[2024-01-25 18:43:35,628] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:35,632] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:35,632] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3ef2cb1-fdcf-41da-87ba-3a9c28c9c89d/dqc_reference
[2024-01-25 18:43:36,824] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:36,825] [INFO] Task started: Prodigal
[2024-01-25 18:43:36,825] [INFO] Running command: gunzip -c /var/lib/cwl/stg7fbe15fc-7ae0-4987-bd88-067334cc2b7b/GCF_022870925.1_ASM2287092v1_genomic.fna.gz | prodigal -d GCF_022870925.1_ASM2287092v1_genomic.fna/cds.fna -a GCF_022870925.1_ASM2287092v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:43:52,487] [INFO] Task succeeded: Prodigal
[2024-01-25 18:43:52,488] [INFO] Task started: HMMsearch
[2024-01-25 18:43:52,488] [INFO] Running command: hmmsearch --tblout GCF_022870925.1_ASM2287092v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3ef2cb1-fdcf-41da-87ba-3a9c28c9c89d/dqc_reference/reference_markers.hmm GCF_022870925.1_ASM2287092v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:43:52,705] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:43:52,706] [INFO] Found 6/6 markers.
[2024-01-25 18:43:52,735] [INFO] Query marker FASTA was written to GCF_022870925.1_ASM2287092v1_genomic.fna/markers.fasta
[2024-01-25 18:43:52,736] [INFO] Task started: Blastn
[2024-01-25 18:43:52,736] [INFO] Running command: blastn -query GCF_022870925.1_ASM2287092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3ef2cb1-fdcf-41da-87ba-3a9c28c9c89d/dqc_reference/reference_markers.fasta -out GCF_022870925.1_ASM2287092v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:53,367] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:53,370] [INFO] Selected 16 target genomes.
[2024-01-25 18:43:53,371] [INFO] Target genome list was writen to GCF_022870925.1_ASM2287092v1_genomic.fna/target_genomes.txt
[2024-01-25 18:43:53,375] [INFO] Task started: fastANI
[2024-01-25 18:43:53,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fbe15fc-7ae0-4987-bd88-067334cc2b7b/GCF_022870925.1_ASM2287092v1_genomic.fna.gz --refList GCF_022870925.1_ASM2287092v1_genomic.fna/target_genomes.txt --output GCF_022870925.1_ASM2287092v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:44:02,954] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:02,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3ef2cb1-fdcf-41da-87ba-3a9c28c9c89d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:44:02,955] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3ef2cb1-fdcf-41da-87ba-3a9c28c9c89d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:44:02,963] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:44:02,963] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:44:02,964] [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
Vitreoscilla massiliensis	strain=SN4	GCA_022870925.1	1689272	1689272	type	True	100.0	1236	1242	95	conclusive
Vitreoscilla massiliensis	strain=SN6	GCA_001457815.1	1689272	1689272	type	True	99.9867	1228	1242	95	conclusive
Vitreoscilla stercoraria	strain=SAG 1488-6	GCA_022870945.1	61	61	type	True	80.1088	454	1242	95	below_threshold
Vitreoscilla stercoraria	strain=DSM 513	GCA_000382305.1	61	61	type	True	79.835	446	1242	95	below_threshold
Neisseria meningitidis	strain=PartJ-Nmeningitidis-RM8376	GCA_022869645.1	487	487	type	True	78.9949	96	1242	95	below_threshold
Neisseria subflava	strain=ATCC 49275	GCA_005221305.1	28449	28449	type	True	78.0175	116	1242	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	77.7293	112	1242	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	77.6031	131	1242	95	below_threshold
Neisseria iguanae	strain=ATCC 51483	GCA_003013245.1	90242	90242	type	True	77.3995	106	1242	95	below_threshold
Alysiella crassa	strain=S6	GCA_022871045.1	153491	153491	type	True	77.2557	107	1242	95	below_threshold
Uruburuella suis	strain=1258/02	GCA_022870845.1	252130	252130	type	True	76.8784	176	1242	95	below_threshold
Uruburuella suis	strain=DSM 17474	GCA_004341385.1	252130	252130	type	True	76.3379	165	1242	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:44:02,965] [INFO] DFAST Taxonomy check result was written to GCF_022870925.1_ASM2287092v1_genomic.fna/tc_result.tsv
[2024-01-25 18:44:02,965] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:44:02,965] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:44:02,966] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3ef2cb1-fdcf-41da-87ba-3a9c28c9c89d/dqc_reference/checkm_data
[2024-01-25 18:44:02,966] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:44:03,005] [INFO] Task started: CheckM
[2024-01-25 18:44:03,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022870925.1_ASM2287092v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022870925.1_ASM2287092v1_genomic.fna/checkm_input GCF_022870925.1_ASM2287092v1_genomic.fna/checkm_result
[2024-01-25 18:44:49,469] [INFO] Task succeeded: CheckM
[2024-01-25 18:44:49,470] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:44:49,483] [INFO] ===== Completeness check finished =====
[2024-01-25 18:44:49,484] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:44:49,484] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022870925.1_ASM2287092v1_genomic.fna/markers.fasta)
[2024-01-25 18:44:49,484] [INFO] Task started: Blastn
[2024-01-25 18:44:49,484] [INFO] Running command: blastn -query GCF_022870925.1_ASM2287092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3ef2cb1-fdcf-41da-87ba-3a9c28c9c89d/dqc_reference/reference_markers_gtdb.fasta -out GCF_022870925.1_ASM2287092v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:50,557] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:50,560] [INFO] Selected 22 target genomes.
[2024-01-25 18:44:50,561] [INFO] Target genome list was writen to GCF_022870925.1_ASM2287092v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:44:50,585] [INFO] Task started: fastANI
[2024-01-25 18:44:50,585] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fbe15fc-7ae0-4987-bd88-067334cc2b7b/GCF_022870925.1_ASM2287092v1_genomic.fna.gz --refList GCF_022870925.1_ASM2287092v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022870925.1_ASM2287092v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:45:01,461] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:01,471] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:45:01,471] [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_001457815.1	s__Vitreoscilla massiliensis	99.9872	1228	1242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Vitreoscilla	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000382305.1	s__Vitreoscilla stercoraria	79.8168	448	1242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Vitreoscilla	95.0	99.33	99.33	0.95	0.95	2	-
GCF_005221305.1	s__Neisseria subflava	78.25	116	1242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.1594	96.50	96.31	0.91	0.87	10	-
GCF_009671065.1	s__Neisseria brasiliensis	78.1604	161	1242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.38	99.05	0.95	0.90	4	-
GCF_014054525.1	s__Alysiella filiformis	77.9658	109	1242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002327085.1	s__Neisseria sp002327085	77.9361	131	1242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.28	99.27	0.86	0.86	3	-
GCF_900637855.1	s__Neisseria animaloris	77.579	104	1242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.11	0.97	0.94	5	-
GCF_003013245.1	s__Neisseria iguanae	77.3584	106	1242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000751855.1	s__Kingella negevensis	77.2714	85	1242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella	95.0	99.09	98.48	0.96	0.94	3	-
GCA_016894345.1	s__26B sp016894345	77.2209	176	1242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__26B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111845.1	s__Kingella kingae	76.8482	90	1242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella	95.0	98.43	98.16	0.96	0.94	37	-
GCA_017987415.1	s__JAGNPU01 sp017987415	76.6422	93	1242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__JAGNPU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745955.1	s__Alysiella crassa	76.6308	99	1242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.94	99.94	0.99	0.99	2	-
GCA_017991555.1	s__JAGNPU01 sp017991555	76.5712	135	1242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__JAGNPU01	95.0	99.61	99.61	0.99	0.99	2	-
GCF_000226875.1	s__Eikenella shayeganii	76.3939	117	1242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	96.47	96.47	0.85	0.85	2	-
GCA_017989485.1	s__JAGNPU01 sp017989485	75.9886	82	1242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__JAGNPU01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:45:01,473] [INFO] GTDB search result was written to GCF_022870925.1_ASM2287092v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:45:01,473] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:45:01,476] [INFO] DFAST_QC result json was written to GCF_022870925.1_ASM2287092v1_genomic.fna/dqc_result.json
[2024-01-25 18:45:01,477] [INFO] DFAST_QC completed!
[2024-01-25 18:45:01,477] [INFO] Total running time: 0h1m26s