[2024-01-24 11:35:10,916] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:10,921] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:10,921] [INFO] DQC Reference Directory: /var/lib/cwl/stgd14707b6-b9d0-4704-85e8-e56af931214b/dqc_reference
[2024-01-24 11:35:12,293] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:12,294] [INFO] Task started: Prodigal
[2024-01-24 11:35:12,294] [INFO] Running command: gunzip -c /var/lib/cwl/stg239dbd71-a448-4cd8-8686-acb37fb2de54/GCF_019047205.1_ASM1904720v1_genomic.fna.gz | prodigal -d GCF_019047205.1_ASM1904720v1_genomic.fna/cds.fna -a GCF_019047205.1_ASM1904720v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:20,703] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:20,703] [INFO] Task started: HMMsearch
[2024-01-24 11:35:20,703] [INFO] Running command: hmmsearch --tblout GCF_019047205.1_ASM1904720v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd14707b6-b9d0-4704-85e8-e56af931214b/dqc_reference/reference_markers.hmm GCF_019047205.1_ASM1904720v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:21,003] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:21,004] [INFO] Found 6/6 markers.
[2024-01-24 11:35:21,037] [INFO] Query marker FASTA was written to GCF_019047205.1_ASM1904720v1_genomic.fna/markers.fasta
[2024-01-24 11:35:21,037] [INFO] Task started: Blastn
[2024-01-24 11:35:21,038] [INFO] Running command: blastn -query GCF_019047205.1_ASM1904720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd14707b6-b9d0-4704-85e8-e56af931214b/dqc_reference/reference_markers.fasta -out GCF_019047205.1_ASM1904720v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:21,823] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:21,828] [INFO] Selected 9 target genomes.
[2024-01-24 11:35:21,828] [INFO] Target genome list was writen to GCF_019047205.1_ASM1904720v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:21,831] [INFO] Task started: fastANI
[2024-01-24 11:35:21,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg239dbd71-a448-4cd8-8686-acb37fb2de54/GCF_019047205.1_ASM1904720v1_genomic.fna.gz --refList GCF_019047205.1_ASM1904720v1_genomic.fna/target_genomes.txt --output GCF_019047205.1_ASM1904720v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:30,047] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:30,047] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd14707b6-b9d0-4704-85e8-e56af931214b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:30,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd14707b6-b9d0-4704-85e8-e56af931214b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:30,055] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:35:30,055] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:30,055] [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 pittii	strain=FDAARGOS 1399	GCA_019047205.1	48296	48296	type	True	100.0	1323	1325	95	conclusive
Acinetobacter pittii	strain=DSM 25618	GCA_000836015.1	48296	48296	type	True	99.9859	1283	1325	95	conclusive
Acinetobacter pittii	strain=CIP 70.29	GCA_000369045.1	48296	48296	type	True	99.9667	1251	1325	95	conclusive
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	96.9873	1163	1325	95	conclusive
Acinetobacter lactucae	strain=NRRL B-41902	GCA_001605885.1	1785128	1785128	type	True	93.4879	1109	1325	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	89.2848	1087	1325	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	89.2745	1088	1325	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	80.6553	489	1325	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:30,058] [INFO] DFAST Taxonomy check result was written to GCF_019047205.1_ASM1904720v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:30,059] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:30,059] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:30,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd14707b6-b9d0-4704-85e8-e56af931214b/dqc_reference/checkm_data
[2024-01-24 11:35:30,061] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:30,109] [INFO] Task started: CheckM
[2024-01-24 11:35:30,109] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019047205.1_ASM1904720v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019047205.1_ASM1904720v1_genomic.fna/checkm_input GCF_019047205.1_ASM1904720v1_genomic.fna/checkm_result
[2024-01-24 11:36:01,855] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:01,856] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:01,876] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:01,877] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:01,877] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019047205.1_ASM1904720v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:01,877] [INFO] Task started: Blastn
[2024-01-24 11:36:01,878] [INFO] Running command: blastn -query GCF_019047205.1_ASM1904720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd14707b6-b9d0-4704-85e8-e56af931214b/dqc_reference/reference_markers_gtdb.fasta -out GCF_019047205.1_ASM1904720v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:02,934] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:02,937] [INFO] Selected 6 target genomes.
[2024-01-24 11:36:02,937] [INFO] Target genome list was writen to GCF_019047205.1_ASM1904720v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:02,941] [INFO] Task started: fastANI
[2024-01-24 11:36:02,941] [INFO] Running command: fastANI --query /var/lib/cwl/stg239dbd71-a448-4cd8-8686-acb37fb2de54/GCF_019047205.1_ASM1904720v1_genomic.fna.gz --refList GCF_019047205.1_ASM1904720v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019047205.1_ASM1904720v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:08,862] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:08,868] [INFO] Found 6 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 11:36:08,868] [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_000369045.1	s__Acinetobacter pittii	99.965	1251	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.31	95.52	0.91	0.84	337	inconclusive
GCF_013009345.1	s__Acinetobacter sp013009345	95.1208	1108	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.73	96.63	0.87	0.86	5	inconclusive
GCF_002928115.1	s__Acinetobacter pittii_H	94.5195	1112	1325	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	93.4989	1108	1325	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	93.2006	900	1325	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	92.5141	1094	1325	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 11:36:08,870] [INFO] GTDB search result was written to GCF_019047205.1_ASM1904720v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:08,870] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:08,873] [INFO] DFAST_QC result json was written to GCF_019047205.1_ASM1904720v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:08,873] [INFO] DFAST_QC completed!
[2024-01-24 11:36:08,873] [INFO] Total running time: 0h0m58s