[2024-01-24 12:30:05,385] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:05,387] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:05,387] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1d6d7e3-a8d5-4063-a565-c9640d21bf61/dqc_reference
[2024-01-24 12:30:07,245] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:07,248] [INFO] Task started: Prodigal
[2024-01-24 12:30:07,249] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b92d94b-46f8-425a-92e0-26fd7a22222b/GCF_016616095.2_ASM1661609v2_genomic.fna.gz | prodigal -d GCF_016616095.2_ASM1661609v2_genomic.fna/cds.fna -a GCF_016616095.2_ASM1661609v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:18,301] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:18,301] [INFO] Task started: HMMsearch
[2024-01-24 12:30:18,301] [INFO] Running command: hmmsearch --tblout GCF_016616095.2_ASM1661609v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1d6d7e3-a8d5-4063-a565-c9640d21bf61/dqc_reference/reference_markers.hmm GCF_016616095.2_ASM1661609v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:18,629] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:18,630] [INFO] Found 6/6 markers.
[2024-01-24 12:30:18,675] [INFO] Query marker FASTA was written to GCF_016616095.2_ASM1661609v2_genomic.fna/markers.fasta
[2024-01-24 12:30:18,675] [INFO] Task started: Blastn
[2024-01-24 12:30:18,676] [INFO] Running command: blastn -query GCF_016616095.2_ASM1661609v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1d6d7e3-a8d5-4063-a565-c9640d21bf61/dqc_reference/reference_markers.fasta -out GCF_016616095.2_ASM1661609v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:19,235] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:19,243] [INFO] Selected 14 target genomes.
[2024-01-24 12:30:19,244] [INFO] Target genome list was writen to GCF_016616095.2_ASM1661609v2_genomic.fna/target_genomes.txt
[2024-01-24 12:30:19,248] [INFO] Task started: fastANI
[2024-01-24 12:30:19,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b92d94b-46f8-425a-92e0-26fd7a22222b/GCF_016616095.2_ASM1661609v2_genomic.fna.gz --refList GCF_016616095.2_ASM1661609v2_genomic.fna/target_genomes.txt --output GCF_016616095.2_ASM1661609v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:30,955] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:30,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1d6d7e3-a8d5-4063-a565-c9640d21bf61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:30,955] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1d6d7e3-a8d5-4063-a565-c9640d21bf61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:30,960] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:30,961] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:30,961] [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
Breznakiella homolactica	strain=RmG30	GCA_016616095.2	2798577	2798577	type	True	100.0	1547	1548	95	conclusive
Brucepastera parasyntrophica	strain=RmG11	GCA_022376835.1	2880008	2880008	type	True	77.9438	69	1548	95	below_threshold
Leadbettera azotonutricia	strain=ZAS-9	GCA_000214355.1	150829	150829	type	True	76.9277	70	1548	95	below_threshold
Gracilinema caldarium	strain=DSM 7334	GCA_000219725.1	215591	215591	type	True	76.8246	73	1548	95	below_threshold
Treponema primitia	strain=ZAS-2	GCA_000214375.1	88058	88058	type	True	76.8117	128	1548	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:30,962] [INFO] DFAST Taxonomy check result was written to GCF_016616095.2_ASM1661609v2_genomic.fna/tc_result.tsv
[2024-01-24 12:30:30,962] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:30,962] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:30,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1d6d7e3-a8d5-4063-a565-c9640d21bf61/dqc_reference/checkm_data
[2024-01-24 12:30:30,963] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:31,007] [INFO] Task started: CheckM
[2024-01-24 12:30:31,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016616095.2_ASM1661609v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016616095.2_ASM1661609v2_genomic.fna/checkm_input GCF_016616095.2_ASM1661609v2_genomic.fna/checkm_result
[2024-01-24 12:31:04,423] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:04,424] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.59%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:04,447] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:04,447] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:04,448] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016616095.2_ASM1661609v2_genomic.fna/markers.fasta)
[2024-01-24 12:31:04,448] [INFO] Task started: Blastn
[2024-01-24 12:31:04,448] [INFO] Running command: blastn -query GCF_016616095.2_ASM1661609v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1d6d7e3-a8d5-4063-a565-c9640d21bf61/dqc_reference/reference_markers_gtdb.fasta -out GCF_016616095.2_ASM1661609v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:05,217] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:05,220] [INFO] Selected 27 target genomes.
[2024-01-24 12:31:05,220] [INFO] Target genome list was writen to GCF_016616095.2_ASM1661609v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:05,259] [INFO] Task started: fastANI
[2024-01-24 12:31:05,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b92d94b-46f8-425a-92e0-26fd7a22222b/GCF_016616095.2_ASM1661609v2_genomic.fna.gz --refList GCF_016616095.2_ASM1661609v2_genomic.fna/target_genomes_gtdb.txt --output GCF_016616095.2_ASM1661609v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:19,949] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:19,956] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:19,956] [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_016616095.1	s__Breznakiella homolactica	99.9999	1547	1548	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Termitinemataceae;g__Breznakiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000214375.1	s__Termitinema primitia	76.8117	128	1548	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Termitinemataceae;g__Termitinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000219725.1	s__Treponema_G caldarium	76.6799	73	1548	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Termitinemataceae;g__Treponema_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214355.1	s__Treponema_H azotonutricium	76.6246	68	1548	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Termitinemataceae;g__Treponema_H	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009782555.1	s__WRIV01 sp009782555	76.2682	54	1548	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Termitinemataceae;g__WRIV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343725.1	s__J25 sp004343725	76.165	53	1548	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Termitinemataceae;g__J25	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003527485.1	s__UBA12037 sp003527485	75.7624	69	1548	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Termitinemataceae;g__UBA12037	95.0	99.92	99.92	0.93	0.93	2	-
GCA_012517385.1	s__Treponema_G sp012517385	75.6711	70	1548	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Termitinemataceae;g__Treponema_G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:19,957] [INFO] GTDB search result was written to GCF_016616095.2_ASM1661609v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:19,957] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:19,960] [INFO] DFAST_QC result json was written to GCF_016616095.2_ASM1661609v2_genomic.fna/dqc_result.json
[2024-01-24 12:31:19,960] [INFO] DFAST_QC completed!
[2024-01-24 12:31:19,960] [INFO] Total running time: 0h1m15s