[2024-01-25 19:11:05,671] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:05,672] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:05,673] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fdf793b-8382-4b65-80ec-f8495b9306c6/dqc_reference
[2024-01-25 19:11:06,818] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:06,819] [INFO] Task started: Prodigal
[2024-01-25 19:11:06,819] [INFO] Running command: gunzip -c /var/lib/cwl/stgf073ab74-7adc-4ff4-bc92-c9da17638a18/GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna.gz | prodigal -d GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna/cds.fna -a GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:11:14,105] [INFO] Task succeeded: Prodigal
[2024-01-25 19:11:14,105] [INFO] Task started: HMMsearch
[2024-01-25 19:11:14,105] [INFO] Running command: hmmsearch --tblout GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fdf793b-8382-4b65-80ec-f8495b9306c6/dqc_reference/reference_markers.hmm GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:11:14,395] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:11:14,396] [INFO] Found 6/6 markers.
[2024-01-25 19:11:14,426] [INFO] Query marker FASTA was written to GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna/markers.fasta
[2024-01-25 19:11:14,427] [INFO] Task started: Blastn
[2024-01-25 19:11:14,427] [INFO] Running command: blastn -query GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fdf793b-8382-4b65-80ec-f8495b9306c6/dqc_reference/reference_markers.fasta -out GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:15,031] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:15,034] [INFO] Selected 15 target genomes.
[2024-01-25 19:11:15,034] [INFO] Target genome list was writen to GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna/target_genomes.txt
[2024-01-25 19:11:15,045] [INFO] Task started: fastANI
[2024-01-25 19:11:15,046] [INFO] Running command: fastANI --query /var/lib/cwl/stgf073ab74-7adc-4ff4-bc92-c9da17638a18/GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna.gz --refList GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna/target_genomes.txt --output GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:11:25,909] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:25,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fdf793b-8382-4b65-80ec-f8495b9306c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:11:25,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fdf793b-8382-4b65-80ec-f8495b9306c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:11:25,930] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:11:25,930] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:11:25,930] [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 bohemicus	strain=ANC 3994	GCA_000367925.1	1435036	1435036	type	True	99.9994	1204	1212	95	conclusive
Acinetobacter terrae	strain=ANC 4282	GCA_013004375.1	2731247	2731247	type	True	84.9137	778	1212	95	below_threshold
Acinetobacter terrestris	strain=ANC 4471	GCA_004331155.1	2529843	2529843	suspected-type	True	84.4396	781	1212	95	below_threshold
Acinetobacter albensis	strain=ANC 4874	GCA_900095025.1	1673609	1673609	type	True	82.9108	721	1212	95	below_threshold
Acinetobacter harbinensis	strain=HITLi 7	GCA_000816495.1	1353941	1353941	type	True	81.8294	647	1212	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	81.8072	583	1212	95	below_threshold
Acinetobacter shaoyimingii	strain=323-1	GCA_011578045.1	2715164	2715164	type	True	80.581	499	1212	95	below_threshold
Acinetobacter wuhouensis	strain=WCHA60	GCA_001696605.3	1879050	1879050	type	True	80.5456	522	1212	95	below_threshold
Acinetobacter indicus	strain=CIP 110367	GCA_000488255.1	756892	756892	type	True	80.0076	483	1212	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	79.8755	439	1212	95	below_threshold
Acinetobacter indicus	strain=DSM 25388	GCA_000830155.1	756892	756892	type	True	79.8573	471	1212	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	79.5447	392	1212	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	79.1785	418	1212	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	79.1044	394	1212	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:11:25,932] [INFO] DFAST Taxonomy check result was written to GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna/tc_result.tsv
[2024-01-25 19:11:25,933] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:11:25,933] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:11:25,933] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fdf793b-8382-4b65-80ec-f8495b9306c6/dqc_reference/checkm_data
[2024-01-25 19:11:25,934] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:11:25,971] [INFO] Task started: CheckM
[2024-01-25 19:11:25,972] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna/checkm_input GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna/checkm_result
[2024-01-25 19:11:52,669] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:52,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:52,705] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:52,705] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:52,705] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna/markers.fasta)
[2024-01-25 19:11:52,705] [INFO] Task started: Blastn
[2024-01-25 19:11:52,705] [INFO] Running command: blastn -query GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fdf793b-8382-4b65-80ec-f8495b9306c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:53,609] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:53,613] [INFO] Selected 14 target genomes.
[2024-01-25 19:11:53,613] [INFO] Target genome list was writen to GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:53,630] [INFO] Task started: fastANI
[2024-01-25 19:11:53,630] [INFO] Running command: fastANI --query /var/lib/cwl/stgf073ab74-7adc-4ff4-bc92-c9da17638a18/GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna.gz --refList GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:12:04,686] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:04,694] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:12:04,694] [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_000367925.1	s__Acinetobacter bohemicus	99.9994	1202	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.89	95.82	0.83	0.82	4	conclusive
GCF_900107285.1	s__Acinetobacter kyonggiensis	93.1137	978	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.53	95.22	0.88	0.86	3	-
GCF_002135335.1	s__Acinetobacter sp002135335	91.3053	864	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004375.1	s__Acinetobacter terrae	84.9478	775	1212	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	84.6539	751	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.82	95.73	0.86	0.83	3	-
GCF_004331155.1	s__Acinetobacter terrestris	84.4365	781	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.13	95.48	0.90	0.88	5	-
GCF_004331285.1	s__Acinetobacter sp004331285	84.0695	822	1212	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	82.6194	717	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902753875.1	s__Acinetobacter bouvetii_A	82.3582	724	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135235.1	s__Acinetobacter sp002135235	81.8203	582	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135345.1	s__Acinetobacter sp002135345	80.8559	535	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024515.2	s__Acinetobacter sichuanensis	80.1218	499	1212	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:12:04,696] [INFO] GTDB search result was written to GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:12:04,697] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:12:04,700] [INFO] DFAST_QC result json was written to GCF_000367925.1_Acin_sp_ANC_3994_V1_genomic.fna/dqc_result.json
[2024-01-25 19:12:04,700] [INFO] DFAST_QC completed!
[2024-01-25 19:12:04,700] [INFO] Total running time: 0h0m59s