[2024-01-24 12:53:37,185] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:37,186] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:37,186] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d036bd3-ba11-4dda-8984-c53937517389/dqc_reference
[2024-01-24 12:53:38,438] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:38,439] [INFO] Task started: Prodigal
[2024-01-24 12:53:38,439] [INFO] Running command: gunzip -c /var/lib/cwl/stg6dfac6c1-081f-4127-beac-1f2272234e4f/GCF_000248155.1_ASM24815v2_genomic.fna.gz | prodigal -d GCF_000248155.1_ASM24815v2_genomic.fna/cds.fna -a GCF_000248155.1_ASM24815v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:44,946] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:44,946] [INFO] Task started: HMMsearch
[2024-01-24 12:53:44,947] [INFO] Running command: hmmsearch --tblout GCF_000248155.1_ASM24815v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d036bd3-ba11-4dda-8984-c53937517389/dqc_reference/reference_markers.hmm GCF_000248155.1_ASM24815v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:45,188] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:45,190] [INFO] Found 6/6 markers.
[2024-01-24 12:53:45,217] [INFO] Query marker FASTA was written to GCF_000248155.1_ASM24815v2_genomic.fna/markers.fasta
[2024-01-24 12:53:45,217] [INFO] Task started: Blastn
[2024-01-24 12:53:45,217] [INFO] Running command: blastn -query GCF_000248155.1_ASM24815v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d036bd3-ba11-4dda-8984-c53937517389/dqc_reference/reference_markers.fasta -out GCF_000248155.1_ASM24815v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:45,917] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:45,922] [INFO] Selected 19 target genomes.
[2024-01-24 12:53:45,923] [INFO] Target genome list was writen to GCF_000248155.1_ASM24815v2_genomic.fna/target_genomes.txt
[2024-01-24 12:53:45,948] [INFO] Task started: fastANI
[2024-01-24 12:53:45,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dfac6c1-081f-4127-beac-1f2272234e4f/GCF_000248155.1_ASM24815v2_genomic.fna.gz --refList GCF_000248155.1_ASM24815v2_genomic.fna/target_genomes.txt --output GCF_000248155.1_ASM24815v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:58,767] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:58,767] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d036bd3-ba11-4dda-8984-c53937517389/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:58,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d036bd3-ba11-4dda-8984-c53937517389/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:58,787] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:53:58,787] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:53:58,787] [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 parvus	strain=DSM 16617	GCA_000248155.2	134533	134533	type	True	100.0	861	869	95	conclusive
Acinetobacter parvus	strain=CIP 108168	GCA_000368025.1	134533	134533	type	True	99.9496	868	869	95	conclusive
Acinetobacter modestus	strain=CCM 8639	GCA_014636095.1	1776740	1776740	type	True	85.8558	625	869	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	84.5385	581	869	95	below_threshold
Acinetobacter junii	strain=CIP 64.5	GCA_000368765.1	40215	40215	type	True	84.3889	589	869	95	below_threshold
Acinetobacter tjernbergiae	strain=DSM 14971	GCA_000374425.1	202955	202955	type	True	83.8533	604	869	95	below_threshold
Acinetobacter tjernbergiae	strain=CIP 107465	GCA_000488175.1	202955	202955	type	True	83.775	603	869	95	below_threshold
Acinetobacter colistiniresistens	strain=NIPH 2036	GCA_000413935.1	280145	280145	type	True	83.2928	637	869	95	below_threshold
Acinetobacter vivianii	strain=CCM 8642	GCA_014635885.1	1776742	1776742	type	True	83.2774	590	869	95	below_threshold
Acinetobacter gyllenbergii	strain=MTCC 11365	GCA_000414075.1	134534	134534	type	True	83.1895	617	869	95	below_threshold
Acinetobacter courvalinii	strain=CCUG 67960	GCA_008802255.1	280147	280147	type	True	83.1165	587	869	95	below_threshold
Acinetobacter haemolyticus	strain=CIP 64.3	GCA_000369065.1	29430	29430	type	True	83.0092	549	869	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	82.9959	557	869	95	below_threshold
Acinetobacter haemolyticus	strain=FDAARGOS_1392	GCA_019355995.1	29430	29430	type	True	82.9347	552	869	95	below_threshold
Acinetobacter courvalinii	strain=CCM 8635	GCA_014635545.1	280147	280147	type	True	82.9102	594	869	95	below_threshold
Acinetobacter haemolyticus	strain=MTCC 9819	GCA_000430205.1	29430	29430	type	True	82.8723	538	869	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	80.5321	362	869	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	79.9619	378	869	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	79.9551	382	869	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:58,789] [INFO] DFAST Taxonomy check result was written to GCF_000248155.1_ASM24815v2_genomic.fna/tc_result.tsv
[2024-01-24 12:53:58,790] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:58,790] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:58,790] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d036bd3-ba11-4dda-8984-c53937517389/dqc_reference/checkm_data
[2024-01-24 12:53:58,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:58,820] [INFO] Task started: CheckM
[2024-01-24 12:53:58,820] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000248155.1_ASM24815v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000248155.1_ASM24815v2_genomic.fna/checkm_input GCF_000248155.1_ASM24815v2_genomic.fna/checkm_result
[2024-01-24 12:54:25,236] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:25,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:25,258] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:25,258] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:25,259] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000248155.1_ASM24815v2_genomic.fna/markers.fasta)
[2024-01-24 12:54:25,259] [INFO] Task started: Blastn
[2024-01-24 12:54:25,259] [INFO] Running command: blastn -query GCF_000248155.1_ASM24815v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d036bd3-ba11-4dda-8984-c53937517389/dqc_reference/reference_markers_gtdb.fasta -out GCF_000248155.1_ASM24815v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:26,342] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:26,346] [INFO] Selected 16 target genomes.
[2024-01-24 12:54:26,346] [INFO] Target genome list was writen to GCF_000248155.1_ASM24815v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:26,379] [INFO] Task started: fastANI
[2024-01-24 12:54:26,379] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dfac6c1-081f-4127-beac-1f2272234e4f/GCF_000248155.1_ASM24815v2_genomic.fna.gz --refList GCF_000248155.1_ASM24815v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000248155.1_ASM24815v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:38,095] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:38,121] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:38,122] [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_000368025.1	s__Acinetobacter parvus	99.9496	868	869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	96.79	0.91	0.83	11	conclusive
GCF_002165255.2	s__Acinetobacter sp002165255	86.7771	649	869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.92	96.70	0.85	0.83	6	-
GCF_014636095.1	s__Acinetobacter modestus	85.8519	625	869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.76	96.94	0.90	0.86	5	-
GCF_000368765.1	s__Acinetobacter junii	84.4028	588	869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.03	97.21	0.88	0.81	75	-
GCF_000374425.1	s__Acinetobacter tjernbergiae	83.8291	605	869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.99	97.83	0.97	0.93	5	-
GCF_009884975.1	s__Acinetobacter dispersus	83.3768	620	869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.44	95.54	0.90	0.89	4	-
GCF_014635885.1	s__Acinetobacter vivianii	83.28	590	869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.48	96.89	0.92	0.86	8	-
GCF_000413935.1	s__Acinetobacter colistiniresistens	83.272	639	869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.98	96.69	0.90	0.86	10	-
GCF_000369525.1	s__Acinetobacter sp000369525	83.2519	660	869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.13	96.00	0.90	0.87	7	-
GCF_000413855.1	s__Acinetobacter gyllenbergii	83.2042	617	869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.05	97.97	0.95	0.91	6	-
GCF_000400715.1	s__Acinetobacter sp000400715	83.1649	638	869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000369805.1	s__Acinetobacter sp000369805	83.0358	636	869	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	82.9893	552	869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.85	97.09	0.87	0.81	55	-
GCF_014635545.1	s__Acinetobacter courvalinii	82.9236	593	869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.40	96.40	0.91	0.86	14	-
GCF_000805455.1	s__Acinetobacter sp000805455	82.5553	564	869	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	79.8467	357	869	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 12:54:38,123] [INFO] GTDB search result was written to GCF_000248155.1_ASM24815v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:38,124] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:38,128] [INFO] DFAST_QC result json was written to GCF_000248155.1_ASM24815v2_genomic.fna/dqc_result.json
[2024-01-24 12:54:38,128] [INFO] DFAST_QC completed!
[2024-01-24 12:54:38,128] [INFO] Total running time: 0h1m1s