[2023-06-28 00:40:53,020] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:40:53,022] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:40:53,023] [INFO] DQC Reference Directory: /var/lib/cwl/stg551a4dc6-8fc4-48c1-af61-27e87644ee0e/dqc_reference
[2023-06-28 00:40:54,354] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:40:54,354] [INFO] Task started: Prodigal
[2023-06-28 00:40:54,355] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b025f58-5636-4438-9251-772fec0e855a/GCA_017965145.1_ASM1796514v1_genomic.fna.gz | prodigal -d GCA_017965145.1_ASM1796514v1_genomic.fna/cds.fna -a GCA_017965145.1_ASM1796514v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:40:59,036] [INFO] Task succeeded: Prodigal
[2023-06-28 00:40:59,036] [INFO] Task started: HMMsearch
[2023-06-28 00:40:59,036] [INFO] Running command: hmmsearch --tblout GCA_017965145.1_ASM1796514v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg551a4dc6-8fc4-48c1-af61-27e87644ee0e/dqc_reference/reference_markers.hmm GCA_017965145.1_ASM1796514v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:40:59,262] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:40:59,263] [INFO] Found 6/6 markers.
[2023-06-28 00:40:59,301] [INFO] Query marker FASTA was written to GCA_017965145.1_ASM1796514v1_genomic.fna/markers.fasta
[2023-06-28 00:40:59,302] [INFO] Task started: Blastn
[2023-06-28 00:40:59,302] [INFO] Running command: blastn -query GCA_017965145.1_ASM1796514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg551a4dc6-8fc4-48c1-af61-27e87644ee0e/dqc_reference/reference_markers.fasta -out GCA_017965145.1_ASM1796514v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:40:59,891] [INFO] Task succeeded: Blastn
[2023-06-28 00:40:59,897] [INFO] Selected 16 target genomes.
[2023-06-28 00:40:59,897] [INFO] Target genome list was writen to GCA_017965145.1_ASM1796514v1_genomic.fna/target_genomes.txt
[2023-06-28 00:40:59,904] [INFO] Task started: fastANI
[2023-06-28 00:40:59,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b025f58-5636-4438-9251-772fec0e855a/GCA_017965145.1_ASM1796514v1_genomic.fna.gz --refList GCA_017965145.1_ASM1796514v1_genomic.fna/target_genomes.txt --output GCA_017965145.1_ASM1796514v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:41:10,678] [INFO] Task succeeded: fastANI
[2023-06-28 00:41:10,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg551a4dc6-8fc4-48c1-af61-27e87644ee0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:41:10,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg551a4dc6-8fc4-48c1-af61-27e87644ee0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:41:10,680] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:41:10,681] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 00:41:10,681] [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
--------------------------------------------------------------------------------
[2023-06-28 00:41:10,683] [INFO] DFAST Taxonomy check result was written to GCA_017965145.1_ASM1796514v1_genomic.fna/tc_result.tsv
[2023-06-28 00:41:10,683] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:41:10,684] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:41:10,684] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg551a4dc6-8fc4-48c1-af61-27e87644ee0e/dqc_reference/checkm_data
[2023-06-28 00:41:10,687] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:41:10,713] [INFO] Task started: CheckM
[2023-06-28 00:41:10,713] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017965145.1_ASM1796514v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017965145.1_ASM1796514v1_genomic.fna/checkm_input GCA_017965145.1_ASM1796514v1_genomic.fna/checkm_result
[2023-06-28 00:41:33,041] [INFO] Task succeeded: CheckM
[2023-06-28 00:41:33,042] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 00:41:33,068] [INFO] ===== Completeness check finished =====
[2023-06-28 00:41:33,069] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:41:33,069] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017965145.1_ASM1796514v1_genomic.fna/markers.fasta)
[2023-06-28 00:41:33,070] [INFO] Task started: Blastn
[2023-06-28 00:41:33,070] [INFO] Running command: blastn -query GCA_017965145.1_ASM1796514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg551a4dc6-8fc4-48c1-af61-27e87644ee0e/dqc_reference/reference_markers_gtdb.fasta -out GCA_017965145.1_ASM1796514v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:41:33,895] [INFO] Task succeeded: Blastn
[2023-06-28 00:41:33,901] [INFO] Selected 10 target genomes.
[2023-06-28 00:41:33,901] [INFO] Target genome list was writen to GCA_017965145.1_ASM1796514v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:41:33,915] [INFO] Task started: fastANI
[2023-06-28 00:41:33,916] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b025f58-5636-4438-9251-772fec0e855a/GCA_017965145.1_ASM1796514v1_genomic.fna.gz --refList GCA_017965145.1_ASM1796514v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017965145.1_ASM1796514v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:41:38,736] [INFO] Task succeeded: fastANI
[2023-06-28 00:41:38,747] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 00:41:38,747] [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_017961705.1	s__Treponema_D sp017961705	95.8943	235	251	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.01	97.01	0.82	0.82	2	conclusive
GCA_017534445.1	s__Treponema_D sp017534445	92.6639	215	251	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.88	96.88	0.85	0.85	2	-
GCA_002373205.1	s__Treponema_D sp002373205	91.3445	208	251	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.79	96.03	0.78	0.67	16	-
GCA_002448445.1	s__Treponema_D sp002448445	91.0803	223	251	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.51	97.25	0.94	0.94	3	-
GCA_017614295.1	s__Treponema_D sp017614295	88.2757	197	251	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 00:41:38,750] [INFO] GTDB search result was written to GCA_017965145.1_ASM1796514v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:41:38,751] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:41:38,754] [INFO] DFAST_QC result json was written to GCA_017965145.1_ASM1796514v1_genomic.fna/dqc_result.json
[2023-06-28 00:41:38,754] [INFO] DFAST_QC completed!
[2023-06-28 00:41:38,754] [INFO] Total running time: 0h0m46s