveri	strain=LMG 5135	GCA_000224255.2	28091	28091	type	True	78.7531	277	760	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	78.1973	323	760	95	below_threshold
Uruburuella suis	strain=DSM 17474	GCA_004341385.1	252130	252130	type	True	77.9871	270	760	95	below_threshold
Uruburuella suis	strain=1258/02	GCA_022870845.1	252130	252130	type	True	77.9367	277	760	95	below_threshold
Neisseria perflava	strain=CCUG 17915	GCA_023472875.1	33053	33053	suspected-type	True	77.8833	212	760	95	below_threshold
Kingella potus	strain=NCTC13336	GCA_900451175.1	265175	265175	type	True	77.7854	164	760	95	below_threshold
Neisseria elongata	strain=NCTC10660	GCA_900453895.1	495	495	type	True	77.7304	200	760	95	below_threshold
Neisseria elongata subsp. elongata	strain=ATCC 25295	GCA_900113545.1	214482	495	type	True	77.6623	202	760	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:00:05,749] [INFO] DFAST Taxonomy check result was written to GCF_024834045.1_ASM2483404v1_genomic.fna/tc_result.tsv
[2024-01-25 19:00:05,750] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:00:05,750] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:00:05,750] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5caaee22-a3b7-44d0-a6cd-b82e1304aa56/dqc_reference/checkm_data
[2024-01-25 19:00:05,751] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:00:05,776] [INFO] Task started: CheckM
[2024-01-25 19:00:05,776] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024834045.1_ASM2483404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024834045.1_ASM2483404v1_genomic.fna/checkm_input GCF_024834045.1_ASM2483404v1_genomic.fna/checkm_result
[2024-01-25 19:00:26,451] [INFO] Task succeeded: CheckM
[2024-01-25 19:00:26,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:00:26,470] [INFO] ===== Completeness check finished =====
[2024-01-25 19:00:26,470] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:00:26,471] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024834045.1_ASM2483404v1_genomic.fna/markers.fasta)
[2024-01-25 19:00:26,471] [INFO] Task started: Blastn
[2024-01-25 19:00:26,471] [INFO] Running command: blastn -query GCF_024834045.1_ASM2483404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5caaee22-a3b7-44d0-a6cd-b82e1304aa56/dqc_reference/reference_markers_gtdb.fasta -out GCF_024834045.1_ASM2483404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:27,615] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:27,619] [INFO] Selected 12 target genomes.
[2024-01-25 19:00:27,619] [INFO] Target genome list was writen to GCF_024834045.1_ASM2483404v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:00:27,634] [INFO] Task started: fastANI
[2024-01-25 19:00:27,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg486aa7fa-b5f7-430a-b18c-687ff8145590/GCF_024834045.1_ASM2483404v1_genomic.fna.gz --refList GCF_024834045.1_ASM2483404v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024834045.1_ASM2483404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:00:33,678] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:33,685] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:00:33,686] [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_008807015.1	s__Neisseria zalophi	90.9104	642	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187305.1	s__Neisseria zoodegmatis	79.6614	388	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.30	96.60	0.95	0.90	3	-
GCF_002108505.1	s__Neisseria dumasiana	79.3892	391	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.54	97.26	0.91	0.89	4	-
GCF_900637855.1	s__Neisseria animaloris	79.2842	333	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.11	0.97	0.94	5	-
GCF_014055005.1	s__Neisseria dentiae	78.8577	358	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.99	99.98	1.00	1.00	3	-
GCF_900638685.1	s__Neisseria weaveri	78.8416	274	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.19	98.86	0.98	0.97	8	-
GCF_004341385.1	s__Neisseria suis	78.0232	267	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.29	97.17	0.93	0.92	3	-
GCF_005886145.1	s__Neisseria sp000090875	77.9847	211	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.69	97.41	0.97	0.94	3	-
GCF_003044565.1	s__Neisseria sicca_A	77.9831	196	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.01	95.27	0.94	0.92	3	-
GCF_001618015.1	s__Neisseria flavescens_B	77.9702	216	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.1594	95.75	95.73	0.88	0.87	5	-
GCF_003045025.1	s__Neisseria subflava_A	77.953	211	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.3115	96.25	95.58	0.94	0.91	14	-
GCF_001027865.1	s__Neisseria arctica	77.6004	213	760	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 19:00:33,687] [INFO] GTDB search result was written to GCF_024834045.1_ASM2483404v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:00:33,687] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:00:33,691] [INFO] DFAST_QC result json was written to GCF_024834045.1_ASM2483404v1_genomic.fna/dqc_result.json
[2024-01-25 19:00:33,691] [INFO] DFAST_QC completed!
[2024-01-25 19:00:33,691] [INFO] Total running time: 0h0m43s