[2024-01-25 17:37:20,754] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:37:20,755] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:37:20,755] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7c96771-27fc-428e-9312-36f643a06a9e/dqc_reference
[2024-01-25 17:37:21,946] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:37:21,947] [INFO] Task started: Prodigal
[2024-01-25 17:37:21,947] [INFO] Running command: gunzip -c /var/lib/cwl/stga717e1e6-a0bf-4440-89f7-39e2db8244f8/GCF_026343955.1_ASM2634395v1_genomic.fna.gz | prodigal -d GCF_026343955.1_ASM2634395v1_genomic.fna/cds.fna -a GCF_026343955.1_ASM2634395v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:37:34,318] [INFO] Task succeeded: Prodigal
[2024-01-25 17:37:34,319] [INFO] Task started: HMMsearch
[2024-01-25 17:37:34,319] [INFO] Running command: hmmsearch --tblout GCF_026343955.1_ASM2634395v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7c96771-27fc-428e-9312-36f643a06a9e/dqc_reference/reference_markers.hmm GCF_026343955.1_ASM2634395v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:37:34,653] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:37:34,654] [INFO] Found 6/6 markers.
[2024-01-25 17:37:34,696] [INFO] Query marker FASTA was written to GCF_026343955.1_ASM2634395v1_genomic.fna/markers.fasta
[2024-01-25 17:37:34,697] [INFO] Task started: Blastn
[2024-01-25 17:37:34,697] [INFO] Running command: blastn -query GCF_026343955.1_ASM2634395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7c96771-27fc-428e-9312-36f643a06a9e/dqc_reference/reference_markers.fasta -out GCF_026343955.1_ASM2634395v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:35,785] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:35,787] [INFO] Selected 15 target genomes.
[2024-01-25 17:37:35,788] [INFO] Target genome list was writen to GCF_026343955.1_ASM2634395v1_genomic.fna/target_genomes.txt
[2024-01-25 17:37:35,823] [INFO] Task started: fastANI
[2024-01-25 17:37:35,823] [INFO] Running command: fastANI --query /var/lib/cwl/stga717e1e6-a0bf-4440-89f7-39e2db8244f8/GCF_026343955.1_ASM2634395v1_genomic.fna.gz --refList GCF_026343955.1_ASM2634395v1_genomic.fna/target_genomes.txt --output GCF_026343955.1_ASM2634395v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:37:51,683] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:51,683] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7c96771-27fc-428e-9312-36f643a06a9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:37:51,683] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7c96771-27fc-428e-9312-36f643a06a9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:37:51,693] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:37:51,693] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:37:51,693] [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
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	86.2011	1173	1623	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	86.1845	1200	1623	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	80.8969	860	1623	95	below_threshold
Kaistia soli	strain=DSM 19436	GCA_900129325.1	446684	446684	type	True	80.3155	733	1623	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	78.8019	436	1623	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	78.2652	507	1623	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	78.2089	424	1623	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	78.1143	456	1623	95	below_threshold
Bauldia litoralis	strain=ATCC 35022	GCA_900104485.1	665467	665467	type	True	78.064	460	1623	95	below_threshold
Aminobacter aminovorans	strain=DSM 7048	GCA_004341645.1	83263	83263	type	True	77.8832	414	1623	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	77.7815	388	1623	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	77.486	291	1623	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	77.4611	275	1623	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	77.2742	372	1623	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	77.2558	363	1623	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:37:51,700] [INFO] DFAST Taxonomy check result was written to GCF_026343955.1_ASM2634395v1_genomic.fna/tc_result.tsv
[2024-01-25 17:37:51,701] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:37:51,701] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:37:51,701] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7c96771-27fc-428e-9312-36f643a06a9e/dqc_reference/checkm_data
[2024-01-25 17:37:51,702] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:37:51,754] [INFO] Task started: CheckM
[2024-01-25 17:37:51,754] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026343955.1_ASM2634395v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026343955.1_ASM2634395v1_genomic.fna/checkm_input GCF_026343955.1_ASM2634395v1_genomic.fna/checkm_result
[2024-01-25 17:38:29,961] [INFO] Task succeeded: CheckM
[2024-01-25 17:38:29,963] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:38:29,984] [INFO] ===== Completeness check finished =====
[2024-01-25 17:38:29,985] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:38:29,986] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026343955.1_ASM2634395v1_genomic.fna/markers.fasta)
[2024-01-25 17:38:29,986] [INFO] Task started: Blastn
[2024-01-25 17:38:29,986] [INFO] Running command: blastn -query GCF_026343955.1_ASM2634395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7c96771-27fc-428e-9312-36f643a06a9e/dqc_reference/reference_markers_gtdb.fasta -out GCF_026343955.1_ASM2634395v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:32,220] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:32,223] [INFO] Selected 8 target genomes.
[2024-01-25 17:38:32,224] [INFO] Target genome list was writen to GCF_026343955.1_ASM2634395v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:38:32,228] [INFO] Task started: fastANI
[2024-01-25 17:38:32,228] [INFO] Running command: fastANI --query /var/lib/cwl/stga717e1e6-a0bf-4440-89f7-39e2db8244f8/GCF_026343955.1_ASM2634395v1_genomic.fna.gz --refList GCF_026343955.1_ASM2634395v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026343955.1_ASM2634395v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:38:41,949] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:41,955] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:38:41,956] [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
GCA_017305815.1	s__Kaistia sp017305815	87.5761	844	1623	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629525.1	s__Kaistia sp016629525	86.2922	1178	1623	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380505.1	s__Kaistia granuli	86.2212	1171	1623	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423225.1	s__Kaistia adipata	86.1903	1199	1623	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307955.1	s__Kaistia sp017307955	81.0324	817	1623	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196455.1	s__Kaistia hirudinis	80.8624	863	1623	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	96.80	96.80	0.96	0.96	2	-
GCF_900129325.1	s__Kaistia soli	80.306	735	1623	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199915.1	s__Prosthecomicrobium pneumaticum	79.7559	718	1623	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Prosthecomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:38:41,957] [INFO] GTDB search result was written to GCF_026343955.1_ASM2634395v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:38:41,957] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:38:41,960] [INFO] DFAST_QC result json was written to GCF_026343955.1_ASM2634395v1_genomic.fna/dqc_result.json
[2024-01-25 17:38:41,960] [INFO] DFAST_QC completed!
[2024-01-25 17:38:41,960] [INFO] Total running time: 0h1m21s