[2023-06-27 13:43:31,355] [INFO] DFAST_QC pipeline started.
[2023-06-27 13:43:31,358] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 13:43:31,358] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e31085f-6198-410c-bcd2-3c2509930763/dqc_reference
[2023-06-27 13:43:32,682] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 13:43:32,683] [INFO] Task started: Prodigal
[2023-06-27 13:43:32,684] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb7b35b4-78fd-4b9e-8b59-219327c4e615/GCA_002385485.1_ASM238548v1_genomic.fna.gz | prodigal -d GCA_002385485.1_ASM238548v1_genomic.fna/cds.fna -a GCA_002385485.1_ASM238548v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 13:43:36,600] [INFO] Task succeeded: Prodigal
[2023-06-27 13:43:36,601] [INFO] Task started: HMMsearch
[2023-06-27 13:43:36,601] [INFO] Running command: hmmsearch --tblout GCA_002385485.1_ASM238548v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e31085f-6198-410c-bcd2-3c2509930763/dqc_reference/reference_markers.hmm GCA_002385485.1_ASM238548v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 13:43:36,821] [INFO] Task succeeded: HMMsearch
[2023-06-27 13:43:36,823] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcb7b35b4-78fd-4b9e-8b59-219327c4e615/GCA_002385485.1_ASM238548v1_genomic.fna.gz]
[2023-06-27 13:43:36,860] [INFO] Query marker FASTA was written to GCA_002385485.1_ASM238548v1_genomic.fna/markers.fasta
[2023-06-27 13:43:36,861] [INFO] Task started: Blastn
[2023-06-27 13:43:36,861] [INFO] Running command: blastn -query GCA_002385485.1_ASM238548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e31085f-6198-410c-bcd2-3c2509930763/dqc_reference/reference_markers.fasta -out GCA_002385485.1_ASM238548v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 13:43:37,516] [INFO] Task succeeded: Blastn
[2023-06-27 13:43:37,520] [INFO] Selected 10 target genomes.
[2023-06-27 13:43:37,520] [INFO] Target genome list was writen to GCA_002385485.1_ASM238548v1_genomic.fna/target_genomes.txt
[2023-06-27 13:43:37,524] [INFO] Task started: fastANI
[2023-06-27 13:43:37,524] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb7b35b4-78fd-4b9e-8b59-219327c4e615/GCA_002385485.1_ASM238548v1_genomic.fna.gz --refList GCA_002385485.1_ASM238548v1_genomic.fna/target_genomes.txt --output GCA_002385485.1_ASM238548v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 13:43:43,559] [INFO] Task succeeded: fastANI
[2023-06-27 13:43:43,560] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e31085f-6198-410c-bcd2-3c2509930763/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 13:43:43,560] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e31085f-6198-410c-bcd2-3c2509930763/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 13:43:43,565] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2023-06-27 13:43:43,566] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-27 13:43:43,566] [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
Acetomicrobium hydrogeniformans	strain=OS1	GCA_000160455.2	649746	649746	type	True	95.5851	432	478	95	inconclusive
Acetomicrobium thermoterrenum	strain=DSM 13490	GCA_900107215.1	1120986	1120986	type	True	95.5049	405	478	95	inconclusive
--------------------------------------------------------------------------------
[2023-06-27 13:43:43,569] [INFO] DFAST Taxonomy check result was written to GCA_002385485.1_ASM238548v1_genomic.fna/tc_result.tsv
[2023-06-27 13:43:43,570] [INFO] ===== Taxonomy check completed =====
[2023-06-27 13:43:43,570] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 13:43:43,570] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e31085f-6198-410c-bcd2-3c2509930763/dqc_reference/checkm_data
[2023-06-27 13:43:43,571] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 13:43:43,594] [INFO] Task started: CheckM
[2023-06-27 13:43:43,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002385485.1_ASM238548v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002385485.1_ASM238548v1_genomic.fna/checkm_input GCA_002385485.1_ASM238548v1_genomic.fna/checkm_result
[2023-06-27 13:44:03,198] [INFO] Task succeeded: CheckM
[2023-06-27 13:44:03,199] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-27 13:44:03,222] [INFO] ===== Completeness check finished =====
[2023-06-27 13:44:03,222] [INFO] ===== Start GTDB Search =====
[2023-06-27 13:44:03,223] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002385485.1_ASM238548v1_genomic.fna/markers.fasta)
[2023-06-27 13:44:03,223] [INFO] Task started: Blastn
[2023-06-27 13:44:03,223] [INFO] Running command: blastn -query GCA_002385485.1_ASM238548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e31085f-6198-410c-bcd2-3c2509930763/dqc_reference/reference_markers_gtdb.fasta -out GCA_002385485.1_ASM238548v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 13:44:04,168] [INFO] Task succeeded: Blastn
[2023-06-27 13:44:04,172] [INFO] Selected 10 target genomes.
[2023-06-27 13:44:04,173] [INFO] Target genome list was writen to GCA_002385485.1_ASM238548v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 13:44:04,181] [INFO] Task started: fastANI
[2023-06-27 13:44:04,181] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb7b35b4-78fd-4b9e-8b59-219327c4e615/GCA_002385485.1_ASM238548v1_genomic.fna.gz --refList GCA_002385485.1_ASM238548v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002385485.1_ASM238548v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 13:44:07,959] [INFO] Task succeeded: fastANI
[2023-06-27 13:44:07,968] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 13:44:07,968] [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_002385485.1	s__Acetomicrobium sp002385485	100.0	472	478	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Acetomicrobiaceae;g__Acetomicrobium	96.1959	98.11	96.55	0.85	0.83	3	conclusive
GCA_002433005.1	s__Acetomicrobium sp002433005	96.1959	399	478	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Acetomicrobiaceae;g__Acetomicrobium	96.2563	N/A	N/A	N/A	N/A	1	-
GCF_000160455.2	s__Acetomicrobium hydrogeniformans	95.5851	432	478	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Acetomicrobiaceae;g__Acetomicrobium	96.8272	100.00	100.00	1.00	1.00	2	-
GCF_900107215.1	s__Acetomicrobium thermoterrenum	95.5049	405	478	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Acetomicrobiaceae;g__Acetomicrobium	96.8272	97.07	97.07	0.93	0.93	2	-
GCA_012518015.1	s__Acetomicrobium sp012518015	78.9401	75	478	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Acetomicrobiaceae;g__Acetomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 13:44:07,970] [INFO] GTDB search result was written to GCA_002385485.1_ASM238548v1_genomic.fna/result_gtdb.tsv
[2023-06-27 13:44:07,971] [INFO] ===== GTDB Search completed =====
[2023-06-27 13:44:07,974] [INFO] DFAST_QC result json was written to GCA_002385485.1_ASM238548v1_genomic.fna/dqc_result.json
[2023-06-27 13:44:07,974] [INFO] DFAST_QC completed!
[2023-06-27 13:44:07,974] [INFO] Total running time: 0h0m37s