[2024-01-25 19:36:20,698] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:36:20,699] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:36:20,699] [INFO] DQC Reference Directory: /var/lib/cwl/stg47f0df1c-a062-4d7b-9f81-d04c4f539513/dqc_reference
[2024-01-25 19:36:21,898] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:36:21,898] [INFO] Task started: Prodigal
[2024-01-25 19:36:21,899] [INFO] Running command: gunzip -c /var/lib/cwl/stg814c67d5-776c-4c97-b499-6bf39fc3ac4b/GCF_018069705.1_ASM1806970v1_genomic.fna.gz | prodigal -d GCF_018069705.1_ASM1806970v1_genomic.fna/cds.fna -a GCF_018069705.1_ASM1806970v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:36:28,583] [INFO] Task succeeded: Prodigal
[2024-01-25 19:36:28,584] [INFO] Task started: HMMsearch
[2024-01-25 19:36:28,584] [INFO] Running command: hmmsearch --tblout GCF_018069705.1_ASM1806970v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47f0df1c-a062-4d7b-9f81-d04c4f539513/dqc_reference/reference_markers.hmm GCF_018069705.1_ASM1806970v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:36:28,784] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:36:28,785] [INFO] Found 6/6 markers.
[2024-01-25 19:36:28,811] [INFO] Query marker FASTA was written to GCF_018069705.1_ASM1806970v1_genomic.fna/markers.fasta
[2024-01-25 19:36:28,811] [INFO] Task started: Blastn
[2024-01-25 19:36:28,811] [INFO] Running command: blastn -query GCF_018069705.1_ASM1806970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47f0df1c-a062-4d7b-9f81-d04c4f539513/dqc_reference/reference_markers.fasta -out GCF_018069705.1_ASM1806970v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:29,374] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:29,378] [INFO] Selected 22 target genomes.
[2024-01-25 19:36:29,378] [INFO] Target genome list was writen to GCF_018069705.1_ASM1806970v1_genomic.fna/target_genomes.txt
[2024-01-25 19:36:29,384] [INFO] Task started: fastANI
[2024-01-25 19:36:29,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg814c67d5-776c-4c97-b499-6bf39fc3ac4b/GCF_018069705.1_ASM1806970v1_genomic.fna.gz --refList GCF_018069705.1_ASM1806970v1_genomic.fna/target_genomes.txt --output GCF_018069705.1_ASM1806970v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:36:45,503] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:45,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47f0df1c-a062-4d7b-9f81-d04c4f539513/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:36:45,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47f0df1c-a062-4d7b-9f81-d04c4f539513/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:36:45,508] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:36:45,508] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:36:45,508] [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
Aminiphilus circumscriptus	strain=DSM 16581	GCA_000526375.1	290732	290732	type	True	77.8887	107	1036	95	below_threshold
Aminomonas paucivorans	strain=DSM 12260	GCA_000165795.1	81412	81412	type	True	77.8611	137	1036	95	below_threshold
Lentzea cavernae	strain=CGMCC 4.7367	GCA_014653695.1	2020703	2020703	type	True	74.5896	51	1036	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:36:45,509] [INFO] DFAST Taxonomy check result was written to GCF_018069705.1_ASM1806970v1_genomic.fna/tc_result.tsv
[2024-01-25 19:36:45,510] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:36:45,510] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:36:45,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47f0df1c-a062-4d7b-9f81-d04c4f539513/dqc_reference/checkm_data
[2024-01-25 19:36:45,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:36:45,542] [INFO] Task started: CheckM
[2024-01-25 19:36:45,542] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018069705.1_ASM1806970v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018069705.1_ASM1806970v1_genomic.fna/checkm_input GCF_018069705.1_ASM1806970v1_genomic.fna/checkm_result
[2024-01-25 19:37:10,061] [INFO] Task succeeded: CheckM
[2024-01-25 19:37:10,062] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:37:10,083] [INFO] ===== Completeness check finished =====
[2024-01-25 19:37:10,083] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:37:10,084] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018069705.1_ASM1806970v1_genomic.fna/markers.fasta)
[2024-01-25 19:37:10,084] [INFO] Task started: Blastn
[2024-01-25 19:37:10,084] [INFO] Running command: blastn -query GCF_018069705.1_ASM1806970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47f0df1c-a062-4d7b-9f81-d04c4f539513/dqc_reference/reference_markers_gtdb.fasta -out GCF_018069705.1_ASM1806970v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:10,931] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:10,935] [INFO] Selected 11 target genomes.
[2024-01-25 19:37:10,935] [INFO] Target genome list was writen to GCF_018069705.1_ASM1806970v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:37:10,987] [INFO] Task started: fastANI
[2024-01-25 19:37:10,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg814c67d5-776c-4c97-b499-6bf39fc3ac4b/GCF_018069705.1_ASM1806970v1_genomic.fna.gz --refList GCF_018069705.1_ASM1806970v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018069705.1_ASM1806970v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:37:17,338] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:17,343] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:37:17,344] [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_018398915.1	s__SV1-B22 sp018398915	99.2079	977	1036	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__SV1-B22;g__SV1-B22	95.0	99.20	99.20	0.94	0.94	2	conclusive
GCA_016756725.1	s__SV1-B22 sp016756725	82.3489	533	1036	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__SV1-B22;g__SV1-B22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018433595.1	s__SV1-B22 sp018433595	81.2979	481	1036	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__SV1-B22;g__SV1-B22	95.0	98.92	97.17	0.90	0.86	7	-
GCF_000165795.1	s__Aminomonas paucivorans	77.8873	134	1036	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Aminomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002425685.1	s__Aminiphilus sp002425685	77.2413	104	1036	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminiphilaceae;g__Aminiphilus	95.0	98.97	98.23	0.86	0.86	3	-
GCA_015657435.1	s__79-D21 sp015657435	77.2322	71	1036	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__79-D21;g__79-D21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002068355.1	s__JAAYLU01 sp002068355	76.0653	51	1036	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminobacteriaceae;g__JAAYLU01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:37:17,345] [INFO] GTDB search result was written to GCF_018069705.1_ASM1806970v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:37:17,346] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:37:17,348] [INFO] DFAST_QC result json was written to GCF_018069705.1_ASM1806970v1_genomic.fna/dqc_result.json
[2024-01-25 19:37:17,348] [INFO] DFAST_QC completed!
[2024-01-25 19:37:17,348] [INFO] Total running time: 0h0m57s