[2024-01-25 17:35:05,488] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:35:05,490] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:35:05,490] [INFO] DQC Reference Directory: /var/lib/cwl/stg430cb472-81f1-404c-bd94-9ad2edeccda5/dqc_reference
[2024-01-25 17:35:06,675] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:35:06,676] [INFO] Task started: Prodigal
[2024-01-25 17:35:06,676] [INFO] Running command: gunzip -c /var/lib/cwl/stgf0df5d8e-ab9c-4827-8422-c0f7f0156101/GCF_021556475.1_ASM2155647v1_genomic.fna.gz | prodigal -d GCF_021556475.1_ASM2155647v1_genomic.fna/cds.fna -a GCF_021556475.1_ASM2155647v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:35:17,048] [INFO] Task succeeded: Prodigal
[2024-01-25 17:35:17,048] [INFO] Task started: HMMsearch
[2024-01-25 17:35:17,048] [INFO] Running command: hmmsearch --tblout GCF_021556475.1_ASM2155647v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg430cb472-81f1-404c-bd94-9ad2edeccda5/dqc_reference/reference_markers.hmm GCF_021556475.1_ASM2155647v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:35:17,256] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:35:17,257] [INFO] Found 6/6 markers.
[2024-01-25 17:35:17,293] [INFO] Query marker FASTA was written to GCF_021556475.1_ASM2155647v1_genomic.fna/markers.fasta
[2024-01-25 17:35:17,293] [INFO] Task started: Blastn
[2024-01-25 17:35:17,293] [INFO] Running command: blastn -query GCF_021556475.1_ASM2155647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg430cb472-81f1-404c-bd94-9ad2edeccda5/dqc_reference/reference_markers.fasta -out GCF_021556475.1_ASM2155647v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:18,097] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:18,100] [INFO] Selected 16 target genomes.
[2024-01-25 17:35:18,100] [INFO] Target genome list was writen to GCF_021556475.1_ASM2155647v1_genomic.fna/target_genomes.txt
[2024-01-25 17:35:18,109] [INFO] Task started: fastANI
[2024-01-25 17:35:18,109] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0df5d8e-ab9c-4827-8422-c0f7f0156101/GCF_021556475.1_ASM2155647v1_genomic.fna.gz --refList GCF_021556475.1_ASM2155647v1_genomic.fna/target_genomes.txt --output GCF_021556475.1_ASM2155647v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:35:31,604] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:31,604] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg430cb472-81f1-404c-bd94-9ad2edeccda5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:35:31,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg430cb472-81f1-404c-bd94-9ad2edeccda5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:35:31,615] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:35:31,615] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:35:31,615] [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
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	100.0	1303	1306	95	conclusive
Acidiphilium multivorum	strain=AIU301	GCA_000964345.1	62140	62140	type	True	80.8053	575	1306	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000202835.1	62140	62140	type	True	80.7298	654	1306	95	below_threshold
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	77.6289	211	1306	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.5193	285	1306	95	below_threshold
Gluconacetobacter dulcium	strain=LMG 1728	GCA_014174165.1	2729096	2729096	type	True	77.1375	191	1306	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	76.7878	253	1306	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	76.6681	252	1306	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	76.5976	193	1306	95	below_threshold
Komagataeibacter swingsii	strain=LMG 22125	GCA_003207895.1	215220	215220	type	True	76.5789	101	1306	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.5497	200	1306	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.3881	175	1306	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.2071	190	1306	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	75.9465	190	1306	95	below_threshold
Thioclava electrotropha	strain=Elox9	GCA_002085925.2	1549850	1549850	type	True	75.6944	88	1306	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	75.3018	62	1306	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:35:31,616] [INFO] DFAST Taxonomy check result was written to GCF_021556475.1_ASM2155647v1_genomic.fna/tc_result.tsv
[2024-01-25 17:35:31,617] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:35:31,617] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:35:31,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg430cb472-81f1-404c-bd94-9ad2edeccda5/dqc_reference/checkm_data
[2024-01-25 17:35:31,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:35:31,658] [INFO] Task started: CheckM
[2024-01-25 17:35:31,658] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021556475.1_ASM2155647v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021556475.1_ASM2155647v1_genomic.fna/checkm_input GCF_021556475.1_ASM2155647v1_genomic.fna/checkm_result
[2024-01-25 17:36:04,388] [INFO] Task succeeded: CheckM
[2024-01-25 17:36:04,389] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:36:04,416] [INFO] ===== Completeness check finished =====
[2024-01-25 17:36:04,416] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:36:04,417] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021556475.1_ASM2155647v1_genomic.fna/markers.fasta)
[2024-01-25 17:36:04,417] [INFO] Task started: Blastn
[2024-01-25 17:36:04,417] [INFO] Running command: blastn -query GCF_021556475.1_ASM2155647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg430cb472-81f1-404c-bd94-9ad2edeccda5/dqc_reference/reference_markers_gtdb.fasta -out GCF_021556475.1_ASM2155647v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:06,117] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:06,120] [INFO] Selected 18 target genomes.
[2024-01-25 17:36:06,120] [INFO] Target genome list was writen to GCF_021556475.1_ASM2155647v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:36:06,129] [INFO] Task started: fastANI
[2024-01-25 17:36:06,130] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0df5d8e-ab9c-4827-8422-c0f7f0156101/GCF_021556475.1_ASM2155647v1_genomic.fna.gz --refList GCF_021556475.1_ASM2155647v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021556475.1_ASM2155647v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:36:20,885] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:20,896] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:36:20,896] [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_000202835.1	s__Acidiphilium multivorum	80.7297	654	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	98.69	98.42	0.90	0.87	6	-
GCF_902712915.1	s__Acidiphilium sp002255515	80.1376	551	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	99.59	99.19	0.97	0.94	3	-
GCF_900156265.1	s__Acidiphilium rubrum	79.6096	565	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	97.80	96.68	0.89	0.85	4	-
GCA_017307285.1	s__JAFKFI01 sp017307285	78.1096	256	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFKFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903907955.1	s__BOG-930 sp903907955	77.6732	269	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.93	99.75	0.97	0.94	12	-
GCF_000964365.1	s__Acidisphaera rubrifaciens	77.6433	210	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899585.1	s__70-18 sp001899585	77.4918	343	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__70-18	95.0	99.94	99.94	0.98	0.98	2	-
GCA_002279355.1	s__Acidiphilium sp002279355	77.3498	262	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	99.80	99.77	0.93	0.92	3	-
GCA_019240395.1	s__JAFAYA01 sp019240395	77.2885	247	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFAYA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240635.1	s__JAFEFJ01 sp018240635	77.2678	251	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFEFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174275.1	s__Gluconacetobacter takamatsuzukensis	77.2029	170	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174165.1	s__Gluconacetobacter dulcium	77.1375	191	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	98.93	97.86	0.94	0.88	3	-
GCA_903865895.1	s__CAIYPH01 sp903865895	76.9081	268	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007922615.2	s__Nitratireductor_D sp007922615	76.3318	118	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003351345.1	s__Bosea caraganae	75.9379	191	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007693835.1	s__Rubrimonas sp007693835	75.5318	122	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109855.1	s__Roseovarius tolerans	75.2876	63	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.73	96.73	0.86	0.86	2	-
GCA_001724605.1	s__Phenylobacterium sp001724605	75.2519	103	1306	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:36:20,898] [INFO] GTDB search result was written to GCF_021556475.1_ASM2155647v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:36:20,898] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:36:20,902] [INFO] DFAST_QC result json was written to GCF_021556475.1_ASM2155647v1_genomic.fna/dqc_result.json
[2024-01-25 17:36:20,902] [INFO] DFAST_QC completed!
[2024-01-25 17:36:20,902] [INFO] Total running time: 0h1m15s