[2023-06-13 10:49:57,881] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:49:57,885] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:49:57,885] [INFO] DQC Reference Directory: /var/lib/cwl/stg52ce93e3-82e9-4d9b-a412-01c4ba174ed7/dqc_reference
[2023-06-13 10:49:59,215] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:49:59,216] [INFO] Task started: Prodigal
[2023-06-13 10:49:59,217] [INFO] Running command: gunzip -c /var/lib/cwl/stg87064e2d-c5a6-400f-ba48-87fff1d26c74/GCA_022775475.1_ASM2277547v1_genomic.fna.gz | prodigal -d GCA_022775475.1_ASM2277547v1_genomic.fna/cds.fna -a GCA_022775475.1_ASM2277547v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:50:02,772] [INFO] Task succeeded: Prodigal
[2023-06-13 10:50:02,773] [INFO] Task started: HMMsearch
[2023-06-13 10:50:02,773] [INFO] Running command: hmmsearch --tblout GCA_022775475.1_ASM2277547v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52ce93e3-82e9-4d9b-a412-01c4ba174ed7/dqc_reference/reference_markers.hmm GCA_022775475.1_ASM2277547v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:50:02,987] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:50:02,989] [INFO] Found 6/6 markers.
[2023-06-13 10:50:03,014] [INFO] Query marker FASTA was written to GCA_022775475.1_ASM2277547v1_genomic.fna/markers.fasta
[2023-06-13 10:50:03,015] [INFO] Task started: Blastn
[2023-06-13 10:50:03,015] [INFO] Running command: blastn -query GCA_022775475.1_ASM2277547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52ce93e3-82e9-4d9b-a412-01c4ba174ed7/dqc_reference/reference_markers.fasta -out GCA_022775475.1_ASM2277547v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:50:03,560] [INFO] Task succeeded: Blastn
[2023-06-13 10:50:03,564] [INFO] Selected 10 target genomes.
[2023-06-13 10:50:03,564] [INFO] Target genome list was writen to GCA_022775475.1_ASM2277547v1_genomic.fna/target_genomes.txt
[2023-06-13 10:50:03,565] [INFO] Task started: fastANI
[2023-06-13 10:50:03,565] [INFO] Running command: fastANI --query /var/lib/cwl/stg87064e2d-c5a6-400f-ba48-87fff1d26c74/GCA_022775475.1_ASM2277547v1_genomic.fna.gz --refList GCA_022775475.1_ASM2277547v1_genomic.fna/target_genomes.txt --output GCA_022775475.1_ASM2277547v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:50:08,972] [INFO] Task succeeded: fastANI
[2023-06-13 10:50:08,973] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52ce93e3-82e9-4d9b-a412-01c4ba174ed7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:50:08,973] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52ce93e3-82e9-4d9b-a412-01c4ba174ed7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:50:08,980] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 10:50:08,980] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 10:50:08,980] [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	97.0552	488	497	95	conclusive
Treponema peruense	strain=RCC2812	GCA_016117655.1	2787628	2787628	type	True	76.5598	54	497	95	below_threshold
Treponema succinifaciens	strain=DSM 2489	GCA_000195275.1	167	167	type	True	75.8753	59	497	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 10:50:08,982] [INFO] DFAST Taxonomy check result was written to GCA_022775475.1_ASM2277547v1_genomic.fna/tc_result.tsv
[2023-06-13 10:50:08,983] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:50:08,983] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:50:08,984] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52ce93e3-82e9-4d9b-a412-01c4ba174ed7/dqc_reference/checkm_data
[2023-06-13 10:50:08,985] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:50:09,008] [INFO] Task started: CheckM
[2023-06-13 10:50:09,008] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022775475.1_ASM2277547v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022775475.1_ASM2277547v1_genomic.fna/checkm_input GCA_022775475.1_ASM2277547v1_genomic.fna/checkm_result
[2023-06-13 10:50:27,742] [INFO] Task succeeded: CheckM
[2023-06-13 10:50:27,743] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 10:50:27,768] [INFO] ===== Completeness check finished =====
[2023-06-13 10:50:27,769] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:50:27,769] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022775475.1_ASM2277547v1_genomic.fna/markers.fasta)
[2023-06-13 10:50:27,769] [INFO] Task started: Blastn
[2023-06-13 10:50:27,770] [INFO] Running command: blastn -query GCA_022775475.1_ASM2277547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52ce93e3-82e9-4d9b-a412-01c4ba174ed7/dqc_reference/reference_markers_gtdb.fasta -out GCA_022775475.1_ASM2277547v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:50:28,562] [INFO] Task succeeded: Blastn
[2023-06-13 10:50:28,567] [INFO] Selected 19 target genomes.
[2023-06-13 10:50:28,567] [INFO] Target genome list was writen to GCA_022775475.1_ASM2277547v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:50:28,596] [INFO] Task started: fastANI
[2023-06-13 10:50:28,597] [INFO] Running command: fastANI --query /var/lib/cwl/stg87064e2d-c5a6-400f-ba48-87fff1d26c74/GCA_022775475.1_ASM2277547v1_genomic.fna.gz --refList GCA_022775475.1_ASM2277547v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022775475.1_ASM2277547v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:50:36,405] [INFO] Task succeeded: fastANI
[2023-06-13 10:50:36,427] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 10:50:36,427] [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_900167145.1	s__Treponema_D porcinum	97.0552	488	497	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.53	96.24	0.92	0.88	5	conclusive
GCA_900541945.1	s__Treponema_D sp900541945	77.6307	121	497	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.94	97.90	0.88	0.87	3	-
GCA_002478955.1	s__Treponema_D sp002478955	77.4685	102	497	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_016297405.1	s__Treponema_D sp016297405	77.3952	78	497	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	77.3731	65	497	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_002437725.1	s__Treponema_D sp002437725	77.3465	96	497	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.48	98.76	0.93	0.84	13	-
GCA_900317625.1	s__Treponema_D sp900317625	77.237	105	497	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_017470605.1	s__Treponema_D sp017470605	77.1632	75	497	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_017392945.1	s__Treponema_D sp017392945	77.123	96	497	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_014803985.1	s__Treponema_D sp014803985	77.0413	67	497	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.03	97.81	0.86	0.80	8	-
GCA_905372235.1	s__Treponema_D sp905372235	76.5927	69	497	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	76.1498	51	497	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.37	99.37	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-06-13 10:50:36,430] [INFO] GTDB search result was written to GCA_022775475.1_ASM2277547v1_genomic.fna/result_gtdb.tsv
[2023-06-13 10:50:36,431] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:50:36,434] [INFO] DFAST_QC result json was written to GCA_022775475.1_ASM2277547v1_genomic.fna/dqc_result.json
[2023-06-13 10:50:36,434] [INFO] DFAST_QC completed!
[2023-06-13 10:50:36,434] [INFO] Total running time: 0h0m39s