[2023-06-30 22:22:18,109] [INFO] DFAST_QC pipeline started.
[2023-06-30 22:22:18,112] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 22:22:18,112] [INFO] DQC Reference Directory: /var/lib/cwl/stge4e3feec-95d8-4917-87cd-fe03f82036bf/dqc_reference
[2023-06-30 22:22:20,467] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 22:22:20,468] [INFO] Task started: Prodigal
[2023-06-30 22:22:20,468] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c6b172a-7a6c-4ea7-aa22-843df0e978b8/GCA_024682965.1_ASM2468296v1_genomic.fna.gz | prodigal -d GCA_024682965.1_ASM2468296v1_genomic.fna/cds.fna -a GCA_024682965.1_ASM2468296v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 22:22:26,651] [INFO] Task succeeded: Prodigal
[2023-06-30 22:22:26,652] [INFO] Task started: HMMsearch
[2023-06-30 22:22:26,652] [INFO] Running command: hmmsearch --tblout GCA_024682965.1_ASM2468296v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4e3feec-95d8-4917-87cd-fe03f82036bf/dqc_reference/reference_markers.hmm GCA_024682965.1_ASM2468296v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 22:22:26,914] [INFO] Task succeeded: HMMsearch
[2023-06-30 22:22:26,915] [INFO] Found 6/6 markers.
[2023-06-30 22:22:26,948] [INFO] Query marker FASTA was written to GCA_024682965.1_ASM2468296v1_genomic.fna/markers.fasta
[2023-06-30 22:22:26,948] [INFO] Task started: Blastn
[2023-06-30 22:22:26,948] [INFO] Running command: blastn -query GCA_024682965.1_ASM2468296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4e3feec-95d8-4917-87cd-fe03f82036bf/dqc_reference/reference_markers.fasta -out GCA_024682965.1_ASM2468296v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:22:27,575] [INFO] Task succeeded: Blastn
[2023-06-30 22:22:27,580] [INFO] Selected 14 target genomes.
[2023-06-30 22:22:27,580] [INFO] Target genome list was writen to GCA_024682965.1_ASM2468296v1_genomic.fna/target_genomes.txt
[2023-06-30 22:22:27,582] [INFO] Task started: fastANI
[2023-06-30 22:22:27,582] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c6b172a-7a6c-4ea7-aa22-843df0e978b8/GCA_024682965.1_ASM2468296v1_genomic.fna.gz --refList GCA_024682965.1_ASM2468296v1_genomic.fna/target_genomes.txt --output GCA_024682965.1_ASM2468296v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 22:22:35,140] [INFO] Task succeeded: fastANI
[2023-06-30 22:22:35,140] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4e3feec-95d8-4917-87cd-fe03f82036bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 22:22:35,141] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4e3feec-95d8-4917-87cd-fe03f82036bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 22:22:35,149] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 22:22:35,149] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 22:22:35,149] [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 ruminis	strain=DSM 103462	GCA_014201975.1	744515	744515	type	True	77.6719	51	1078	95	below_threshold
Treponema berlinense	strain=ATCC BAA-909	GCA_900167025.1	225004	225004	type	True	76.8733	73	1078	95	below_threshold
Treponema porcinum	strain=ATCC BAA-908	GCA_900167145.1	261392	261392	type	True	76.7495	61	1078	95	below_threshold
Treponema rectale	strain=DSM 103679	GCA_014202035.1	744512	744512	suspected-type	True	76.4381	94	1078	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 22:22:35,151] [INFO] DFAST Taxonomy check result was written to GCA_024682965.1_ASM2468296v1_genomic.fna/tc_result.tsv
[2023-06-30 22:22:35,152] [INFO] ===== Taxonomy check completed =====
[2023-06-30 22:22:35,152] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 22:22:35,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4e3feec-95d8-4917-87cd-fe03f82036bf/dqc_reference/checkm_data
[2023-06-30 22:22:35,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 22:22:35,194] [INFO] Task started: CheckM
[2023-06-30 22:22:35,194] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024682965.1_ASM2468296v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024682965.1_ASM2468296v1_genomic.fna/checkm_input GCA_024682965.1_ASM2468296v1_genomic.fna/checkm_result
[2023-06-30 22:23:00,190] [INFO] Task succeeded: CheckM
[2023-06-30 22:23:00,191] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.94%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 22:23:00,214] [INFO] ===== Completeness check finished =====
[2023-06-30 22:23:00,214] [INFO] ===== Start GTDB Search =====
[2023-06-30 22:23:00,214] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024682965.1_ASM2468296v1_genomic.fna/markers.fasta)
[2023-06-30 22:23:00,215] [INFO] Task started: Blastn
[2023-06-30 22:23:00,215] [INFO] Running command: blastn -query GCA_024682965.1_ASM2468296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4e3feec-95d8-4917-87cd-fe03f82036bf/dqc_reference/reference_markers_gtdb.fasta -out GCA_024682965.1_ASM2468296v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:23:00,981] [INFO] Task succeeded: Blastn
[2023-06-30 22:23:00,986] [INFO] Selected 24 target genomes.
[2023-06-30 22:23:00,986] [INFO] Target genome list was writen to GCA_024682965.1_ASM2468296v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 22:23:01,019] [INFO] Task started: fastANI
[2023-06-30 22:23:01,019] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c6b172a-7a6c-4ea7-aa22-843df0e978b8/GCA_024682965.1_ASM2468296v1_genomic.fna.gz --refList GCA_024682965.1_ASM2468296v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024682965.1_ASM2468296v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 22:23:13,880] [INFO] Task succeeded: fastANI
[2023-06-30 22:23:13,899] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 22:23:13,899] [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_017940255.1	s__Treponema_D sp017940255	79.217	270	1078	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	79.196	278	1078	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.78	97.65	0.86	0.82	3	-
GCA_017470605.1	s__Treponema_D sp017470605	78.8632	285	1078	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_900111035.1	s__Treponema_D bryantii_C	78.4667	277	1078	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_900113965.1	s__Treponema_D bryantii_A	78.4389	259	1078	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_016293915.1	s__Treponema_D sp016293915	78.3462	247	1078	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.46	98.17	0.88	0.85	4	-
GCA_902789325.1	s__Treponema_D sp902789325	78.3008	256	1078	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_004554075.1	s__Treponema_D sp004554075	78.1963	249	1078	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_902802305.1	s__Treponema_D sp902802305	78.1651	294	1078	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_018385315.1	s__Treponema_D sp018385315	78.0958	231	1078	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_017962415.1	s__Treponema_D sp017962415	78.0369	206	1078	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_017617145.1	s__Treponema_D sp017617145	77.918	217	1078	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_016297805.1	s__Treponema_D sp016297805	77.8635	223	1078	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_016290335.1	s__Treponema_D sp016290335	77.7912	234	1078	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_017551545.1	s__Treponema_D sp017551545	77.7433	198	1078	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_016292805.1	s__Treponema_D sp016292805	77.7172	185	1078	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_017619795.1	s__Treponema_D sp017619795	77.6988	215	1078	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_017963165.1	s__Treponema_D sp017963165	77.5812	230	1078	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_002350445.1	s__Treponema_D sp002350445	77.5127	185	1078	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.37	99.37	0.88	0.88	2	-
GCA_900769975.1	s__Treponema_D sp900769975	77.3348	193	1078	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_018385415.1	s__Treponema_D sp018385415	77.2485	93	1078	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_017521105.1	s__Treponema_D sp017521105	77.0968	181	1078	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.98	96.98	0.70	0.70	2	-
GCA_017622055.1	s__Treponema_D sp017622055	76.9107	148	1078	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_015061465.1	s__Treponema_D bryantii_D	76.8643	157	1078	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.46	96.39	0.85	0.81	3	-
--------------------------------------------------------------------------------
[2023-06-30 22:23:13,901] [INFO] GTDB search result was written to GCA_024682965.1_ASM2468296v1_genomic.fna/result_gtdb.tsv
[2023-06-30 22:23:13,902] [INFO] ===== GTDB Search completed =====
[2023-06-30 22:23:13,906] [INFO] DFAST_QC result json was written to GCA_024682965.1_ASM2468296v1_genomic.fna/dqc_result.json
[2023-06-30 22:23:13,906] [INFO] DFAST_QC completed!
[2023-06-30 22:23:13,906] [INFO] Total running time: 0h0m56s