[2024-01-24 13:36:44,358] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:44,360] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:44,360] [INFO] DQC Reference Directory: /var/lib/cwl/stgabe09f94-d793-442f-8479-378998a9c6ea/dqc_reference
[2024-01-24 13:36:45,714] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:45,715] [INFO] Task started: Prodigal
[2024-01-24 13:36:45,716] [INFO] Running command: gunzip -c /var/lib/cwl/stg7918de29-1684-462f-aabb-4fdcc33d2c99/GCF_009372215.1_ASM937221v1_genomic.fna.gz | prodigal -d GCF_009372215.1_ASM937221v1_genomic.fna/cds.fna -a GCF_009372215.1_ASM937221v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:51,582] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:51,582] [INFO] Task started: HMMsearch
[2024-01-24 13:36:51,583] [INFO] Running command: hmmsearch --tblout GCF_009372215.1_ASM937221v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabe09f94-d793-442f-8479-378998a9c6ea/dqc_reference/reference_markers.hmm GCF_009372215.1_ASM937221v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:51,806] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:51,807] [INFO] Found 6/6 markers.
[2024-01-24 13:36:51,832] [INFO] Query marker FASTA was written to GCF_009372215.1_ASM937221v1_genomic.fna/markers.fasta
[2024-01-24 13:36:51,833] [INFO] Task started: Blastn
[2024-01-24 13:36:51,833] [INFO] Running command: blastn -query GCF_009372215.1_ASM937221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabe09f94-d793-442f-8479-378998a9c6ea/dqc_reference/reference_markers.fasta -out GCF_009372215.1_ASM937221v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:52,572] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:52,575] [INFO] Selected 21 target genomes.
[2024-01-24 13:36:52,575] [INFO] Target genome list was writen to GCF_009372215.1_ASM937221v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:52,608] [INFO] Task started: fastANI
[2024-01-24 13:36:52,608] [INFO] Running command: fastANI --query /var/lib/cwl/stg7918de29-1684-462f-aabb-4fdcc33d2c99/GCF_009372215.1_ASM937221v1_genomic.fna.gz --refList GCF_009372215.1_ASM937221v1_genomic.fna/target_genomes.txt --output GCF_009372215.1_ASM937221v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:05,795] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:05,796] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabe09f94-d793-442f-8479-378998a9c6ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:05,796] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabe09f94-d793-442f-8479-378998a9c6ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:05,813] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:05,814] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:05,814] [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 portensis	strain=AC 877	GCA_009372215.1	1839785	1839785	type	True	100.0	909	914	95	conclusive
Acinetobacter equi	strain=114	GCA_001307195.1	1324350	1324350	type	True	81.1186	539	914	95	below_threshold
Acinetobacter cumulans	strain=WCHAc060092	GCA_003024525.3	2136182	2136182	type	True	81.0688	485	914	95	below_threshold
Acinetobacter wanghuae	strain=dk386	GCA_009557235.1	2662362	2662362	type	True	80.9855	450	914	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	80.979	449	914	95	below_threshold
Acinetobacter gandensis	strain=ANC 4275	GCA_001678755.1	1443941	1443941	type	True	80.9211	486	914	95	below_threshold
Acinetobacter chengduensis	strain=WCHAc060005	GCA_003664645.1	2420890	2420890	type	True	80.8785	483	914	95	below_threshold
Acinetobacter gandensis	strain=CCUG 68482	GCA_008802205.1	1443941	1443941	type	True	80.8522	487	914	95	below_threshold
Acinetobacter johnsonii	strain=DSM 6963	GCA_000949655.1	40214	40214	suspected-type	True	80.6705	434	914	95	below_threshold
Acinetobacter bohemicus	strain=ANC 3994	GCA_000367925.1	1435036	1435036	type	True	80.604	490	914	95	below_threshold
Acinetobacter shaoyimingii	strain=323-1	GCA_011578045.1	2715164	2715164	type	True	80.5412	430	914	95	below_threshold
Acinetobacter terrae	strain=ANC 4282	GCA_013004375.1	2731247	2731247	type	True	80.5243	457	914	95	below_threshold
Acinetobacter celticus	strain=ANC 4603	GCA_001707755.1	1891224	1891224	type	True	80.4763	465	914	95	below_threshold
Acinetobacter pseudolwoffii	strain=ANC 5044	GCA_002803605.1	2053287	2053287	type	True	80.4398	376	914	95	below_threshold
Acinetobacter wuhouensis	strain=WCHA60	GCA_001696605.3	1879050	1879050	type	True	80.2941	443	914	95	below_threshold
Acinetobacter kanungonis	strain=PS-1	GCA_009939195.1	2699469	2699469	type	True	80.2193	387	914	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	80.1936	403	914	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	80.0283	360	914	95	below_threshold
Acinetobacter pragensis	strain=ANC 4149	GCA_001605895.1	1806892	1806892	type	True	79.9584	372	914	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	79.0297	343	914	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	78.9332	350	914	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:05,816] [INFO] DFAST Taxonomy check result was written to GCF_009372215.1_ASM937221v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:05,817] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:05,817] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:05,817] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabe09f94-d793-442f-8479-378998a9c6ea/dqc_reference/checkm_data
[2024-01-24 13:37:05,819] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:05,851] [INFO] Task started: CheckM
[2024-01-24 13:37:05,851] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009372215.1_ASM937221v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009372215.1_ASM937221v1_genomic.fna/checkm_input GCF_009372215.1_ASM937221v1_genomic.fna/checkm_result
[2024-01-24 13:37:31,193] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:31,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:31,211] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:31,211] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:31,211] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009372215.1_ASM937221v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:31,212] [INFO] Task started: Blastn
[2024-01-24 13:37:31,212] [INFO] Running command: blastn -query GCF_009372215.1_ASM937221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabe09f94-d793-442f-8479-378998a9c6ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_009372215.1_ASM937221v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:32,383] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:32,387] [INFO] Selected 19 target genomes.
[2024-01-24 13:37:32,387] [INFO] Target genome list was writen to GCF_009372215.1_ASM937221v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:32,423] [INFO] Task started: fastANI
[2024-01-24 13:37:32,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg7918de29-1684-462f-aabb-4fdcc33d2c99/GCF_009372215.1_ASM937221v1_genomic.fna.gz --refList GCF_009372215.1_ASM937221v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009372215.1_ASM937221v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:44,790] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:44,806] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:44,806] [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_009372215.1	s__Acinetobacter portensis	100.0	909	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.69	98.69	0.93	0.93	2	conclusive
GCF_009707625.1	s__Acinetobacter sp009707625	87.3635	688	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001307195.1	s__Acinetobacter equi	81.1072	541	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024525.3	s__Acinetobacter cumulans	81.0848	486	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	97.84	0.86	0.82	9	-
GCF_009557235.1	s__Acinetobacter wanghuae	80.9742	450	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.95	99.95	0.94	0.94	2	-
GCF_001678755.1	s__Acinetobacter gandensis	80.9273	486	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.74	98.30	0.89	0.84	6	-
GCF_902753875.1	s__Acinetobacter bouvetii_A	80.6997	420	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004336635.1	s__Acinetobacter sp004336635	80.6882	476	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.82	95.73	0.86	0.83	3	-
GCF_002135295.1	s__Acinetobacter sp002135295	80.6807	474	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002018365.1	s__Acinetobacter sp002018365	80.6622	466	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.65	95.34	0.86	0.83	71	-
GCF_000367925.1	s__Acinetobacter bohemicus	80.6211	489	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.89	95.82	0.83	0.82	4	-
GCF_011578045.1	s__Acinetobacter shaoyimingii	80.527	431	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.63	98.63	0.95	0.95	2	-
GCF_002135355.1	s__Acinetobacter sp002135355	80.5219	425	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107285.1	s__Acinetobacter kyonggiensis	80.4436	510	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.53	95.22	0.88	0.86	3	-
GCF_002803605.1	s__Acinetobacter pseudolwoffii	80.4405	376	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.62	97.19	0.89	0.84	25	-
GCF_002135335.1	s__Acinetobacter sp002135335	80.375	494	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331285.1	s__Acinetobacter sp004331285	80.3044	438	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009939195.1	s__Acinetobacter kanungonis	80.2099	388	914	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.15	96.11	0.90	0.89	4	-
GCF_004331255.1	s__Acinetobacter sp004331255	80.0405	422	914	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 13:37:44,808] [INFO] GTDB search result was written to GCF_009372215.1_ASM937221v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:44,808] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:44,813] [INFO] DFAST_QC result json was written to GCF_009372215.1_ASM937221v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:44,813] [INFO] DFAST_QC completed!
[2024-01-24 13:37:44,813] [INFO] Total running time: 0h1m0s