[2023-06-27 19:44:36,749] [INFO] DFAST_QC pipeline started.
[2023-06-27 19:44:36,755] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 19:44:36,755] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b8af1cf-9e9f-49bb-b88a-d901410f6c98/dqc_reference
[2023-06-27 19:44:39,850] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 19:44:39,851] [INFO] Task started: Prodigal
[2023-06-27 19:44:39,852] [INFO] Running command: gunzip -c /var/lib/cwl/stgfaf9ae42-2e6f-4ef1-a9bf-05d3057534cb/GCA_002430345.1_ASM243034v1_genomic.fna.gz | prodigal -d GCA_002430345.1_ASM243034v1_genomic.fna/cds.fna -a GCA_002430345.1_ASM243034v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 19:44:45,707] [INFO] Task succeeded: Prodigal
[2023-06-27 19:44:45,708] [INFO] Task started: HMMsearch
[2023-06-27 19:44:45,708] [INFO] Running command: hmmsearch --tblout GCA_002430345.1_ASM243034v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b8af1cf-9e9f-49bb-b88a-d901410f6c98/dqc_reference/reference_markers.hmm GCA_002430345.1_ASM243034v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 19:44:46,001] [INFO] Task succeeded: HMMsearch
[2023-06-27 19:44:46,003] [INFO] Found 6/6 markers.
[2023-06-27 19:44:46,069] [INFO] Query marker FASTA was written to GCA_002430345.1_ASM243034v1_genomic.fna/markers.fasta
[2023-06-27 19:44:46,069] [INFO] Task started: Blastn
[2023-06-27 19:44:46,070] [INFO] Running command: blastn -query GCA_002430345.1_ASM243034v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b8af1cf-9e9f-49bb-b88a-d901410f6c98/dqc_reference/reference_markers.fasta -out GCA_002430345.1_ASM243034v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 19:44:46,744] [INFO] Task succeeded: Blastn
[2023-06-27 19:44:46,749] [INFO] Selected 10 target genomes.
[2023-06-27 19:44:46,750] [INFO] Target genome list was writen to GCA_002430345.1_ASM243034v1_genomic.fna/target_genomes.txt
[2023-06-27 19:44:46,755] [INFO] Task started: fastANI
[2023-06-27 19:44:46,756] [INFO] Running command: fastANI --query /var/lib/cwl/stgfaf9ae42-2e6f-4ef1-a9bf-05d3057534cb/GCA_002430345.1_ASM243034v1_genomic.fna.gz --refList GCA_002430345.1_ASM243034v1_genomic.fna/target_genomes.txt --output GCA_002430345.1_ASM243034v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 19:44:54,641] [INFO] Task succeeded: fastANI
[2023-06-27 19:44:54,642] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b8af1cf-9e9f-49bb-b88a-d901410f6c98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 19:44:54,642] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b8af1cf-9e9f-49bb-b88a-d901410f6c98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 19:44:54,658] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2023-06-27 19:44:54,658] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-27 19:44:54,658] [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 nosocomialis	strain=LMG 10619	GCA_000836055.1	106654	106654	type	True	97.9738	836	943	95	conclusive
Acinetobacter nosocomialis	strain=NIPH 2119	GCA_000368085.1	106654	106654	type	True	97.8994	846	943	95	conclusive
Acinetobacter seifertii	strain=NIPH 973	GCA_000368065.1	1530123	1530123	type	True	92.0442	836	943	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_014116795.1	470	470	type	True	91.5528	805	943	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_000737145.1	470	470	type	True	91.5218	806	943	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	91.4937	803	943	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	91.4754	806	943	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	88.33	775	943	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	80.2298	395	943	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 19:44:54,660] [INFO] DFAST Taxonomy check result was written to GCA_002430345.1_ASM243034v1_genomic.fna/tc_result.tsv
[2023-06-27 19:44:54,661] [INFO] ===== Taxonomy check completed =====
[2023-06-27 19:44:54,661] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 19:44:54,661] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b8af1cf-9e9f-49bb-b88a-d901410f6c98/dqc_reference/checkm_data
[2023-06-27 19:44:54,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 19:44:54,700] [INFO] Task started: CheckM
[2023-06-27 19:44:54,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002430345.1_ASM243034v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002430345.1_ASM243034v1_genomic.fna/checkm_input GCA_002430345.1_ASM243034v1_genomic.fna/checkm_result
[2023-06-27 19:45:19,199] [INFO] Task succeeded: CheckM
[2023-06-27 19:45:19,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 19:45:19,227] [INFO] ===== Completeness check finished =====
[2023-06-27 19:45:19,228] [INFO] ===== Start GTDB Search =====
[2023-06-27 19:45:19,228] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002430345.1_ASM243034v1_genomic.fna/markers.fasta)
[2023-06-27 19:45:19,229] [INFO] Task started: Blastn
[2023-06-27 19:45:19,229] [INFO] Running command: blastn -query GCA_002430345.1_ASM243034v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b8af1cf-9e9f-49bb-b88a-d901410f6c98/dqc_reference/reference_markers_gtdb.fasta -out GCA_002430345.1_ASM243034v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 19:45:20,188] [INFO] Task succeeded: Blastn
[2023-06-27 19:45:20,193] [INFO] Selected 13 target genomes.
[2023-06-27 19:45:20,193] [INFO] Target genome list was writen to GCA_002430345.1_ASM243034v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 19:45:20,207] [INFO] Task started: fastANI
[2023-06-27 19:45:20,207] [INFO] Running command: fastANI --query /var/lib/cwl/stgfaf9ae42-2e6f-4ef1-a9bf-05d3057534cb/GCA_002430345.1_ASM243034v1_genomic.fna.gz --refList GCA_002430345.1_ASM243034v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002430345.1_ASM243034v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 19:45:30,879] [INFO] Task succeeded: fastANI
[2023-06-27 19:45:30,897] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 19:45:30,897] [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_000368085.1	s__Acinetobacter nosocomialis	97.8994	846	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.94	97.50	0.90	0.85	250	conclusive
GCF_000368065.1	s__Acinetobacter seifertii	92.0466	836	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.88	96.48	0.87	0.81	81	-
GCF_009759685.1	s__Acinetobacter baumannii	91.5143	803	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.86	96.67	0.89	0.80	5417	-
GCF_002928115.1	s__Acinetobacter pittii_H	88.1538	769	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.46	96.15	0.91	0.87	9	-
GCF_000369045.1	s__Acinetobacter pittii	88.1262	767	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.31	95.52	0.91	0.84	337	-
GCF_013009345.1	s__Acinetobacter sp013009345	87.9337	756	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.73	96.63	0.87	0.86	5	-
GCF_013344765.1	s__Acinetobacter lactucae_A	87.8347	670	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.51	97.14	0.90	0.87	4	-
GCF_000399685.1	s__Acinetobacter pittii_E	87.7455	768	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000313935.1	s__Acinetobacter sp000313935	87.7363	787	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.37	99.37	0.94	0.94	2	-
GCF_001605885.1	s__Acinetobacter lactucae	87.61	756	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.34	96.55	0.91	0.85	16	-
GCF_016508255.1	s__Acinetobacter calcoaceticus_E	87.3202	750	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000399665.1	s__Acinetobacter calcoaceticus_B	87.2057	753	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900520355.1	s__Acinetobacter calcoaceticus_C	86.4876	769	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.76	96.36	0.92	0.90	4	-
--------------------------------------------------------------------------------
[2023-06-27 19:45:30,899] [INFO] GTDB search result was written to GCA_002430345.1_ASM243034v1_genomic.fna/result_gtdb.tsv
[2023-06-27 19:45:30,900] [INFO] ===== GTDB Search completed =====
[2023-06-27 19:45:30,904] [INFO] DFAST_QC result json was written to GCA_002430345.1_ASM243034v1_genomic.fna/dqc_result.json
[2023-06-27 19:45:30,904] [INFO] DFAST_QC completed!
[2023-06-27 19:45:30,904] [INFO] Total running time: 0h0m54s