[2024-01-24 12:40:20,800] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:20,801] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:20,802] [INFO] DQC Reference Directory: /var/lib/cwl/stge3456e04-b139-47ed-afad-12a0b2ce85e7/dqc_reference
[2024-01-24 12:40:22,038] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:22,039] [INFO] Task started: Prodigal
[2024-01-24 12:40:22,039] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4482b8b-11e2-4cfb-80f4-4a114a5d4405/GCF_008802255.1_ASM880225v1_genomic.fna.gz | prodigal -d GCF_008802255.1_ASM880225v1_genomic.fna/cds.fna -a GCF_008802255.1_ASM880225v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:31,751] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:31,751] [INFO] Task started: HMMsearch
[2024-01-24 12:40:31,752] [INFO] Running command: hmmsearch --tblout GCF_008802255.1_ASM880225v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3456e04-b139-47ed-afad-12a0b2ce85e7/dqc_reference/reference_markers.hmm GCF_008802255.1_ASM880225v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:32,013] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:32,015] [INFO] Found 6/6 markers.
[2024-01-24 12:40:32,049] [INFO] Query marker FASTA was written to GCF_008802255.1_ASM880225v1_genomic.fna/markers.fasta
[2024-01-24 12:40:32,049] [INFO] Task started: Blastn
[2024-01-24 12:40:32,050] [INFO] Running command: blastn -query GCF_008802255.1_ASM880225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3456e04-b139-47ed-afad-12a0b2ce85e7/dqc_reference/reference_markers.fasta -out GCF_008802255.1_ASM880225v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:32,754] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:32,758] [INFO] Selected 19 target genomes.
[2024-01-24 12:40:32,759] [INFO] Target genome list was writen to GCF_008802255.1_ASM880225v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:32,767] [INFO] Task started: fastANI
[2024-01-24 12:40:32,767] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4482b8b-11e2-4cfb-80f4-4a114a5d4405/GCF_008802255.1_ASM880225v1_genomic.fna.gz --refList GCF_008802255.1_ASM880225v1_genomic.fna/target_genomes.txt --output GCF_008802255.1_ASM880225v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:46,943] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:46,943] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3456e04-b139-47ed-afad-12a0b2ce85e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:46,944] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3456e04-b139-47ed-afad-12a0b2ce85e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:46,958] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:40:46,959] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:46,959] [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 courvalinii	strain=CCUG 67960	GCA_008802255.1	280147	280147	type	True	100.0	1298	1298	95	conclusive
Acinetobacter courvalinii	strain=CCM 8635	GCA_014635545.1	280147	280147	type	True	99.9961	1294	1298	95	conclusive
Acinetobacter vivianii	strain=CCM 8642	GCA_014635885.1	1776742	1776742	type	True	90.1415	1083	1298	95	below_threshold
Acinetobacter proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	86.0965	996	1298	95	below_threshold
Acinetobacter gyllenbergii	strain=CIP 110306	GCA_000413855.1	134534	134534	type	True	85.3346	987	1298	95	below_threshold
Acinetobacter gyllenbergii	strain=MTCC 11365	GCA_000414075.1	134534	134534	type	True	85.2729	995	1298	95	below_threshold
Acinetobacter colistiniresistens	strain=NIPH 2036	GCA_000413935.1	280145	280145	type	True	85.27	925	1298	95	below_threshold
Acinetobacter venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	82.8432	725	1298	95	below_threshold
Acinetobacter venetianus	strain=CIP 110063	GCA_000368585.1	52133	52133	type	True	82.797	746	1298	95	below_threshold
Acinetobacter tjernbergiae	strain=DSM 14971	GCA_000374425.1	202955	202955	type	True	82.7938	736	1298	95	below_threshold
Acinetobacter tjernbergiae	strain=CIP 107465	GCA_000488175.1	202955	202955	type	True	82.7762	737	1298	95	below_threshold
Acinetobacter haemolyticus	strain=MTCC 9819	GCA_000430205.1	29430	29430	type	True	82.3741	655	1298	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	82.3424	686	1298	95	below_threshold
Acinetobacter haemolyticus	strain=CIP 64.3	GCA_000369065.1	29430	29430	type	True	82.3213	682	1298	95	below_threshold
Acinetobacter haemolyticus	strain=FDAARGOS_1392	GCA_019355995.1	29430	29430	type	True	82.2537	694	1298	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	82.1252	650	1298	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	80.0507	516	1298	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	79.9106	520	1298	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	79.8591	525	1298	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:46,960] [INFO] DFAST Taxonomy check result was written to GCF_008802255.1_ASM880225v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:46,961] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:46,961] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:46,961] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3456e04-b139-47ed-afad-12a0b2ce85e7/dqc_reference/checkm_data
[2024-01-24 12:40:46,962] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:47,000] [INFO] Task started: CheckM
[2024-01-24 12:40:47,000] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008802255.1_ASM880225v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008802255.1_ASM880225v1_genomic.fna/checkm_input GCF_008802255.1_ASM880225v1_genomic.fna/checkm_result
[2024-01-24 12:41:21,046] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:21,048] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:21,067] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:21,067] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:21,067] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008802255.1_ASM880225v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:21,068] [INFO] Task started: Blastn
[2024-01-24 12:41:21,068] [INFO] Running command: blastn -query GCF_008802255.1_ASM880225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3456e04-b139-47ed-afad-12a0b2ce85e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_008802255.1_ASM880225v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:22,137] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:22,141] [INFO] Selected 13 target genomes.
[2024-01-24 12:41:22,141] [INFO] Target genome list was writen to GCF_008802255.1_ASM880225v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:22,146] [INFO] Task started: fastANI
[2024-01-24 12:41:22,146] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4482b8b-11e2-4cfb-80f4-4a114a5d4405/GCF_008802255.1_ASM880225v1_genomic.fna.gz --refList GCF_008802255.1_ASM880225v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008802255.1_ASM880225v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:33,450] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:33,465] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:33,466] [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_014635545.1	s__Acinetobacter courvalinii	99.9961	1294	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.40	96.40	0.91	0.86	14	conclusive
GCF_014635885.1	s__Acinetobacter vivianii	90.1415	1083	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.48	96.89	0.92	0.86	8	-
GCF_000805455.1	s__Acinetobacter sp000805455	88.0275	1021	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000367945.1	s__Acinetobacter proteolyticus	86.0782	998	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.84	97.76	0.89	0.87	5	-
GCF_000369525.1	s__Acinetobacter sp000369525	85.665	998	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.13	96.00	0.90	0.87	7	-
GCF_009884975.1	s__Acinetobacter dispersus	85.6636	1003	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.44	95.54	0.90	0.89	4	-
GCF_000369645.1	s__Acinetobacter sp000369645	85.4401	922	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.86	98.16	0.89	0.84	9	-
GCF_000413855.1	s__Acinetobacter gyllenbergii	85.3423	985	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.05	97.97	0.95	0.91	6	-
GCF_013072695.1	s__Acinetobacter sp013072695	85.3161	980	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000413935.1	s__Acinetobacter colistiniresistens	85.277	924	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.98	96.69	0.90	0.86	10	-
GCF_000368585.1	s__Acinetobacter venetianus	82.8088	744	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.49	96.30	0.89	0.81	21	-
GCF_900406815.1	s__Acinetobacter haemolyticus_A	82.4582	710	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000369065.1	s__Acinetobacter haemolyticus	82.3131	683	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.85	97.09	0.87	0.81	55	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:33,467] [INFO] GTDB search result was written to GCF_008802255.1_ASM880225v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:33,468] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:33,549] [INFO] DFAST_QC result json was written to GCF_008802255.1_ASM880225v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:33,550] [INFO] DFAST_QC completed!
[2024-01-24 12:41:33,550] [INFO] Total running time: 0h1m13s