[2023-07-01 00:16:32,286] [INFO] DFAST_QC pipeline started.
[2023-07-01 00:16:32,289] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 00:16:32,289] [INFO] DQC Reference Directory: /var/lib/cwl/stg58fe97ca-dc35-4b5d-947d-ae14ac7f53b0/dqc_reference
[2023-07-01 00:16:34,986] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 00:16:34,987] [INFO] Task started: Prodigal
[2023-07-01 00:16:34,987] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e0fcaf5-b3c2-4df4-84c1-aa3680edc08c/GCA_024693045.1_ASM2469304v1_genomic.fna.gz | prodigal -d GCA_024693045.1_ASM2469304v1_genomic.fna/cds.fna -a GCA_024693045.1_ASM2469304v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 00:16:39,912] [INFO] Task succeeded: Prodigal
[2023-07-01 00:16:39,912] [INFO] Task started: HMMsearch
[2023-07-01 00:16:39,912] [INFO] Running command: hmmsearch --tblout GCA_024693045.1_ASM2469304v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58fe97ca-dc35-4b5d-947d-ae14ac7f53b0/dqc_reference/reference_markers.hmm GCA_024693045.1_ASM2469304v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 00:16:40,217] [INFO] Task succeeded: HMMsearch
[2023-07-01 00:16:40,218] [INFO] Found 6/6 markers.
[2023-07-01 00:16:40,267] [INFO] Query marker FASTA was written to GCA_024693045.1_ASM2469304v1_genomic.fna/markers.fasta
[2023-07-01 00:16:40,268] [INFO] Task started: Blastn
[2023-07-01 00:16:40,268] [INFO] Running command: blastn -query GCA_024693045.1_ASM2469304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58fe97ca-dc35-4b5d-947d-ae14ac7f53b0/dqc_reference/reference_markers.fasta -out GCA_024693045.1_ASM2469304v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 00:16:40,875] [INFO] Task succeeded: Blastn
[2023-07-01 00:16:40,879] [INFO] Selected 15 target genomes.
[2023-07-01 00:16:40,879] [INFO] Target genome list was writen to GCA_024693045.1_ASM2469304v1_genomic.fna/target_genomes.txt
[2023-07-01 00:16:40,882] [INFO] Task started: fastANI
[2023-07-01 00:16:40,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e0fcaf5-b3c2-4df4-84c1-aa3680edc08c/GCA_024693045.1_ASM2469304v1_genomic.fna.gz --refList GCA_024693045.1_ASM2469304v1_genomic.fna/target_genomes.txt --output GCA_024693045.1_ASM2469304v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 00:16:49,454] [INFO] Task succeeded: fastANI
[2023-07-01 00:16:49,455] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58fe97ca-dc35-4b5d-947d-ae14ac7f53b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 00:16:49,455] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58fe97ca-dc35-4b5d-947d-ae14ac7f53b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 00:16:49,468] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 00:16:49,468] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 00:16:49,468] [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
Treponema porcinum	strain=ATCC BAA-908	GCA_900167145.1	261392	261392	type	True	77.6642	102	810	95	below_threshold
Treponema rectale	strain=DSM 103679	GCA_014202035.1	744512	744512	suspected-type	True	76.8936	98	810	95	below_threshold
Treponema berlinense	strain=ATCC BAA-909	GCA_900167025.1	225004	225004	type	True	76.717	74	810	95	below_threshold
Treponema ruminis	strain=DSM 103462	GCA_014201975.1	744515	744515	type	True	76.6653	63	810	95	below_threshold
Treponema peruense	strain=RCC2812	GCA_016117655.1	2787628	2787628	type	True	76.3794	54	810	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 00:16:49,470] [INFO] DFAST Taxonomy check result was written to GCA_024693045.1_ASM2469304v1_genomic.fna/tc_result.tsv
[2023-07-01 00:16:49,471] [INFO] ===== Taxonomy check completed =====
[2023-07-01 00:16:49,471] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 00:16:49,472] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58fe97ca-dc35-4b5d-947d-ae14ac7f53b0/dqc_reference/checkm_data
[2023-07-01 00:16:49,473] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 00:16:49,507] [INFO] Task started: CheckM
[2023-07-01 00:16:49,507] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024693045.1_ASM2469304v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024693045.1_ASM2469304v1_genomic.fna/checkm_input GCA_024693045.1_ASM2469304v1_genomic.fna/checkm_result
[2023-07-01 00:17:11,692] [INFO] Task succeeded: CheckM
[2023-07-01 00:17:11,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 00:17:11,712] [INFO] ===== Completeness check finished =====
[2023-07-01 00:17:11,712] [INFO] ===== Start GTDB Search =====
[2023-07-01 00:17:11,713] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024693045.1_ASM2469304v1_genomic.fna/markers.fasta)
[2023-07-01 00:17:11,713] [INFO] Task started: Blastn
[2023-07-01 00:17:11,713] [INFO] Running command: blastn -query GCA_024693045.1_ASM2469304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58fe97ca-dc35-4b5d-947d-ae14ac7f53b0/dqc_reference/reference_markers_gtdb.fasta -out GCA_024693045.1_ASM2469304v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 00:17:12,476] [INFO] Task succeeded: Blastn
[2023-07-01 00:17:12,497] [INFO] Selected 20 target genomes.
[2023-07-01 00:17:12,497] [INFO] Target genome list was writen to GCA_024693045.1_ASM2469304v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 00:17:12,505] [INFO] Task started: fastANI
[2023-07-01 00:17:12,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e0fcaf5-b3c2-4df4-84c1-aa3680edc08c/GCA_024693045.1_ASM2469304v1_genomic.fna.gz --refList GCA_024693045.1_ASM2469304v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024693045.1_ASM2469304v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 00:17:21,223] [INFO] Task succeeded: fastANI
[2023-07-01 00:17:21,244] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 00:17:21,244] [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
GCA_017392945.1	s__Treponema_D sp017392945	79.8101	264	810	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017381365.1	s__Treponema_D sp017381365	79.4376	269	810	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.14	97.14	0.75	0.75	2	-
GCA_017390125.1	s__Treponema_D sp017390125	78.9701	215	810	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017386165.1	s__Treponema_D sp017386165	78.7181	170	810	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797305.1	s__Treponema_D sp902797305	78.4158	182	810	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002395155.1	s__Treponema_D sp002395155	78.2423	139	810	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.78	97.65	0.86	0.82	3	-
GCF_000619925.1	s__Treponema_D sp000619925	78.1932	129	810	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541945.1	s__Treponema_D sp900541945	78.1728	134	810	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.94	97.90	0.88	0.87	3	-
GCF_000421345.1	s__Treponema_D bryantii_B	78.0448	113	810	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017550685.1	s__Treponema_D sp017550685	77.919	83	810	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002478955.1	s__Treponema_D sp002478955	77.9097	149	810	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.79	97.79	0.82	0.82	2	-
GCA_900769325.1	s__Treponema_D sp900769325	77.747	117	810	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167145.1	s__Treponema_D porcinum	77.6964	101	810	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.53	96.24	0.92	0.88	5	-
GCA_900317625.1	s__Treponema_D sp900317625	77.4733	172	810	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.21	99.03	0.90	0.87	4	-
GCA_016292805.1	s__Treponema_D sp016292805	77.4391	115	810	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.76	98.76	0.90	0.90	2	-
GCA_900769985.1	s__Treponema_D sp900769985	77.0169	92	810	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.33	98.33	0.87	0.87	2	-
GCA_900767955.1	s__Treponema_D sp900767955	76.9343	147	810	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.06	96.06	0.87	0.77	5	-
GCA_015061465.1	s__Treponema_D bryantii_D	76.9205	80	810	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.46	96.39	0.85	0.81	3	-
GCA_017553635.1	s__Treponema_D sp017553635	76.9055	98	810	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.74	98.74	0.94	0.94	2	-
GCF_014334335.1	s__Treponema_D sp014334335	76.5728	66	810	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 00:17:21,258] [INFO] GTDB search result was written to GCA_024693045.1_ASM2469304v1_genomic.fna/result_gtdb.tsv
[2023-07-01 00:17:21,259] [INFO] ===== GTDB Search completed =====
[2023-07-01 00:17:21,266] [INFO] DFAST_QC result json was written to GCA_024693045.1_ASM2469304v1_genomic.fna/dqc_result.json
[2023-07-01 00:17:21,266] [INFO] DFAST_QC completed!
[2023-07-01 00:17:21,266] [INFO] Total running time: 0h0m49s