[2024-01-24 12:36:57,858] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:57,859] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:57,860] [INFO] DQC Reference Directory: /var/lib/cwl/stgc018cde0-382d-4b47-8e33-e7c7e612ba94/dqc_reference
[2024-01-24 12:36:59,200] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:59,201] [INFO] Task started: Prodigal
[2024-01-24 12:36:59,201] [INFO] Running command: gunzip -c /var/lib/cwl/stg3fa1bde5-6cda-4e33-86ac-f97448a8aaef/GCF_018324105.1_ASM1832410v1_genomic.fna.gz | prodigal -d GCF_018324105.1_ASM1832410v1_genomic.fna/cds.fna -a GCF_018324105.1_ASM1832410v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:07,946] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:07,947] [INFO] Task started: HMMsearch
[2024-01-24 12:37:07,947] [INFO] Running command: hmmsearch --tblout GCF_018324105.1_ASM1832410v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc018cde0-382d-4b47-8e33-e7c7e612ba94/dqc_reference/reference_markers.hmm GCF_018324105.1_ASM1832410v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:08,302] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:08,305] [INFO] Found 6/6 markers.
[2024-01-24 12:37:08,345] [INFO] Query marker FASTA was written to GCF_018324105.1_ASM1832410v1_genomic.fna/markers.fasta
[2024-01-24 12:37:08,346] [INFO] Task started: Blastn
[2024-01-24 12:37:08,346] [INFO] Running command: blastn -query GCF_018324105.1_ASM1832410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc018cde0-382d-4b47-8e33-e7c7e612ba94/dqc_reference/reference_markers.fasta -out GCF_018324105.1_ASM1832410v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:09,256] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:09,260] [INFO] Selected 18 target genomes.
[2024-01-24 12:37:09,260] [INFO] Target genome list was writen to GCF_018324105.1_ASM1832410v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:09,273] [INFO] Task started: fastANI
[2024-01-24 12:37:09,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fa1bde5-6cda-4e33-86ac-f97448a8aaef/GCF_018324105.1_ASM1832410v1_genomic.fna.gz --refList GCF_018324105.1_ASM1832410v1_genomic.fna/target_genomes.txt --output GCF_018324105.1_ASM1832410v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:21,782] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:21,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc018cde0-382d-4b47-8e33-e7c7e612ba94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:21,783] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc018cde0-382d-4b47-8e33-e7c7e612ba94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:21,797] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:37:21,798] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:21,799] [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 bouvetii	strain=DSM 14964	GCA_000373725.1	202951	202951	type	True	99.9839	1107	1133	95	conclusive
Acinetobacter bouvetii	strain=CIP 107468	GCA_000368865.1	202951	202951	type	True	99.9821	1122	1133	95	conclusive
Acinetobacter pragensis	strain=ANC 4149	GCA_001605895.1	1806892	1806892	type	True	85.6172	855	1133	95	below_threshold
Acinetobacter tianfuensis	strain=WCHAc060012	GCA_003611465.1	2419603	2419603	type	True	81.5334	648	1133	95	below_threshold
Acinetobacter celticus	strain=ANC 4603	GCA_001707755.1	1891224	1891224	type	True	81.4985	603	1133	95	below_threshold
Acinetobacter johnsonii	strain=FDAARGOS_910	GCA_016027055.1	40214	40214	suspected-type	True	81.443	486	1133	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	81.3744	501	1133	95	below_threshold
Acinetobacter johnsonii	strain=DSM 6963	GCA_000949655.1	40214	40214	suspected-type	True	81.1058	475	1133	95	below_threshold
Acinetobacter cumulans	strain=WCHAc060092	GCA_003024525.3	2136182	2136182	type	True	81.0807	575	1133	95	below_threshold
Acinetobacter chengduensis	strain=WCHAc060005	GCA_003664645.1	2420890	2420890	type	True	80.7637	561	1133	95	below_threshold
Acinetobacter gandensis	strain=ANC 4275	GCA_001678755.1	1443941	1443941	type	True	80.6405	518	1133	95	below_threshold
Acinetobacter pseudolwoffii	strain=ANC 5044	GCA_002803605.1	2053287	2053287	type	True	80.3105	459	1133	95	below_threshold
Acinetobacter indicus	strain=CIP 110367	GCA_000488255.1	756892	756892	type	True	80.2177	479	1133	95	below_threshold
Acinetobacter indicus	strain=DSM 25388	GCA_000830155.1	756892	756892	type	True	79.951	455	1133	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	79.8798	458	1133	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	79.601	352	1133	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	79.1708	289	1133	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	78.347	310	1133	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:21,801] [INFO] DFAST Taxonomy check result was written to GCF_018324105.1_ASM1832410v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:21,802] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:21,802] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:21,802] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc018cde0-382d-4b47-8e33-e7c7e612ba94/dqc_reference/checkm_data
[2024-01-24 12:37:21,803] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:21,848] [INFO] Task started: CheckM
[2024-01-24 12:37:21,848] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018324105.1_ASM1832410v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018324105.1_ASM1832410v1_genomic.fna/checkm_input GCF_018324105.1_ASM1832410v1_genomic.fna/checkm_result
[2024-01-24 12:37:55,464] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:55,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:55,485] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:55,486] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:55,487] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018324105.1_ASM1832410v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:55,487] [INFO] Task started: Blastn
[2024-01-24 12:37:55,487] [INFO] Running command: blastn -query GCF_018324105.1_ASM1832410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc018cde0-382d-4b47-8e33-e7c7e612ba94/dqc_reference/reference_markers_gtdb.fasta -out GCF_018324105.1_ASM1832410v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:56,693] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:56,696] [INFO] Selected 12 target genomes.
[2024-01-24 12:37:56,696] [INFO] Target genome list was writen to GCF_018324105.1_ASM1832410v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:56,705] [INFO] Task started: fastANI
[2024-01-24 12:37:56,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fa1bde5-6cda-4e33-86ac-f97448a8aaef/GCF_018324105.1_ASM1832410v1_genomic.fna.gz --refList GCF_018324105.1_ASM1832410v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018324105.1_ASM1832410v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:05,803] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:05,816] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:05,816] [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_000368865.1	s__Acinetobacter bouvetii	99.9821	1122	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.30	95.72	0.97	0.92	6	conclusive
GCF_001605895.1	s__Acinetobacter pragensis	85.6066	856	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135435.1	s__Acinetobacter sp002135435	84.103	863	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001696615.3	s__Acinetobacter sp001696615	82.3706	718	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611465.1	s__Acinetobacter tianfuensis	81.5445	647	1133	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	81.0786	542	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.65	95.34	0.86	0.83	71	-
GCF_002135295.1	s__Acinetobacter sp002135295	81.049	574	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664645.1	s__Acinetobacter chengduensis	80.7415	563	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.56	99.34	0.91	0.89	3	-
GCF_900096895.1	s__Acinetobacter kookii	80.4954	550	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.51	97.51	0.92	0.92	2	-
GCF_002135355.1	s__Acinetobacter sp002135355	80.4525	560	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002803605.1	s__Acinetobacter pseudolwoffii	80.3229	458	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.62	97.19	0.89	0.84	25	-
GCF_004331285.1	s__Acinetobacter sp004331285	79.841	503	1133	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 12:38:05,818] [INFO] GTDB search result was written to GCF_018324105.1_ASM1832410v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:05,819] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:05,823] [INFO] DFAST_QC result json was written to GCF_018324105.1_ASM1832410v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:05,823] [INFO] DFAST_QC completed!
[2024-01-24 12:38:05,823] [INFO] Total running time: 0h1m8s