[2023-06-28 10:15:24,885] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:15:24,887] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:15:24,887] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1e6c7f3-23b6-4d04-9014-ba104839f77a/dqc_reference
[2023-06-28 10:15:26,146] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:15:26,147] [INFO] Task started: Prodigal
[2023-06-28 10:15:26,148] [INFO] Running command: gunzip -c /var/lib/cwl/stg1cbfb7d7-e6de-4545-8378-5cd32649b97b/GCA_002708935.1_ASM270893v1_genomic.fna.gz | prodigal -d GCA_002708935.1_ASM270893v1_genomic.fna/cds.fna -a GCA_002708935.1_ASM270893v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:15:32,732] [INFO] Task succeeded: Prodigal
[2023-06-28 10:15:32,732] [INFO] Task started: HMMsearch
[2023-06-28 10:15:32,732] [INFO] Running command: hmmsearch --tblout GCA_002708935.1_ASM270893v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1e6c7f3-23b6-4d04-9014-ba104839f77a/dqc_reference/reference_markers.hmm GCA_002708935.1_ASM270893v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:15:32,957] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:15:32,959] [INFO] Found 6/6 markers.
[2023-06-28 10:15:32,983] [INFO] Query marker FASTA was written to GCA_002708935.1_ASM270893v1_genomic.fna/markers.fasta
[2023-06-28 10:15:32,983] [INFO] Task started: Blastn
[2023-06-28 10:15:32,983] [INFO] Running command: blastn -query GCA_002708935.1_ASM270893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1e6c7f3-23b6-4d04-9014-ba104839f77a/dqc_reference/reference_markers.fasta -out GCA_002708935.1_ASM270893v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:15:33,580] [INFO] Task succeeded: Blastn
[2023-06-28 10:15:33,585] [INFO] Selected 17 target genomes.
[2023-06-28 10:15:33,586] [INFO] Target genome list was writen to GCA_002708935.1_ASM270893v1_genomic.fna/target_genomes.txt
[2023-06-28 10:15:33,589] [INFO] Task started: fastANI
[2023-06-28 10:15:33,589] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cbfb7d7-e6de-4545-8378-5cd32649b97b/GCA_002708935.1_ASM270893v1_genomic.fna.gz --refList GCA_002708935.1_ASM270893v1_genomic.fna/target_genomes.txt --output GCA_002708935.1_ASM270893v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:15:41,273] [INFO] Task succeeded: fastANI
[2023-06-28 10:15:41,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1e6c7f3-23b6-4d04-9014-ba104839f77a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:15:41,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1e6c7f3-23b6-4d04-9014-ba104839f77a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:15:41,284] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:15:41,285] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 10:15:41,285] [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 10:15:41,287] [INFO] DFAST Taxonomy check result was written to GCA_002708935.1_ASM270893v1_genomic.fna/tc_result.tsv
[2023-06-28 10:15:41,287] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:15:41,287] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:15:41,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1e6c7f3-23b6-4d04-9014-ba104839f77a/dqc_reference/checkm_data
[2023-06-28 10:15:41,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:15:41,333] [INFO] Task started: CheckM
[2023-06-28 10:15:41,333] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708935.1_ASM270893v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708935.1_ASM270893v1_genomic.fna/checkm_input GCA_002708935.1_ASM270893v1_genomic.fna/checkm_result
[2023-06-28 10:16:08,447] [INFO] Task succeeded: CheckM
[2023-06-28 10:16:08,449] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 10:16:08,473] [INFO] ===== Completeness check finished =====
[2023-06-28 10:16:08,473] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:16:08,473] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708935.1_ASM270893v1_genomic.fna/markers.fasta)
[2023-06-28 10:16:08,474] [INFO] Task started: Blastn
[2023-06-28 10:16:08,474] [INFO] Running command: blastn -query GCA_002708935.1_ASM270893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1e6c7f3-23b6-4d04-9014-ba104839f77a/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708935.1_ASM270893v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:16:09,190] [INFO] Task succeeded: Blastn
[2023-06-28 10:16:09,194] [INFO] Selected 14 target genomes.
[2023-06-28 10:16:09,194] [INFO] Target genome list was writen to GCA_002708935.1_ASM270893v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:16:09,204] [INFO] Task started: fastANI
[2023-06-28 10:16:09,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cbfb7d7-e6de-4545-8378-5cd32649b97b/GCA_002708935.1_ASM270893v1_genomic.fna.gz --refList GCA_002708935.1_ASM270893v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708935.1_ASM270893v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:16:16,919] [INFO] Task succeeded: fastANI
[2023-06-28 10:16:16,928] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:16:16,928] [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_002708935.1	s__MedAcidi-G3 sp002708935	100.0	789	790	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__MedAcidi-G3	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002713975.1	s__MedAcidi-G3 sp002713975	94.7182	468	790	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__MedAcidi-G3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004214275.1	s__MedAcidi-G3 sp004214275	94.2987	473	790	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__MedAcidi-G3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457435.1	s__MedAcidi-G3 sp002457435	88.6264	568	790	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__MedAcidi-G3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722565.1	s__MedAcidi-G3 sp002722565	78.3524	315	790	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__MedAcidi-G3	95.0	96.30	96.09	0.94	0.94	4	-
GCA_000817105.1	s__MedAcidi-G3 sp000817105	77.9533	236	790	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__MedAcidi-G3	95.0	99.01	98.43	0.87	0.75	11	-
GCA_002721305.1	s__UBA6944 sp002721305	77.5419	156	790	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA6944	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002296525.1	s__UBA6944 sp002296525	77.187	141	790	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA6944	95.0	98.78	97.54	0.95	0.91	12	-
GCA_012960315.1	s__UBA2110 sp012960315	76.618	107	790	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	99.85	99.85	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-28 10:16:16,930] [INFO] GTDB search result was written to GCA_002708935.1_ASM270893v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:16:16,931] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:16:16,935] [INFO] DFAST_QC result json was written to GCA_002708935.1_ASM270893v1_genomic.fna/dqc_result.json
[2023-06-28 10:16:16,935] [INFO] DFAST_QC completed!
[2023-06-28 10:16:16,936] [INFO] Total running time: 0h0m52s