[2024-01-25 19:43:05,516] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:05,520] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:05,520] [INFO] DQC Reference Directory: /var/lib/cwl/stg1237fce6-0cb3-48be-962d-406e58a2c683/dqc_reference
[2024-01-25 19:43:06,652] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:06,654] [INFO] Task started: Prodigal
[2024-01-25 19:43:06,654] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5eae6a6-fee1-4dff-88c7-2c4e45428489/GCF_900111845.1_PRJEB17081_genomic.fna.gz | prodigal -d GCF_900111845.1_PRJEB17081_genomic.fna/cds.fna -a GCF_900111845.1_PRJEB17081_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:43:12,388] [INFO] Task succeeded: Prodigal
[2024-01-25 19:43:12,389] [INFO] Task started: HMMsearch
[2024-01-25 19:43:12,389] [INFO] Running command: hmmsearch --tblout GCF_900111845.1_PRJEB17081_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1237fce6-0cb3-48be-962d-406e58a2c683/dqc_reference/reference_markers.hmm GCF_900111845.1_PRJEB17081_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:43:12,598] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:43:12,599] [INFO] Found 6/6 markers.
[2024-01-25 19:43:12,617] [INFO] Query marker FASTA was written to GCF_900111845.1_PRJEB17081_genomic.fna/markers.fasta
[2024-01-25 19:43:12,618] [INFO] Task started: Blastn
[2024-01-25 19:43:12,618] [INFO] Running command: blastn -query GCF_900111845.1_PRJEB17081_genomic.fna/markers.fasta -db /var/lib/cwl/stg1237fce6-0cb3-48be-962d-406e58a2c683/dqc_reference/reference_markers.fasta -out GCF_900111845.1_PRJEB17081_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:13,237] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:13,240] [INFO] Selected 11 target genomes.
[2024-01-25 19:43:13,240] [INFO] Target genome list was writen to GCF_900111845.1_PRJEB17081_genomic.fna/target_genomes.txt
[2024-01-25 19:43:13,248] [INFO] Task started: fastANI
[2024-01-25 19:43:13,248] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5eae6a6-fee1-4dff-88c7-2c4e45428489/GCF_900111845.1_PRJEB17081_genomic.fna.gz --refList GCF_900111845.1_PRJEB17081_genomic.fna/target_genomes.txt --output GCF_900111845.1_PRJEB17081_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:43:20,547] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:20,547] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1237fce6-0cb3-48be-962d-406e58a2c683/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:43:20,548] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1237fce6-0cb3-48be-962d-406e58a2c683/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:43:20,556] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 19:43:20,556] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:43:20,556] [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 kingae	strain=ATCC 23330	GCA_900111845.1	504	504	type	True	100.0	620	621	95	conclusive
Kingella kingae	strain=4177/66	GCA_022871005.1	504	504	type	True	99.9905	621	621	95	conclusive
Kingella kingae	strain=NCTC10529	GCA_900475905.1	504	504	type	True	99.9881	621	621	95	conclusive
Kingella kingae	strain=ATCC 23330	GCA_000213535.1	504	504	type	True	99.9419	613	621	95	conclusive
Simonsiella muelleri	strain=ATCC 29453	GCA_002951835.1	72	72	type	True	79.997	250	621	95	below_threshold
Alysiella crassa	strain=S6	GCA_022871045.1	153491	153491	type	True	79.607	338	621	95	below_threshold
Alysiella filiformis	strain=DSM 16848	GCA_014054525.1	194196	194196	type	True	79.5519	354	621	95	below_threshold
Kingella denitrificans	strain=ATCC 33394	GCA_000190695.1	502	502	type	True	78.2001	267	621	95	below_threshold
Conchiformibius steedae	strain=DSM 2580	GCA_023547005.1	153493	153493	type	True	77.5281	202	621	95	below_threshold
Neisseria cinerea	strain=CCUG 2156	GCA_021025975.1	483	483	type	True	77.4549	104	621	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	76.7217	108	621	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:43:20,558] [INFO] DFAST Taxonomy check result was written to GCF_900111845.1_PRJEB17081_genomic.fna/tc_result.tsv
[2024-01-25 19:43:20,558] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:43:20,558] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:43:20,558] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1237fce6-0cb3-48be-962d-406e58a2c683/dqc_reference/checkm_data
[2024-01-25 19:43:20,559] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:43:20,583] [INFO] Task started: CheckM
[2024-01-25 19:43:20,583] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111845.1_PRJEB17081_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111845.1_PRJEB17081_genomic.fna/checkm_input GCF_900111845.1_PRJEB17081_genomic.fna/checkm_result
[2024-01-25 19:43:41,767] [INFO] Task succeeded: CheckM
[2024-01-25 19:43:41,768] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:43:41,782] [INFO] ===== Completeness check finished =====
[2024-01-25 19:43:41,782] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:43:41,782] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111845.1_PRJEB17081_genomic.fna/markers.fasta)
[2024-01-25 19:43:41,783] [INFO] Task started: Blastn
[2024-01-25 19:43:41,783] [INFO] Running command: blastn -query GCF_900111845.1_PRJEB17081_genomic.fna/markers.fasta -db /var/lib/cwl/stg1237fce6-0cb3-48be-962d-406e58a2c683/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111845.1_PRJEB17081_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:42,812] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:42,814] [INFO] Selected 10 target genomes.
[2024-01-25 19:43:42,814] [INFO] Target genome list was writen to GCF_900111845.1_PRJEB17081_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:43:42,819] [INFO] Task started: fastANI
[2024-01-25 19:43:42,819] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5eae6a6-fee1-4dff-88c7-2c4e45428489/GCF_900111845.1_PRJEB17081_genomic.fna.gz --refList GCF_900111845.1_PRJEB17081_genomic.fna/target_genomes_gtdb.txt --output GCF_900111845.1_PRJEB17081_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:43:49,795] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:49,803] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:43:49,803] [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_900111845.1	s__Kingella kingae	100.0	620	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella	95.0	98.43	98.16	0.96	0.94	37	conclusive
GCF_000751855.1	s__Kingella negevensis	84.963	316	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella	95.0	99.09	98.48	0.96	0.94	3	-
GCF_002951835.1	s__Simonsiella muelleri	80.0351	250	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Simonsiella	95.0	99.93	99.93	0.98	0.98	2	-
GCF_000745955.1	s__Alysiella crassa	79.6741	324	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.94	99.94	0.99	0.99	2	-
GCF_014054525.1	s__Alysiella filiformis	79.545	354	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000190695.1	s__Kingella_A denitrificans	78.2588	264	621	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_014054985.1	s__Kingella_B oralis	78.0529	244	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_B	95.0	98.22	96.45	0.95	0.91	3	-
GCA_017446355.1	s__RGIG3394 sp017446355	77.4452	114	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__RGIG3394	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001027865.1	s__Neisseria arctica	77.2324	60	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637855.1	s__Neisseria animaloris	77.0507	100	621	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.11	0.97	0.94	5	-
--------------------------------------------------------------------------------
[2024-01-25 19:43:49,809] [INFO] GTDB search result was written to GCF_900111845.1_PRJEB17081_genomic.fna/result_gtdb.tsv
[2024-01-25 19:43:49,810] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:43:49,812] [INFO] DFAST_QC result json was written to GCF_900111845.1_PRJEB17081_genomic.fna/dqc_result.json
[2024-01-25 19:43:49,813] [INFO] DFAST_QC completed!
[2024-01-25 19:43:49,813] [INFO] Total running time: 0h0m44s