[2024-01-24 15:09:55,434] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:09:55,446] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:09:55,447] [INFO] DQC Reference Directory: /var/lib/cwl/stg925a1d7d-6def-4e8b-8d70-c4b923590ddd/dqc_reference
[2024-01-24 15:09:58,165] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:09:58,166] [INFO] Task started: Prodigal
[2024-01-24 15:09:58,167] [INFO] Running command: gunzip -c /var/lib/cwl/stg09d6d030-da7d-460d-939d-724fcf2a56d6/GCF_004331155.1_ASM433115v1_genomic.fna.gz | prodigal -d GCF_004331155.1_ASM433115v1_genomic.fna/cds.fna -a GCF_004331155.1_ASM433115v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:06,448] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:06,449] [INFO] Task started: HMMsearch
[2024-01-24 15:10:06,449] [INFO] Running command: hmmsearch --tblout GCF_004331155.1_ASM433115v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg925a1d7d-6def-4e8b-8d70-c4b923590ddd/dqc_reference/reference_markers.hmm GCF_004331155.1_ASM433115v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:06,811] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:06,812] [INFO] Found 6/6 markers.
[2024-01-24 15:10:06,866] [INFO] Query marker FASTA was written to GCF_004331155.1_ASM433115v1_genomic.fna/markers.fasta
[2024-01-24 15:10:06,866] [INFO] Task started: Blastn
[2024-01-24 15:10:06,867] [INFO] Running command: blastn -query GCF_004331155.1_ASM433115v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg925a1d7d-6def-4e8b-8d70-c4b923590ddd/dqc_reference/reference_markers.fasta -out GCF_004331155.1_ASM433115v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:07,667] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:07,670] [INFO] Selected 16 target genomes.
[2024-01-24 15:10:07,671] [INFO] Target genome list was writen to GCF_004331155.1_ASM433115v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:07,712] [INFO] Task started: fastANI
[2024-01-24 15:10:07,712] [INFO] Running command: fastANI --query /var/lib/cwl/stg09d6d030-da7d-460d-939d-724fcf2a56d6/GCF_004331155.1_ASM433115v1_genomic.fna.gz --refList GCF_004331155.1_ASM433115v1_genomic.fna/target_genomes.txt --output GCF_004331155.1_ASM433115v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:21,652] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:21,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg925a1d7d-6def-4e8b-8d70-c4b923590ddd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:21,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg925a1d7d-6def-4e8b-8d70-c4b923590ddd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:21,666] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:21,666] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:21,667] [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 terrestris	strain=ANC 4471	GCA_004331155.1	2529843	2529843	suspected-type	True	100.0	1067	1070	95	conclusive
Acinetobacter terrae	strain=ANC 4282	GCA_013004375.1	2731247	2731247	type	True	91.1323	918	1070	95	below_threshold
Acinetobacter bohemicus	strain=ANC 3994	GCA_000367925.1	1435036	1435036	type	True	84.386	776	1070	95	below_threshold
Acinetobacter albensis	strain=ANC 4874	GCA_900095025.1	1673609	1673609	type	True	81.7428	629	1070	95	below_threshold
Acinetobacter harbinensis	strain=HITLi 7	GCA_000816495.1	1353941	1353941	type	True	81.4872	629	1070	95	below_threshold
Acinetobacter lwoffii	strain=FDAARGOS 1393	GCA_019048305.1	28090	28090	type	True	81.1805	574	1070	95	below_threshold
Acinetobacter lwoffii	strain=NCTC5866	GCA_900699155.1	28090	28090	type	True	81.1317	573	1070	95	below_threshold
Acinetobacter gandensis	strain=ANC 4275	GCA_001678755.1	1443941	1443941	type	True	81.0058	537	1070	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	80.9719	542	1070	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	80.5007	551	1070	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	80.2926	455	1070	95	below_threshold
Acinetobacter chengduensis	strain=WCHAc060005	GCA_003664645.1	2420890	2420890	type	True	80.2278	516	1070	95	below_threshold
Acinetobacter shaoyimingii	strain=323-1	GCA_011578045.1	2715164	2715164	type	True	80.1098	474	1070	95	below_threshold
Acinetobacter gerneri	strain=KCTC 12415	GCA_000747725.1	202952	202952	type	True	79.6089	401	1070	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	78.9371	390	1070	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:21,668] [INFO] DFAST Taxonomy check result was written to GCF_004331155.1_ASM433115v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:21,669] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:21,669] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:21,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg925a1d7d-6def-4e8b-8d70-c4b923590ddd/dqc_reference/checkm_data
[2024-01-24 15:10:21,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:21,703] [INFO] Task started: CheckM
[2024-01-24 15:10:21,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004331155.1_ASM433115v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004331155.1_ASM433115v1_genomic.fna/checkm_input GCF_004331155.1_ASM433115v1_genomic.fna/checkm_result
[2024-01-24 15:10:52,217] [INFO] Task succeeded: CheckM
[2024-01-24 15:10:52,218] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 15:10:52,239] [INFO] ===== Completeness check finished =====
[2024-01-24 15:10:52,239] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:10:52,240] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004331155.1_ASM433115v1_genomic.fna/markers.fasta)
[2024-01-24 15:10:52,240] [INFO] Task started: Blastn
[2024-01-24 15:10:52,240] [INFO] Running command: blastn -query GCF_004331155.1_ASM433115v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg925a1d7d-6def-4e8b-8d70-c4b923590ddd/dqc_reference/reference_markers_gtdb.fasta -out GCF_004331155.1_ASM433115v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:53,360] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:53,366] [INFO] Selected 7 target genomes.
[2024-01-24 15:10:53,366] [INFO] Target genome list was writen to GCF_004331155.1_ASM433115v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:10:53,373] [INFO] Task started: fastANI
[2024-01-24 15:10:53,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg09d6d030-da7d-460d-939d-724fcf2a56d6/GCF_004331155.1_ASM433115v1_genomic.fna.gz --refList GCF_004331155.1_ASM433115v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004331155.1_ASM433115v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:10:59,340] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:59,347] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:10:59,347] [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_004331155.1	s__Acinetobacter terrestris	100.0	1067	1070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.13	95.48	0.90	0.88	5	conclusive
GCF_013004375.1	s__Acinetobacter terrae	91.1216	919	1070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.86	96.05	0.92	0.88	8	-
GCF_004336635.1	s__Acinetobacter sp004336635	89.8492	865	1070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.82	95.73	0.86	0.83	3	-
GCF_001647545.1	s__Acinetobacter sp001647545	89.4305	866	1070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.85	96.85	0.89	0.89	2	-
GCF_004331285.1	s__Acinetobacter sp004331285	88.8808	866	1070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135315.1	s__Acinetobacter sp002135315	84.4807	783	1070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015602705.1	s__Acinetobacter lwoffii_E	80.6887	560	1070	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.0499	96.41	96.41	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:10:59,349] [INFO] GTDB search result was written to GCF_004331155.1_ASM433115v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:10:59,349] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:10:59,353] [INFO] DFAST_QC result json was written to GCF_004331155.1_ASM433115v1_genomic.fna/dqc_result.json
[2024-01-24 15:10:59,353] [INFO] DFAST_QC completed!
[2024-01-24 15:10:59,353] [INFO] Total running time: 0h1m4s