[2024-01-24 14:55:50,237] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:50,242] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:50,243] [INFO] DQC Reference Directory: /var/lib/cwl/stg43904c66-c72a-46ac-b379-a8bb86d670fa/dqc_reference
[2024-01-24 14:55:51,531] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:51,532] [INFO] Task started: Prodigal
[2024-01-24 14:55:51,532] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a6b3594-c4a2-49c8-905b-5d6e03af3114/GCF_003024525.3_ASM302452v3_genomic.fna.gz | prodigal -d GCF_003024525.3_ASM302452v3_genomic.fna/cds.fna -a GCF_003024525.3_ASM302452v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:00,440] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:00,440] [INFO] Task started: HMMsearch
[2024-01-24 14:56:00,441] [INFO] Running command: hmmsearch --tblout GCF_003024525.3_ASM302452v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43904c66-c72a-46ac-b379-a8bb86d670fa/dqc_reference/reference_markers.hmm GCF_003024525.3_ASM302452v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:00,725] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:00,726] [INFO] Found 6/6 markers.
[2024-01-24 14:56:00,759] [INFO] Query marker FASTA was written to GCF_003024525.3_ASM302452v3_genomic.fna/markers.fasta
[2024-01-24 14:56:00,760] [INFO] Task started: Blastn
[2024-01-24 14:56:00,760] [INFO] Running command: blastn -query GCF_003024525.3_ASM302452v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg43904c66-c72a-46ac-b379-a8bb86d670fa/dqc_reference/reference_markers.fasta -out GCF_003024525.3_ASM302452v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:01,497] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:01,500] [INFO] Selected 17 target genomes.
[2024-01-24 14:56:01,500] [INFO] Target genome list was writen to GCF_003024525.3_ASM302452v3_genomic.fna/target_genomes.txt
[2024-01-24 14:56:01,509] [INFO] Task started: fastANI
[2024-01-24 14:56:01,509] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a6b3594-c4a2-49c8-905b-5d6e03af3114/GCF_003024525.3_ASM302452v3_genomic.fna.gz --refList GCF_003024525.3_ASM302452v3_genomic.fna/target_genomes.txt --output GCF_003024525.3_ASM302452v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:14,775] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:14,776] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43904c66-c72a-46ac-b379-a8bb86d670fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:14,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43904c66-c72a-46ac-b379-a8bb86d670fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:14,801] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:56:14,801] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:14,801] [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 cumulans	strain=WCHAc060092	GCA_003024525.3	2136182	2136182	type	True	100.0	1200	1233	95	conclusive
Acinetobacter chengduensis	strain=WCHAc060005	GCA_003664645.1	2420890	2420890	type	True	88.8365	936	1233	95	below_threshold
Acinetobacter tianfuensis	strain=WCHAc060012	GCA_003611465.1	2419603	2419603	type	True	82.7626	692	1233	95	below_threshold
Acinetobacter gandensis	strain=ANC 4275	GCA_001678755.1	1443941	1443941	type	True	81.8964	580	1233	95	below_threshold
Acinetobacter gandensis	strain=CCUG 68482	GCA_008802205.1	1443941	1443941	type	True	81.8124	591	1233	95	below_threshold
Acinetobacter johnsonii	strain=FDAARGOS_910	GCA_016027055.1	40214	40214	suspected-type	True	81.4287	523	1233	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	81.2567	547	1233	95	below_threshold
Acinetobacter schindleri	strain=CIP 107287	GCA_000368625.1	108981	108981	type	True	81.1638	475	1233	95	below_threshold
Acinetobacter portensis	strain=AC 877	GCA_009372215.1	1839785	1839785	type	True	81.0466	488	1233	95	below_threshold
Acinetobacter wuhouensis	strain=WCHA60	GCA_001696605.3	1879050	1879050	type	True	81.0256	517	1233	95	below_threshold
Acinetobacter celticus	strain=ANC 4603	GCA_001707755.1	1891224	1891224	type	True	80.7705	577	1233	95	below_threshold
Acinetobacter johnsonii	strain=DSM 6963	GCA_000949655.1	40214	40214	suspected-type	True	80.7419	518	1233	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	80.3324	442	1233	95	below_threshold
Acinetobacter gerneri	strain=KCTC 12415	GCA_000747725.1	202952	202952	type	True	79.7473	401	1233	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	79.7413	413	1233	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	79.5533	364	1233	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	79.5401	364	1233	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:14,803] [INFO] DFAST Taxonomy check result was written to GCF_003024525.3_ASM302452v3_genomic.fna/tc_result.tsv
[2024-01-24 14:56:14,803] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:14,803] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:14,803] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43904c66-c72a-46ac-b379-a8bb86d670fa/dqc_reference/checkm_data
[2024-01-24 14:56:14,804] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:14,840] [INFO] Task started: CheckM
[2024-01-24 14:56:14,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003024525.3_ASM302452v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003024525.3_ASM302452v3_genomic.fna/checkm_input GCF_003024525.3_ASM302452v3_genomic.fna/checkm_result
[2024-01-24 14:56:48,232] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:48,234] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:48,256] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:48,256] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:48,257] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003024525.3_ASM302452v3_genomic.fna/markers.fasta)
[2024-01-24 14:56:48,257] [INFO] Task started: Blastn
[2024-01-24 14:56:48,258] [INFO] Running command: blastn -query GCF_003024525.3_ASM302452v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg43904c66-c72a-46ac-b379-a8bb86d670fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_003024525.3_ASM302452v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:49,445] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:49,448] [INFO] Selected 17 target genomes.
[2024-01-24 14:56:49,448] [INFO] Target genome list was writen to GCF_003024525.3_ASM302452v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:49,469] [INFO] Task started: fastANI
[2024-01-24 14:56:49,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a6b3594-c4a2-49c8-905b-5d6e03af3114/GCF_003024525.3_ASM302452v3_genomic.fna.gz --refList GCF_003024525.3_ASM302452v3_genomic.fna/target_genomes_gtdb.txt --output GCF_003024525.3_ASM302452v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:03,204] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:03,227] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:03,228] [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_003024525.3	s__Acinetobacter cumulans	100.0	1197	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	97.84	0.86	0.82	9	conclusive
GCF_003664645.1	s__Acinetobacter chengduensis	88.8233	936	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.56	99.34	0.91	0.89	3	-
GCF_003611465.1	s__Acinetobacter tianfuensis	82.7586	692	1233	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	82.6503	644	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.65	95.34	0.86	0.83	71	-
GCF_001678755.1	s__Acinetobacter gandensis	81.8941	580	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.74	98.30	0.89	0.84	6	-
GCF_002135295.1	s__Acinetobacter sp002135295	81.6098	619	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001647675.1	s__Acinetobacter sp001647675	81.5984	532	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368045.1	s__Acinetobacter johnsonii	81.4018	540	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.19	95.36	0.86	0.80	59	-
GCF_002165305.2	s__Acinetobacter sp002165305	81.1393	539	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009372215.1	s__Acinetobacter portensis	81.071	487	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.69	98.69	0.93	0.93	2	-
GCF_001696605.3	s__Acinetobacter wuhouensis	80.9938	524	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.82	96.71	0.87	0.86	6	-
GCF_002688565.1	s__Acinetobacter sp002688565	80.9713	479	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001707755.1	s__Acinetobacter celticus	80.7731	577	1233	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	80.7423	451	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711395.1	s__Acinetobacter sp003711395	80.6486	447	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.62	98.61	0.92	0.90	3	-
GCF_002135205.1	s__Acinetobacter sp002135205	80.6334	515	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.42	98.15	0.90	0.88	5	-
GCA_002365595.1	s__Acinetobacter sp002365595	80.6091	503	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.10	98.08	0.91	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:03,229] [INFO] GTDB search result was written to GCF_003024525.3_ASM302452v3_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:03,230] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:03,234] [INFO] DFAST_QC result json was written to GCF_003024525.3_ASM302452v3_genomic.fna/dqc_result.json
[2024-01-24 14:57:03,235] [INFO] DFAST_QC completed!
[2024-01-24 14:57:03,235] [INFO] Total running time: 0h1m13s