[2024-01-24 13:01:52,108] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:52,109] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:52,109] [INFO] DQC Reference Directory: /var/lib/cwl/stgdeeb6201-9005-4757-888c-f98edd161b60/dqc_reference
[2024-01-24 13:01:53,428] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:53,429] [INFO] Task started: Prodigal
[2024-01-24 13:01:53,430] [INFO] Running command: gunzip -c /var/lib/cwl/stga4e3074d-cd84-4fc3-b12b-98690b668090/GCF_011578045.1_ASM1157804v1_genomic.fna.gz | prodigal -d GCF_011578045.1_ASM1157804v1_genomic.fna/cds.fna -a GCF_011578045.1_ASM1157804v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:01,833] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:01,833] [INFO] Task started: HMMsearch
[2024-01-24 13:02:01,833] [INFO] Running command: hmmsearch --tblout GCF_011578045.1_ASM1157804v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdeeb6201-9005-4757-888c-f98edd161b60/dqc_reference/reference_markers.hmm GCF_011578045.1_ASM1157804v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:02,121] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:02,122] [INFO] Found 6/6 markers.
[2024-01-24 13:02:02,155] [INFO] Query marker FASTA was written to GCF_011578045.1_ASM1157804v1_genomic.fna/markers.fasta
[2024-01-24 13:02:02,155] [INFO] Task started: Blastn
[2024-01-24 13:02:02,155] [INFO] Running command: blastn -query GCF_011578045.1_ASM1157804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdeeb6201-9005-4757-888c-f98edd161b60/dqc_reference/reference_markers.fasta -out GCF_011578045.1_ASM1157804v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:02,932] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:02,940] [INFO] Selected 20 target genomes.
[2024-01-24 13:02:02,941] [INFO] Target genome list was writen to GCF_011578045.1_ASM1157804v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:02,975] [INFO] Task started: fastANI
[2024-01-24 13:02:02,975] [INFO] Running command: fastANI --query /var/lib/cwl/stga4e3074d-cd84-4fc3-b12b-98690b668090/GCF_011578045.1_ASM1157804v1_genomic.fna.gz --refList GCF_011578045.1_ASM1157804v1_genomic.fna/target_genomes.txt --output GCF_011578045.1_ASM1157804v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:20,318] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:20,318] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdeeb6201-9005-4757-888c-f98edd161b60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:20,319] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdeeb6201-9005-4757-888c-f98edd161b60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:20,343] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:20,343] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:20,343] [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 shaoyimingii	strain=323-1	GCA_011578045.1	2715164	2715164	type	True	100.0	1188	1190	95	conclusive
Acinetobacter lanii	strain=185	GCA_011578285.1	2715163	2715163	type	True	81.4321	635	1190	95	below_threshold
Acinetobacter wanghuae	strain=dk386	GCA_009557235.1	2662362	2662362	type	True	80.7962	445	1190	95	below_threshold
Acinetobacter portensis	strain=AC 877	GCA_009372215.1	1839785	1839785	type	True	80.6544	444	1190	95	below_threshold
Acinetobacter wuhouensis	strain=WCHA60	GCA_001696605.3	1879050	1879050	type	True	80.5251	510	1190	95	below_threshold
Acinetobacter bohemicus	strain=ANC 3994	GCA_000367925.1	1435036	1435036	type	True	80.4418	502	1190	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	80.4007	457	1190	95	below_threshold
Acinetobacter terrae	strain=ANC 4282	GCA_013004375.1	2731247	2731247	type	True	80.254	469	1190	95	below_threshold
Acinetobacter equi	strain=114	GCA_001307195.1	1324350	1324350	type	True	80.2452	422	1190	95	below_threshold
Acinetobacter guillouiae	strain=CIP 63.46	GCA_000368145.1	106649	106649	type	True	80.1862	504	1190	95	below_threshold
Acinetobacter sichuanensis	strain=WCHAc060041	GCA_003024515.2	2136183	2136183	type	True	80.046	508	1190	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	80.0449	453	1190	95	below_threshold
Acinetobacter gerneri	strain=CIP 107464	GCA_000368565.1	202952	202952	type	True	80.0434	450	1190	95	below_threshold
Acinetobacter tandoii	strain=CIP 107469	GCA_000400735.1	202954	202954	type	True	80.0117	424	1190	95	below_threshold
Acinetobacter guillouiae	strain=CCUG 2491	GCA_008802215.1	106649	106649	type	True	79.9683	490	1190	95	below_threshold
Acinetobacter gerneri	strain=MTCC 9824	GCA_000430245.1	202952	202952	type	True	79.8128	447	1190	95	below_threshold
Acinetobacter gerneri	strain=KCTC 12415	GCA_000747725.1	202952	202952	type	True	79.7338	445	1190	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	79.5215	345	1190	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	78.8062	363	1190	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:20,345] [INFO] DFAST Taxonomy check result was written to GCF_011578045.1_ASM1157804v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:20,345] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:20,346] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:20,346] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdeeb6201-9005-4757-888c-f98edd161b60/dqc_reference/checkm_data
[2024-01-24 13:02:20,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:20,384] [INFO] Task started: CheckM
[2024-01-24 13:02:20,385] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011578045.1_ASM1157804v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011578045.1_ASM1157804v1_genomic.fna/checkm_input GCF_011578045.1_ASM1157804v1_genomic.fna/checkm_result
[2024-01-24 13:02:53,098] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:53,099] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:53,118] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:53,118] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:53,119] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011578045.1_ASM1157804v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:53,119] [INFO] Task started: Blastn
[2024-01-24 13:02:53,119] [INFO] Running command: blastn -query GCF_011578045.1_ASM1157804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdeeb6201-9005-4757-888c-f98edd161b60/dqc_reference/reference_markers_gtdb.fasta -out GCF_011578045.1_ASM1157804v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:54,172] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:54,175] [INFO] Selected 19 target genomes.
[2024-01-24 13:02:54,175] [INFO] Target genome list was writen to GCF_011578045.1_ASM1157804v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:54,195] [INFO] Task started: fastANI
[2024-01-24 13:02:54,195] [INFO] Running command: fastANI --query /var/lib/cwl/stga4e3074d-cd84-4fc3-b12b-98690b668090/GCF_011578045.1_ASM1157804v1_genomic.fna.gz --refList GCF_011578045.1_ASM1157804v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011578045.1_ASM1157804v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:08,062] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:08,081] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:08,081] [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_011578045.1	s__Acinetobacter shaoyimingii	100.0	1188	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.63	98.63	0.95	0.95	2	conclusive
GCF_011578285.1	s__Acinetobacter lanii	81.4147	633	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.20	97.20	0.92	0.92	2	-
GCF_009557235.1	s__Acinetobacter wanghuae	80.8342	444	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.95	99.95	0.94	0.94	2	-
GCF_001612555.1	s__Acinetobacter sp001612555	80.7795	568	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009372215.1	s__Acinetobacter portensis	80.6547	444	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.69	98.69	0.93	0.93	2	-
GCF_001696605.3	s__Acinetobacter wuhouensis	80.6219	510	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.82	96.71	0.87	0.86	6	-
GCF_002135315.1	s__Acinetobacter sp002135315	80.4922	430	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000367925.1	s__Acinetobacter bohemicus	80.4486	506	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.89	95.82	0.83	0.82	4	-
GCF_001307195.1	s__Acinetobacter equi	80.4428	426	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000632455.1	s__Acinetobacter sp000632455	80.4356	442	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.93	97.36	0.88	0.86	4	-
GCF_004336635.1	s__Acinetobacter sp004336635	80.352	485	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.82	95.73	0.86	0.83	3	-
GCF_002135335.1	s__Acinetobacter sp002135335	80.3173	490	1190	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	80.2552	469	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.86	96.05	0.92	0.88	8	-
GCF_000368145.1	s__Acinetobacter guillouiae	80.1948	507	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.78	96.36	0.91	0.85	14	-
GCF_003024515.2	s__Acinetobacter sichuanensis	80.0401	507	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331035.1	s__Acinetobacter sp004331035	80.0061	436	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003105055.1	s__Acinetobacter sp003105055	79.9504	439	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135415.1	s__Acinetobacter sp002135415	79.8436	542	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009912575.1	s__Acinetobacter bereziniae_A	79.5456	447	1190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:08,083] [INFO] GTDB search result was written to GCF_011578045.1_ASM1157804v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:08,084] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:08,089] [INFO] DFAST_QC result json was written to GCF_011578045.1_ASM1157804v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:08,089] [INFO] DFAST_QC completed!
[2024-01-24 13:03:08,089] [INFO] Total running time: 0h1m16s