[2024-01-25 19:49:50,668] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:49:50,671] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:49:50,672] [INFO] DQC Reference Directory: /var/lib/cwl/stg32ead3b0-b2cf-4f60-94b7-ba0a6cbdf4fe/dqc_reference
[2024-01-25 19:49:51,909] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:49:51,909] [INFO] Task started: Prodigal
[2024-01-25 19:49:51,910] [INFO] Running command: gunzip -c /var/lib/cwl/stg1cccc390-bdf9-42a5-a443-9a9fdcb4b72e/GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna.gz | prodigal -d GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna/cds.fna -a GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:59,679] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:59,680] [INFO] Task started: HMMsearch
[2024-01-25 19:49:59,680] [INFO] Running command: hmmsearch --tblout GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32ead3b0-b2cf-4f60-94b7-ba0a6cbdf4fe/dqc_reference/reference_markers.hmm GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:59,917] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:59,918] [INFO] Found 6/6 markers.
[2024-01-25 19:49:59,954] [INFO] Query marker FASTA was written to GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna/markers.fasta
[2024-01-25 19:49:59,954] [INFO] Task started: Blastn
[2024-01-25 19:49:59,954] [INFO] Running command: blastn -query GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32ead3b0-b2cf-4f60-94b7-ba0a6cbdf4fe/dqc_reference/reference_markers.fasta -out GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:00,627] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:00,630] [INFO] Selected 9 target genomes.
[2024-01-25 19:50:00,631] [INFO] Target genome list was writen to GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna/target_genomes.txt
[2024-01-25 19:50:00,633] [INFO] Task started: fastANI
[2024-01-25 19:50:00,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cccc390-bdf9-42a5-a443-9a9fdcb4b72e/GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna.gz --refList GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna/target_genomes.txt --output GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:50:09,023] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:09,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32ead3b0-b2cf-4f60-94b7-ba0a6cbdf4fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:50:09,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32ead3b0-b2cf-4f60-94b7-ba0a6cbdf4fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:50:09,032] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:50:09,032] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:50:09,032] [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 seifertii	strain=NIPH 973	GCA_000368065.1	1530123	1530123	type	True	99.9968	1399	1403	95	conclusive
Acinetobacter nosocomialis	strain=LMG 10619	GCA_000836055.1	106654	106654	type	True	92.086	1082	1403	95	below_threshold
Acinetobacter nosocomialis	strain=NIPH 2119	GCA_000368085.1	106654	106654	type	True	92.0835	1106	1403	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	90.1864	1074	1403	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	90.1758	1074	1403	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_014116795.1	470	470	type	True	90.1538	1069	1403	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	88.9832	1041	1403	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	79.7812	422	1403	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	79.2529	280	1403	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:50:09,034] [INFO] DFAST Taxonomy check result was written to GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna/tc_result.tsv
[2024-01-25 19:50:09,036] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:50:09,036] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:50:09,036] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32ead3b0-b2cf-4f60-94b7-ba0a6cbdf4fe/dqc_reference/checkm_data
[2024-01-25 19:50:09,037] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:50:09,085] [INFO] Task started: CheckM
[2024-01-25 19:50:09,085] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna/checkm_input GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna/checkm_result
[2024-01-25 19:50:36,806] [INFO] Task succeeded: CheckM
[2024-01-25 19:50:36,806] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:50:36,834] [INFO] ===== Completeness check finished =====
[2024-01-25 19:50:36,835] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:50:36,835] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna/markers.fasta)
[2024-01-25 19:50:36,835] [INFO] Task started: Blastn
[2024-01-25 19:50:36,835] [INFO] Running command: blastn -query GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32ead3b0-b2cf-4f60-94b7-ba0a6cbdf4fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:37,889] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:37,892] [INFO] Selected 12 target genomes.
[2024-01-25 19:50:37,892] [INFO] Target genome list was writen to GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:50:37,893] [INFO] Task started: fastANI
[2024-01-25 19:50:37,893] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cccc390-bdf9-42a5-a443-9a9fdcb4b72e/GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna.gz --refList GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:50:49,411] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:49,421] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:50:49,421] [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_000368065.1	s__Acinetobacter seifertii	99.9968	1399	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.88	96.48	0.87	0.81	81	conclusive
GCF_000368085.1	s__Acinetobacter nosocomialis	92.0835	1106	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.94	97.50	0.90	0.85	250	-
GCF_009759685.1	s__Acinetobacter baumannii	90.1443	1079	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.86	96.67	0.89	0.80	5417	-
GCF_000369045.1	s__Acinetobacter pittii	88.8708	1040	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.31	95.52	0.91	0.84	337	-
GCF_000196795.1	s__Acinetobacter oleivorans	88.8437	1100	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.22	95.12	0.90	0.85	40	-
GCF_002928115.1	s__Acinetobacter pittii_H	88.6437	1024	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.46	96.15	0.91	0.87	9	-
GCF_013344765.1	s__Acinetobacter lactucae_A	88.54	878	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.51	97.14	0.90	0.87	4	-
GCF_001605885.1	s__Acinetobacter lactucae	88.3385	1025	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.34	96.55	0.91	0.85	16	-
GCF_000313935.1	s__Acinetobacter sp000313935	88.1844	1056	1403	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	88.1227	1015	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000399685.1	s__Acinetobacter pittii_E	88.0406	1003	1403	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	87.667	1043	1403	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:50:49,423] [INFO] GTDB search result was written to GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:50:49,427] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:50:49,443] [INFO] DFAST_QC result json was written to GCF_000368065.1_Acin_sp_NIPH_973_V1_genomic.fna/dqc_result.json
[2024-01-25 19:50:49,444] [INFO] DFAST_QC completed!
[2024-01-25 19:50:49,444] [INFO] Total running time: 0h0m59s