[2024-01-24 10:47:06,585] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,591] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,591] [INFO] DQC Reference Directory: /var/lib/cwl/stg4736b4bf-1a3a-4154-bc67-80a575577a56/dqc_reference
[2024-01-24 10:47:12,680] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,825] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,826] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ef3cf67-c19b-4132-b310-e84de048d48a/GCF_004339085.1_ASM433908v1_genomic.fna.gz | prodigal -d GCF_004339085.1_ASM433908v1_genomic.fna/cds.fna -a GCF_004339085.1_ASM433908v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:21,813] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:21,814] [INFO] Task started: HMMsearch
[2024-01-24 10:47:21,814] [INFO] Running command: hmmsearch --tblout GCF_004339085.1_ASM433908v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4736b4bf-1a3a-4154-bc67-80a575577a56/dqc_reference/reference_markers.hmm GCF_004339085.1_ASM433908v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:22,078] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:22,085] [INFO] Found 6/6 markers.
[2024-01-24 10:47:22,114] [INFO] Query marker FASTA was written to GCF_004339085.1_ASM433908v1_genomic.fna/markers.fasta
[2024-01-24 10:47:22,114] [INFO] Task started: Blastn
[2024-01-24 10:47:22,115] [INFO] Running command: blastn -query GCF_004339085.1_ASM433908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4736b4bf-1a3a-4154-bc67-80a575577a56/dqc_reference/reference_markers.fasta -out GCF_004339085.1_ASM433908v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:22,949] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:22,955] [INFO] Selected 29 target genomes.
[2024-01-24 10:47:22,956] [INFO] Target genome list was writen to GCF_004339085.1_ASM433908v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:24,301] [INFO] Task started: fastANI
[2024-01-24 10:47:24,301] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ef3cf67-c19b-4132-b310-e84de048d48a/GCF_004339085.1_ASM433908v1_genomic.fna.gz --refList GCF_004339085.1_ASM433908v1_genomic.fna/target_genomes.txt --output GCF_004339085.1_ASM433908v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:44,672] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:44,672] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4736b4bf-1a3a-4154-bc67-80a575577a56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:44,673] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4736b4bf-1a3a-4154-bc67-80a575577a56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:44,680] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:44,680] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:44,680] [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
Thiogranum longum	strain=DSM 19610	GCA_004339085.1	1537524	1537524	type	True	100.0	972	972	95	conclusive
Acidihalobacter prosperus	strain=DSM 5130	GCA_000754095.2	160660	160660	type	True	77.1126	57	972	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.9046	122	972	95	below_threshold
Thiohalophilus thiocyanatoxydans	strain=DSM 16326	GCA_004366735.1	381308	381308	type	True	76.7872	69	972	95	below_threshold
Thioalkalivibrio versutus	strain=AL 2	GCA_001999325.1	106634	106634	type	True	76.4826	57	972	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	75.9586	52	972	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:44,682] [INFO] DFAST Taxonomy check result was written to GCF_004339085.1_ASM433908v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:44,682] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:44,683] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:44,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4736b4bf-1a3a-4154-bc67-80a575577a56/dqc_reference/checkm_data
[2024-01-24 10:47:44,684] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:44,720] [INFO] Task started: CheckM
[2024-01-24 10:47:44,720] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004339085.1_ASM433908v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004339085.1_ASM433908v1_genomic.fna/checkm_input GCF_004339085.1_ASM433908v1_genomic.fna/checkm_result
[2024-01-24 10:48:16,716] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:16,717] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:16,738] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:16,738] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:16,739] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004339085.1_ASM433908v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:16,739] [INFO] Task started: Blastn
[2024-01-24 10:48:16,739] [INFO] Running command: blastn -query GCF_004339085.1_ASM433908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4736b4bf-1a3a-4154-bc67-80a575577a56/dqc_reference/reference_markers_gtdb.fasta -out GCF_004339085.1_ASM433908v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:18,168] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:18,174] [INFO] Selected 18 target genomes.
[2024-01-24 10:48:18,174] [INFO] Target genome list was writen to GCF_004339085.1_ASM433908v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:18,500] [INFO] Task started: fastANI
[2024-01-24 10:48:18,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ef3cf67-c19b-4132-b310-e84de048d48a/GCF_004339085.1_ASM433908v1_genomic.fna.gz --refList GCF_004339085.1_ASM433908v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004339085.1_ASM433908v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:27,807] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:27,817] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:27,817] [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_004339085.1	s__Thiogranum longum	100.0	972	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015494295.1	s__Thiogranum sp015494295	79.4051	422	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	99.47	99.47	0.86	0.86	2	-
GCA_011374975.1	s__Thiogranum sp011374975	78.2655	239	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011371465.1	s__Thiogranum sp011371465	77.7157	234	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011321775.1	s__Thiogranum sp011321775	77.6534	188	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003230545.1	s__SZUA-186 sp003230545	77.0662	65	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA9214;f__UBA9214;g__SZUA-186	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	76.9805	85	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013343005.1	s__Reidiella endopervernicosa	76.7144	53	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCF-013343005;f__GCF-013343005;g__Reidiella	95.0	99.22	99.22	0.89	0.89	2	-
GCA_016214925.1	s__JAHJQQ01 sp016214925	76.4405	66	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JAHJQQ01;f__JAHJQQ01;g__JAHJQQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487785.1	s__S012-40 sp015487785	76.2195	60	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S140-43;f__S140-43;g__S012-40	95.0	99.75	99.72	0.93	0.92	3	-
GCA_905480065.1	s__UBA9214 sp905480065	76.1541	81	972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA9214;f__UBA9214;g__UBA9214	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:27,819] [INFO] GTDB search result was written to GCF_004339085.1_ASM433908v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:27,819] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:27,822] [INFO] DFAST_QC result json was written to GCF_004339085.1_ASM433908v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:27,822] [INFO] DFAST_QC completed!
[2024-01-24 10:48:27,822] [INFO] Total running time: 0h1m21s