[2024-01-24 11:06:04,654] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:06:04,656] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:06:04,656] [INFO] DQC Reference Directory: /var/lib/cwl/stg32caf674-e6ce-498a-9736-b45e2bc157a7/dqc_reference
[2024-01-24 11:06:07,010] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:06:07,011] [INFO] Task started: Prodigal
[2024-01-24 11:06:07,012] [INFO] Running command: gunzip -c /var/lib/cwl/stgb273d7d3-9705-4a11-a689-f17a125ad599/GCF_019048305.1_ASM1904830v1_genomic.fna.gz | prodigal -d GCF_019048305.1_ASM1904830v1_genomic.fna/cds.fna -a GCF_019048305.1_ASM1904830v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:15,508] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:15,509] [INFO] Task started: HMMsearch
[2024-01-24 11:06:15,509] [INFO] Running command: hmmsearch --tblout GCF_019048305.1_ASM1904830v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32caf674-e6ce-498a-9736-b45e2bc157a7/dqc_reference/reference_markers.hmm GCF_019048305.1_ASM1904830v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:15,769] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:15,771] [INFO] Found 6/6 markers.
[2024-01-24 11:06:15,802] [INFO] Query marker FASTA was written to GCF_019048305.1_ASM1904830v1_genomic.fna/markers.fasta
[2024-01-24 11:06:15,802] [INFO] Task started: Blastn
[2024-01-24 11:06:15,802] [INFO] Running command: blastn -query GCF_019048305.1_ASM1904830v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32caf674-e6ce-498a-9736-b45e2bc157a7/dqc_reference/reference_markers.fasta -out GCF_019048305.1_ASM1904830v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:16,470] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:16,474] [INFO] Selected 13 target genomes.
[2024-01-24 11:06:16,474] [INFO] Target genome list was writen to GCF_019048305.1_ASM1904830v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:16,487] [INFO] Task started: fastANI
[2024-01-24 11:06:16,487] [INFO] Running command: fastANI --query /var/lib/cwl/stgb273d7d3-9705-4a11-a689-f17a125ad599/GCF_019048305.1_ASM1904830v1_genomic.fna.gz --refList GCF_019048305.1_ASM1904830v1_genomic.fna/target_genomes.txt --output GCF_019048305.1_ASM1904830v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:26,595] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:26,596] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32caf674-e6ce-498a-9736-b45e2bc157a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:26,597] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32caf674-e6ce-498a-9736-b45e2bc157a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:26,613] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:06:26,613] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:26,614] [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
Acinetobacter lwoffii	strain=FDAARGOS 1393	GCA_019048305.1	28090	28090	type	True	100.0	1161	1164	95	conclusive
Acinetobacter lwoffii	strain=NCTC5866	GCA_900699155.1	28090	28090	type	True	99.9983	1145	1164	95	conclusive
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	90.6028	891	1164	95	below_threshold
Acinetobacter pseudolwoffii	strain=ANC 5044	GCA_002803605.1	2053287	2053287	type	True	88.8784	845	1164	95	below_threshold
Acinetobacter variabilis	strain=NIPH 2171	GCA_000369625.1	70346	70346	type	True	84.6901	816	1164	95	below_threshold
Acinetobacter schindleri	strain=CIP 107287	GCA_000368625.1	108981	108981	type	True	83.3794	719	1164	95	below_threshold
Acinetobacter wanghuae	strain=dk386	GCA_009557235.1	2662362	2662362	type	True	81.2059	559	1164	95	below_threshold
Acinetobacter terrae	strain=ANC 4282	GCA_013004375.1	2731247	2731247	type	True	80.6898	560	1164	95	below_threshold
Acinetobacter chengduensis	strain=WCHAc060005	GCA_003664645.1	2420890	2420890	type	True	80.6436	447	1164	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	79.8821	352	1164	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	79.7358	301	1164	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	79.5956	311	1164	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	79.456	311	1164	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:26,615] [INFO] DFAST Taxonomy check result was written to GCF_019048305.1_ASM1904830v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:26,616] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:26,616] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:26,616] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32caf674-e6ce-498a-9736-b45e2bc157a7/dqc_reference/checkm_data
[2024-01-24 11:06:26,617] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:26,651] [INFO] Task started: CheckM
[2024-01-24 11:06:26,651] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019048305.1_ASM1904830v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019048305.1_ASM1904830v1_genomic.fna/checkm_input GCF_019048305.1_ASM1904830v1_genomic.fna/checkm_result
[2024-01-24 11:06:57,804] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:57,806] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:57,822] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:57,822] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:57,823] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019048305.1_ASM1904830v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:57,823] [INFO] Task started: Blastn
[2024-01-24 11:06:57,823] [INFO] Running command: blastn -query GCF_019048305.1_ASM1904830v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32caf674-e6ce-498a-9736-b45e2bc157a7/dqc_reference/reference_markers_gtdb.fasta -out GCF_019048305.1_ASM1904830v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:58,700] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:58,703] [INFO] Selected 7 target genomes.
[2024-01-24 11:06:58,703] [INFO] Target genome list was writen to GCF_019048305.1_ASM1904830v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:58,709] [INFO] Task started: fastANI
[2024-01-24 11:06:58,709] [INFO] Running command: fastANI --query /var/lib/cwl/stgb273d7d3-9705-4a11-a689-f17a125ad599/GCF_019048305.1_ASM1904830v1_genomic.fna.gz --refList GCF_019048305.1_ASM1904830v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019048305.1_ASM1904830v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:04,746] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:04,759] [INFO] Found 7 fastANI hits (3 hits with ANI > circumscription radius)
[2024-01-24 11:07:04,760] [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_000487975.1	s__Acinetobacter lwoffii	99.9737	1109	1164	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.2485	99.52	96.36	0.98	0.86	9	inconclusive
GCF_014769185.1	s__Acinetobacter lwoffii_D	96.2588	945	1164	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.2371	96.35	96.24	0.87	0.85	7	inconclusive
GCF_011058205.1	s__Acinetobacter fasciculus	96.1665	890	1164	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.2485	96.87	96.57	0.87	0.83	19	-
GCF_015602705.1	s__Acinetobacter lwoffii_E	96.0677	930	1164	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.0499	96.41	96.41	0.92	0.92	2	inconclusive
GCA_000761495.1	s__Acinetobacter idrijaensis	96.051	926	1164	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.2371	96.62	96.35	0.87	0.83	6	-
GCA_002367455.1	s__Acinetobacter sp002367455	95.7078	735	1164	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.0792	96.40	96.39	0.89	0.87	3	-
GCF_001647535.1	s__Acinetobacter sp001647535	90.5275	881	1164	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.56	98.54	0.92	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:04,762] [INFO] GTDB search result was written to GCF_019048305.1_ASM1904830v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:04,762] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:04,767] [INFO] DFAST_QC result json was written to GCF_019048305.1_ASM1904830v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:04,767] [INFO] DFAST_QC completed!
[2024-01-24 11:07:04,767] [INFO] Total running time: 0h1m0s