[2024-01-24 13:31:33,454] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:33,461] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:33,461] [INFO] DQC Reference Directory: /var/lib/cwl/stg250e59b3-e2b4-431c-8f42-c9f4aec6c31e/dqc_reference
[2024-01-24 13:31:34,804] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:34,805] [INFO] Task started: Prodigal
[2024-01-24 13:31:34,805] [INFO] Running command: gunzip -c /var/lib/cwl/stg132263a2-6355-4e92-b75c-99901eee14c7/GCF_026344055.1_ASM2634405v1_genomic.fna.gz | prodigal -d GCF_026344055.1_ASM2634405v1_genomic.fna/cds.fna -a GCF_026344055.1_ASM2634405v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:47,814] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:47,815] [INFO] Task started: HMMsearch
[2024-01-24 13:31:47,815] [INFO] Running command: hmmsearch --tblout GCF_026344055.1_ASM2634405v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg250e59b3-e2b4-431c-8f42-c9f4aec6c31e/dqc_reference/reference_markers.hmm GCF_026344055.1_ASM2634405v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:48,103] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:48,104] [INFO] Found 6/6 markers.
[2024-01-24 13:31:48,147] [INFO] Query marker FASTA was written to GCF_026344055.1_ASM2634405v1_genomic.fna/markers.fasta
[2024-01-24 13:31:48,148] [INFO] Task started: Blastn
[2024-01-24 13:31:48,148] [INFO] Running command: blastn -query GCF_026344055.1_ASM2634405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg250e59b3-e2b4-431c-8f42-c9f4aec6c31e/dqc_reference/reference_markers.fasta -out GCF_026344055.1_ASM2634405v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:49,275] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:49,278] [INFO] Selected 15 target genomes.
[2024-01-24 13:31:49,279] [INFO] Target genome list was writen to GCF_026344055.1_ASM2634405v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:49,286] [INFO] Task started: fastANI
[2024-01-24 13:31:49,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg132263a2-6355-4e92-b75c-99901eee14c7/GCF_026344055.1_ASM2634405v1_genomic.fna.gz --refList GCF_026344055.1_ASM2634405v1_genomic.fna/target_genomes.txt --output GCF_026344055.1_ASM2634405v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:04,227] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:04,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg250e59b3-e2b4-431c-8f42-c9f4aec6c31e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:04,228] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg250e59b3-e2b4-431c-8f42-c9f4aec6c31e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:04,241] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:32:04,241] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:32:04,241] [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 soli	strain=DSM 19436	GCA_900129325.1	446684	446684	type	True	82.6135	1088	1525	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	81.9737	971	1525	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	81.5776	813	1525	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	81.1339	782	1525	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	78.3604	527	1525	95	below_threshold
Bauldia litoralis	strain=ATCC 35022	GCA_900104485.1	665467	665467	type	True	77.9961	472	1525	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.9932	498	1525	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	77.8606	440	1525	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	77.7461	386	1525	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.6641	479	1525	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	77.5982	465	1525	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	77.5658	346	1525	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	77.5514	322	1525	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	77.1228	299	1525	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.9152	480	1525	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:04,243] [INFO] DFAST Taxonomy check result was written to GCF_026344055.1_ASM2634405v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:04,243] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:04,243] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:04,244] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg250e59b3-e2b4-431c-8f42-c9f4aec6c31e/dqc_reference/checkm_data
[2024-01-24 13:32:04,245] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:04,295] [INFO] Task started: CheckM
[2024-01-24 13:32:04,295] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026344055.1_ASM2634405v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026344055.1_ASM2634405v1_genomic.fna/checkm_input GCF_026344055.1_ASM2634405v1_genomic.fna/checkm_result
[2024-01-24 13:32:49,276] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:49,277] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:49,295] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:49,295] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:49,295] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026344055.1_ASM2634405v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:49,296] [INFO] Task started: Blastn
[2024-01-24 13:32:49,296] [INFO] Running command: blastn -query GCF_026344055.1_ASM2634405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg250e59b3-e2b4-431c-8f42-c9f4aec6c31e/dqc_reference/reference_markers_gtdb.fasta -out GCF_026344055.1_ASM2634405v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:51,547] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:51,551] [INFO] Selected 8 target genomes.
[2024-01-24 13:32:51,551] [INFO] Target genome list was writen to GCF_026344055.1_ASM2634405v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:51,561] [INFO] Task started: fastANI
[2024-01-24 13:32:51,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg132263a2-6355-4e92-b75c-99901eee14c7/GCF_026344055.1_ASM2634405v1_genomic.fna.gz --refList GCF_026344055.1_ASM2634405v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026344055.1_ASM2634405v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:01,449] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:01,458] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:33:01,458] [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_017307955.1	s__Kaistia sp017307955	91.1005	1362	1525	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129325.1	s__Kaistia soli	82.5967	1090	1525	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	81.9525	973	1525	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	96.80	96.80	0.96	0.96	2	-
GCF_016629525.1	s__Kaistia sp016629525	81.626	818	1525	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	81.5557	815	1525	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	81.1176	785	1525	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305815.1	s__Kaistia sp017305815	81.0371	608	1525	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	80.3788	763	1525	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Prosthecomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:01,460] [INFO] GTDB search result was written to GCF_026344055.1_ASM2634405v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:01,460] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:01,465] [INFO] DFAST_QC result json was written to GCF_026344055.1_ASM2634405v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:01,465] [INFO] DFAST_QC completed!
[2024-01-24 13:33:01,465] [INFO] Total running time: 0h1m28s