[2024-01-24 10:47:08,892] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:08,895] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:08,896] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8c60408-4308-465e-b8ee-9c3f0adb8175/dqc_reference
[2024-01-24 10:47:11,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,917] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,918] [INFO] Running command: gunzip -c /var/lib/cwl/stg2076d953-625d-4ed5-be76-93631b6b3649/GCF_020911985.1_ASM2091198v1_genomic.fna.gz | prodigal -d GCF_020911985.1_ASM2091198v1_genomic.fna/cds.fna -a GCF_020911985.1_ASM2091198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:21,506] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:21,507] [INFO] Task started: HMMsearch
[2024-01-24 10:47:21,507] [INFO] Running command: hmmsearch --tblout GCF_020911985.1_ASM2091198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8c60408-4308-465e-b8ee-9c3f0adb8175/dqc_reference/reference_markers.hmm GCF_020911985.1_ASM2091198v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:21,782] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:21,784] [INFO] Found 6/6 markers.
[2024-01-24 10:47:21,826] [INFO] Query marker FASTA was written to GCF_020911985.1_ASM2091198v1_genomic.fna/markers.fasta
[2024-01-24 10:47:21,826] [INFO] Task started: Blastn
[2024-01-24 10:47:21,826] [INFO] Running command: blastn -query GCF_020911985.1_ASM2091198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8c60408-4308-465e-b8ee-9c3f0adb8175/dqc_reference/reference_markers.fasta -out GCF_020911985.1_ASM2091198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:22,485] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:22,489] [INFO] Selected 8 target genomes.
[2024-01-24 10:47:22,489] [INFO] Target genome list was writen to GCF_020911985.1_ASM2091198v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:23,520] [INFO] Task started: fastANI
[2024-01-24 10:47:23,520] [INFO] Running command: fastANI --query /var/lib/cwl/stg2076d953-625d-4ed5-be76-93631b6b3649/GCF_020911985.1_ASM2091198v1_genomic.fna.gz --refList GCF_020911985.1_ASM2091198v1_genomic.fna/target_genomes.txt --output GCF_020911985.1_ASM2091198v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:30,696] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:30,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8c60408-4308-465e-b8ee-9c3f0adb8175/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:30,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8c60408-4308-465e-b8ee-9c3f0adb8175/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:30,706] [INFO] Found 8 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 10:47:30,706] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:30,706] [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 baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	100.0	1326	1332	95	conclusive
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	99.9999	1320	1332	95	conclusive
Acinetobacter baumannii	strain=ATCC 19606	GCA_009035845.1	470	470	type	True	99.9983	1322	1332	95	conclusive
Acinetobacter baumannii	strain=ATCC 19606	GCA_014116795.1	470	470	type	True	99.9903	1292	1332	95	conclusive
Acinetobacter baumannii	strain=ATCC 19606	GCA_000737145.1	470	470	type	True	99.98	1310	1332	95	conclusive
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	89.1433	1048	1332	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	80.5879	475	1332	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	79.0279	281	1332	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:30,709] [INFO] DFAST Taxonomy check result was written to GCF_020911985.1_ASM2091198v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:30,710] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:30,710] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:30,710] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8c60408-4308-465e-b8ee-9c3f0adb8175/dqc_reference/checkm_data
[2024-01-24 10:47:30,711] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:30,754] [INFO] Task started: CheckM
[2024-01-24 10:47:30,754] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020911985.1_ASM2091198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020911985.1_ASM2091198v1_genomic.fna/checkm_input GCF_020911985.1_ASM2091198v1_genomic.fna/checkm_result
[2024-01-24 10:48:04,900] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:04,902] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:04,923] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:04,923] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:04,923] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020911985.1_ASM2091198v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:04,924] [INFO] Task started: Blastn
[2024-01-24 10:48:04,924] [INFO] Running command: blastn -query GCF_020911985.1_ASM2091198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8c60408-4308-465e-b8ee-9c3f0adb8175/dqc_reference/reference_markers_gtdb.fasta -out GCF_020911985.1_ASM2091198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:05,833] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:05,837] [INFO] Selected 11 target genomes.
[2024-01-24 10:48:05,837] [INFO] Target genome list was writen to GCF_020911985.1_ASM2091198v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:06,045] [INFO] Task started: fastANI
[2024-01-24 10:48:06,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg2076d953-625d-4ed5-be76-93631b6b3649/GCF_020911985.1_ASM2091198v1_genomic.fna.gz --refList GCF_020911985.1_ASM2091198v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020911985.1_ASM2091198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:16,789] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:16,803] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:16,803] [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_009759685.1	s__Acinetobacter baumannii	99.999	1326	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.86	96.67	0.89	0.80	5417	conclusive
GCF_000368085.1	s__Acinetobacter nosocomialis	92.0522	1102	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.94	97.50	0.90	0.85	250	-
GCF_000368065.1	s__Acinetobacter seifertii	90.2132	1071	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.88	96.48	0.87	0.81	81	-
GCF_002928115.1	s__Acinetobacter pittii_H	89.2865	1061	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.46	96.15	0.91	0.87	9	-
GCF_001605885.1	s__Acinetobacter lactucae	88.5994	1048	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.34	96.55	0.91	0.85	16	-
GCF_013344765.1	s__Acinetobacter lactucae_A	88.5848	861	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.51	97.14	0.90	0.87	4	-
GCF_000399685.1	s__Acinetobacter pittii_E	88.4576	1070	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196795.1	s__Acinetobacter oleivorans	88.184	1093	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.22	95.12	0.90	0.85	40	-
GCF_000313935.1	s__Acinetobacter sp000313935	88.0984	1056	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.37	99.37	0.94	0.94	2	-
GCF_000399665.1	s__Acinetobacter calcoaceticus_B	87.773	1031	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016508255.1	s__Acinetobacter calcoaceticus_E	87.4028	1018	1332	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 10:48:16,806] [INFO] GTDB search result was written to GCF_020911985.1_ASM2091198v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:16,807] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:16,811] [INFO] DFAST_QC result json was written to GCF_020911985.1_ASM2091198v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:16,811] [INFO] DFAST_QC completed!
[2024-01-24 10:48:16,812] [INFO] Total running time: 0h1m8s