[2024-01-24 14:39:03,019] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:03,024] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:03,024] [INFO] DQC Reference Directory: /var/lib/cwl/stg643fa4f0-8afe-4a5d-a98e-d9cc26eb6a60/dqc_reference
[2024-01-24 14:39:04,424] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:04,425] [INFO] Task started: Prodigal
[2024-01-24 14:39:04,426] [INFO] Running command: gunzip -c /var/lib/cwl/stg5fec2c79-bf34-4960-b4bb-fe56c264e8cc/GCF_013009345.1_ASM1300934v1_genomic.fna.gz | prodigal -d GCF_013009345.1_ASM1300934v1_genomic.fna/cds.fna -a GCF_013009345.1_ASM1300934v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:12,191] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:12,192] [INFO] Task started: HMMsearch
[2024-01-24 14:39:12,192] [INFO] Running command: hmmsearch --tblout GCF_013009345.1_ASM1300934v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg643fa4f0-8afe-4a5d-a98e-d9cc26eb6a60/dqc_reference/reference_markers.hmm GCF_013009345.1_ASM1300934v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:12,446] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:12,448] [INFO] Found 6/6 markers.
[2024-01-24 14:39:12,500] [INFO] Query marker FASTA was written to GCF_013009345.1_ASM1300934v1_genomic.fna/markers.fasta
[2024-01-24 14:39:12,500] [INFO] Task started: Blastn
[2024-01-24 14:39:12,501] [INFO] Running command: blastn -query GCF_013009345.1_ASM1300934v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg643fa4f0-8afe-4a5d-a98e-d9cc26eb6a60/dqc_reference/reference_markers.fasta -out GCF_013009345.1_ASM1300934v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:13,181] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:13,184] [INFO] Selected 9 target genomes.
[2024-01-24 14:39:13,185] [INFO] Target genome list was writen to GCF_013009345.1_ASM1300934v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:13,189] [INFO] Task started: fastANI
[2024-01-24 14:39:13,189] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fec2c79-bf34-4960-b4bb-fe56c264e8cc/GCF_013009345.1_ASM1300934v1_genomic.fna.gz --refList GCF_013009345.1_ASM1300934v1_genomic.fna/target_genomes.txt --output GCF_013009345.1_ASM1300934v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:22,187] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:22,188] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg643fa4f0-8afe-4a5d-a98e-d9cc26eb6a60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:22,188] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg643fa4f0-8afe-4a5d-a98e-d9cc26eb6a60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:22,197] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:39:22,197] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:22,197] [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=CIP70.29	GCA_024390955.1	48296	48296	type	True	95.2365	1083	1238	95	conclusive
Acinetobacter pittii	strain=DSM 25618	GCA_000836015.1	48296	48296	type	True	95.0538	1093	1238	95	conclusive
Acinetobacter pittii	strain=FDAARGOS 1399	GCA_019047205.1	48296	48296	type	True	95.0299	1109	1238	95	conclusive
Acinetobacter pittii	strain=CIP 70.29	GCA_000369045.1	48296	48296	type	True	94.9664	1068	1238	95	below_threshold
Acinetobacter lactucae	strain=NRRL B-41902	GCA_001605885.1	1785128	1785128	type	True	93.0581	1033	1238	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	88.8688	1023	1238	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	88.8111	1027	1238	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	80.5669	477	1238	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	80.2367	481	1238	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:22,199] [INFO] DFAST Taxonomy check result was written to GCF_013009345.1_ASM1300934v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:22,200] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:22,200] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:22,200] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg643fa4f0-8afe-4a5d-a98e-d9cc26eb6a60/dqc_reference/checkm_data
[2024-01-24 14:39:22,201] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:22,241] [INFO] Task started: CheckM
[2024-01-24 14:39:22,241] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013009345.1_ASM1300934v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013009345.1_ASM1300934v1_genomic.fna/checkm_input GCF_013009345.1_ASM1300934v1_genomic.fna/checkm_result
[2024-01-24 14:39:51,761] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:51,762] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:51,781] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:51,782] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:51,782] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013009345.1_ASM1300934v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:51,783] [INFO] Task started: Blastn
[2024-01-24 14:39:51,783] [INFO] Running command: blastn -query GCF_013009345.1_ASM1300934v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg643fa4f0-8afe-4a5d-a98e-d9cc26eb6a60/dqc_reference/reference_markers_gtdb.fasta -out GCF_013009345.1_ASM1300934v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:52,616] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:52,619] [INFO] Selected 8 target genomes.
[2024-01-24 14:39:52,620] [INFO] Target genome list was writen to GCF_013009345.1_ASM1300934v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:52,626] [INFO] Task started: fastANI
[2024-01-24 14:39:52,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fec2c79-bf34-4960-b4bb-fe56c264e8cc/GCF_013009345.1_ASM1300934v1_genomic.fna.gz --refList GCF_013009345.1_ASM1300934v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013009345.1_ASM1300934v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:00,451] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:00,460] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:00,460] [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_013009345.1	s__Acinetobacter sp013009345	100.0	1236	1238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.73	96.63	0.87	0.86	5	conclusive
GCF_000369045.1	s__Acinetobacter pittii	94.9834	1067	1238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.31	95.52	0.91	0.84	337	-
GCF_002928115.1	s__Acinetobacter pittii_H	93.5528	1038	1238	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	93.0427	1034	1238	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	92.8457	874	1238	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	92.1154	1014	1238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000369625.1	s__Acinetobacter variabilis	80.3171	293	1238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.87	95.07	0.88	0.83	48	-
GCF_013072695.1	s__Acinetobacter sp013072695	80.0497	499	1238	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 14:40:00,462] [INFO] GTDB search result was written to GCF_013009345.1_ASM1300934v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:00,463] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:00,466] [INFO] DFAST_QC result json was written to GCF_013009345.1_ASM1300934v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:00,467] [INFO] DFAST_QC completed!
[2024-01-24 14:40:00,467] [INFO] Total running time: 0h0m57s