[2024-01-24 11:06:04,656] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:06:04,658] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:06:04,658] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5cec036-ac96-49c2-becc-da5cefc80d6f/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/stg203e39e7-e6d0-4699-925a-56221aa9835e/GCF_002174125.1_ASM217412v1_genomic.fna.gz | prodigal -d GCF_002174125.1_ASM217412v1_genomic.fna/cds.fna -a GCF_002174125.1_ASM217412v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:16,243] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:16,243] [INFO] Task started: HMMsearch
[2024-01-24 11:06:16,243] [INFO] Running command: hmmsearch --tblout GCF_002174125.1_ASM217412v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5cec036-ac96-49c2-becc-da5cefc80d6f/dqc_reference/reference_markers.hmm GCF_002174125.1_ASM217412v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:16,484] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:16,485] [INFO] Found 6/6 markers.
[2024-01-24 11:06:16,517] [INFO] Query marker FASTA was written to GCF_002174125.1_ASM217412v1_genomic.fna/markers.fasta
[2024-01-24 11:06:16,518] [INFO] Task started: Blastn
[2024-01-24 11:06:16,518] [INFO] Running command: blastn -query GCF_002174125.1_ASM217412v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5cec036-ac96-49c2-becc-da5cefc80d6f/dqc_reference/reference_markers.fasta -out GCF_002174125.1_ASM217412v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:17,160] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:17,164] [INFO] Selected 28 target genomes.
[2024-01-24 11:06:17,165] [INFO] Target genome list was writen to GCF_002174125.1_ASM217412v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:17,175] [INFO] Task started: fastANI
[2024-01-24 11:06:17,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg203e39e7-e6d0-4699-925a-56221aa9835e/GCF_002174125.1_ASM217412v1_genomic.fna.gz --refList GCF_002174125.1_ASM217412v1_genomic.fna/target_genomes.txt --output GCF_002174125.1_ASM217412v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:33,627] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:33,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5cec036-ac96-49c2-becc-da5cefc80d6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:33,628] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5cec036-ac96-49c2-becc-da5cefc80d6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:33,648] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:33,648] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:33,648] [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 populi	strain=PBJ7	GCA_002174125.1	1582270	1582270	type	True	100.0	1224	1224	95	conclusive
Acinetobacter junii	strain=CIP 64.5	GCA_000368765.1	40215	40215	type	True	78.2999	184	1224	95	below_threshold
Acinetobacter stercoris	strain=KPC-SM-21	GCA_900323515.1	2126983	2126983	type	True	78.2957	194	1224	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	78.2859	184	1224	95	below_threshold
Acinetobacter wuhouensis	strain=WCHA60	GCA_001696605.3	1879050	1879050	type	True	78.2382	212	1224	95	below_threshold
Acinetobacter defluvii	strain=WCHA30	GCA_001704615.3	1871111	1871111	type	True	78.1968	211	1224	95	below_threshold
Acinetobacter venetianus	strain=CIP 110063	GCA_000368585.1	52133	52133	type	True	78.1514	195	1224	95	below_threshold
Acinetobacter soli	strain=KCTC 22184	GCA_000760595.1	487316	487316	type	True	78.1234	190	1224	95	below_threshold
Acinetobacter gerneri	strain=CIP 107464	GCA_000368565.1	202952	202952	type	True	78.1216	219	1224	95	below_threshold
Acinetobacter seifertii	strain=NIPH 973	GCA_000368065.1	1530123	1530123	type	True	78.097	206	1224	95	below_threshold
Acinetobacter cumulans	strain=WCHAc060092	GCA_003024525.3	2136182	2136182	type	True	78.0898	169	1224	95	below_threshold
Acinetobacter venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	78.0547	191	1224	95	below_threshold
Acinetobacter harbinensis	strain=HITLi 7	GCA_000816495.1	1353941	1353941	type	True	78.0045	190	1224	95	below_threshold
Acinetobacter guerrae	strain=AC 1271	GCA_009372255.1	1843371	1843371	type	True	77.999	253	1224	95	below_threshold
Acinetobacter variabilis	strain=NIPH 2171	GCA_000369625.1	70346	70346	type	True	77.9672	204	1224	95	below_threshold
Acinetobacter nosocomialis	strain=NIPH 2119	GCA_000368085.1	106654	106654	type	True	77.9627	199	1224	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	77.959	203	1224	95	below_threshold
Acinetobacter baylyi	strain=CIP 107474	GCA_000368685.1	202950	202950	type	True	77.9371	242	1224	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	77.9246	205	1224	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	77.9212	206	1224	95	below_threshold
Acinetobacter gerneri	strain=MTCC 9824	GCA_000430245.1	202952	202952	type	True	77.8979	214	1224	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	77.8943	277	1224	95	below_threshold
Acinetobacter pragensis	strain=ANC 4149	GCA_001605895.1	1806892	1806892	type	True	77.8529	156	1224	95	below_threshold
Acinetobacter gerneri	strain=KCTC 12415	GCA_000747725.1	202952	202952	type	True	77.8012	210	1224	95	below_threshold
Acinetobacter vivianii	strain=CCM 8642	GCA_014635885.1	1776742	1776742	type	True	77.8002	246	1224	95	below_threshold
Acinetobacter sichuanensis	strain=WCHAc060041	GCA_003024515.2	2136183	2136183	type	True	77.5149	236	1224	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	77.3555	220	1224	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:33,650] [INFO] DFAST Taxonomy check result was written to GCF_002174125.1_ASM217412v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:33,652] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:33,652] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:33,653] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5cec036-ac96-49c2-becc-da5cefc80d6f/dqc_reference/checkm_data
[2024-01-24 11:06:33,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:33,694] [INFO] Task started: CheckM
[2024-01-24 11:06:33,694] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002174125.1_ASM217412v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002174125.1_ASM217412v1_genomic.fna/checkm_input GCF_002174125.1_ASM217412v1_genomic.fna/checkm_result
[2024-01-24 11:07:05,734] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:05,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:05,755] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:05,756] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:05,756] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002174125.1_ASM217412v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:05,756] [INFO] Task started: Blastn
[2024-01-24 11:07:05,757] [INFO] Running command: blastn -query GCF_002174125.1_ASM217412v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5cec036-ac96-49c2-becc-da5cefc80d6f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002174125.1_ASM217412v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:06,607] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:06,611] [INFO] Selected 14 target genomes.
[2024-01-24 11:07:06,612] [INFO] Target genome list was writen to GCF_002174125.1_ASM217412v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:06,633] [INFO] Task started: fastANI
[2024-01-24 11:07:06,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg203e39e7-e6d0-4699-925a-56221aa9835e/GCF_002174125.1_ASM217412v1_genomic.fna.gz --refList GCF_002174125.1_ASM217412v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002174125.1_ASM217412v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:15,031] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:15,046] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:15,046] [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_002174125.1	s__Acinetobacter populi	100.0	1224	1224	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900096995.1	s__Acinetobacter puyangensis	91.6953	954	1224	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008693185.1	s__Acinetobacter qingfengensis	79.3492	395	1224	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCA_008017315.1	s__Acinetobacter sp008017315	78.5394	281	1224	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900096915.1	s__Acinetobacter marinus	78.1028	269	1224	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368065.1	s__Acinetobacter seifertii	78.0988	204	1224	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.88	96.48	0.87	0.81	81	-
GCF_013343215.1	s__Acinetobacter lwoffii_C	78.0228	189	1224	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	97.90	0.93	0.91	5	-
GCA_001626925.1	s__Acinetobacter sp001626925	78.0143	237	1224	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.78	99.66	0.96	0.94	7	-
GCF_000773685.1	s__Acinetobacter sp000773685	77.9162	181	1224	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902809855.1	s__Acinetobacter sp902809855	77.9028	226	1224	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900625095.1	s__Acinetobacter sp900625095	77.897	276	1224	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012371325.1	s__Acinetobacter sp012371325	77.5765	213	1224	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.91	97.28	0.89	0.84	6	-
GCA_002296655.1	s__Acinetobacter sp002296655	77.3411	190	1224	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.95	99.95	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:15,048] [INFO] GTDB search result was written to GCF_002174125.1_ASM217412v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:15,048] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:15,052] [INFO] DFAST_QC result json was written to GCF_002174125.1_ASM217412v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:15,052] [INFO] DFAST_QC completed!
[2024-01-24 11:07:15,053] [INFO] Total running time: 0h1m10s