[2024-01-25 18:00:35,357] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:00:35,358] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:00:35,358] [INFO] DQC Reference Directory: /var/lib/cwl/stg5749d017-c5a2-4bb4-8f53-38781ae6f019/dqc_reference
[2024-01-25 18:00:36,482] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:00:36,482] [INFO] Task started: Prodigal
[2024-01-25 18:00:36,482] [INFO] Running command: gunzip -c /var/lib/cwl/stg3eb0fe52-ba6c-4a3a-8025-59a3388eaa31/GCF_014196455.1_ASM1419645v1_genomic.fna.gz | prodigal -d GCF_014196455.1_ASM1419645v1_genomic.fna/cds.fna -a GCF_014196455.1_ASM1419645v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:00:49,414] [INFO] Task succeeded: Prodigal
[2024-01-25 18:00:49,414] [INFO] Task started: HMMsearch
[2024-01-25 18:00:49,414] [INFO] Running command: hmmsearch --tblout GCF_014196455.1_ASM1419645v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5749d017-c5a2-4bb4-8f53-38781ae6f019/dqc_reference/reference_markers.hmm GCF_014196455.1_ASM1419645v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:00:49,663] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:00:49,664] [INFO] Found 6/6 markers.
[2024-01-25 18:00:49,709] [INFO] Query marker FASTA was written to GCF_014196455.1_ASM1419645v1_genomic.fna/markers.fasta
[2024-01-25 18:00:49,709] [INFO] Task started: Blastn
[2024-01-25 18:00:49,710] [INFO] Running command: blastn -query GCF_014196455.1_ASM1419645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5749d017-c5a2-4bb4-8f53-38781ae6f019/dqc_reference/reference_markers.fasta -out GCF_014196455.1_ASM1419645v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:50,763] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:50,765] [INFO] Selected 14 target genomes.
[2024-01-25 18:00:50,765] [INFO] Target genome list was writen to GCF_014196455.1_ASM1419645v1_genomic.fna/target_genomes.txt
[2024-01-25 18:00:50,777] [INFO] Task started: fastANI
[2024-01-25 18:00:50,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eb0fe52-ba6c-4a3a-8025-59a3388eaa31/GCF_014196455.1_ASM1419645v1_genomic.fna.gz --refList GCF_014196455.1_ASM1419645v1_genomic.fna/target_genomes.txt --output GCF_014196455.1_ASM1419645v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:01:07,583] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:07,584] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5749d017-c5a2-4bb4-8f53-38781ae6f019/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:01:07,584] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5749d017-c5a2-4bb4-8f53-38781ae6f019/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:01:07,593] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:01:07,593] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:01:07,593] [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 hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	100.0	1745	1746	95	conclusive
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	81.4256	878	1746	95	below_threshold
Kaistia soli	strain=DSM 19436	GCA_900129325.1	446684	446684	type	True	81.0829	899	1746	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	81.0802	847	1746	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	78.1176	497	1746	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.9618	451	1746	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.7501	486	1746	95	below_threshold
Chthonobacter albigriseus	strain=KCTC 42450	GCA_013839445.1	1683161	1683161	type	True	77.6089	386	1746	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.5766	464	1746	95	below_threshold
Propylenella binzhouense	strain=L72	GCA_009866965.1	2555902	2555902	type	True	77.4564	369	1746	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	77.4055	378	1746	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	77.2984	276	1746	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	77.1802	254	1746	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	76.9266	400	1746	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:01:07,599] [INFO] DFAST Taxonomy check result was written to GCF_014196455.1_ASM1419645v1_genomic.fna/tc_result.tsv
[2024-01-25 18:01:07,600] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:01:07,600] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:01:07,600] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5749d017-c5a2-4bb4-8f53-38781ae6f019/dqc_reference/checkm_data
[2024-01-25 18:01:07,601] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:01:07,650] [INFO] Task started: CheckM
[2024-01-25 18:01:07,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196455.1_ASM1419645v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196455.1_ASM1419645v1_genomic.fna/checkm_input GCF_014196455.1_ASM1419645v1_genomic.fna/checkm_result
[2024-01-25 18:01:48,382] [INFO] Task succeeded: CheckM
[2024-01-25 18:01:48,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:01:48,403] [INFO] ===== Completeness check finished =====
[2024-01-25 18:01:48,403] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:01:48,404] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196455.1_ASM1419645v1_genomic.fna/markers.fasta)
[2024-01-25 18:01:48,404] [INFO] Task started: Blastn
[2024-01-25 18:01:48,404] [INFO] Running command: blastn -query GCF_014196455.1_ASM1419645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5749d017-c5a2-4bb4-8f53-38781ae6f019/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196455.1_ASM1419645v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:50,611] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:50,613] [INFO] Selected 7 target genomes.
[2024-01-25 18:01:50,613] [INFO] Target genome list was writen to GCF_014196455.1_ASM1419645v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:01:50,619] [INFO] Task started: fastANI
[2024-01-25 18:01:50,619] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eb0fe52-ba6c-4a3a-8025-59a3388eaa31/GCF_014196455.1_ASM1419645v1_genomic.fna.gz --refList GCF_014196455.1_ASM1419645v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196455.1_ASM1419645v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:01:59,439] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:59,444] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:01:59,444] [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_014196455.1	s__Kaistia hirudinis	100.0	1745	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	96.80	96.80	0.96	0.96	2	conclusive
GCA_017307955.1	s__Kaistia sp017307955	82.4022	973	1746	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	81.4063	881	1746	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	81.3854	904	1746	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	81.1801	645	1746	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	81.118	895	1746	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	81.1032	846	1746	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:01:59,446] [INFO] GTDB search result was written to GCF_014196455.1_ASM1419645v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:01:59,447] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:01:59,449] [INFO] DFAST_QC result json was written to GCF_014196455.1_ASM1419645v1_genomic.fna/dqc_result.json
[2024-01-25 18:01:59,449] [INFO] DFAST_QC completed!
[2024-01-25 18:01:59,449] [INFO] Total running time: 0h1m24s