[2024-01-25 19:50:20,445] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:50:20,446] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:50:20,447] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b12c44a-582b-4c01-85ba-f2b54dd1b8f9/dqc_reference
[2024-01-25 19:50:21,617] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:50:21,617] [INFO] Task started: Prodigal
[2024-01-25 19:50:21,618] [INFO] Running command: gunzip -c /var/lib/cwl/stg70ddc738-4e43-4523-9e09-0fd8fecfe697/GCF_023499985.1_ASM2349998v1_genomic.fna.gz | prodigal -d GCF_023499985.1_ASM2349998v1_genomic.fna/cds.fna -a GCF_023499985.1_ASM2349998v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:50:28,724] [INFO] Task succeeded: Prodigal
[2024-01-25 19:50:28,725] [INFO] Task started: HMMsearch
[2024-01-25 19:50:28,725] [INFO] Running command: hmmsearch --tblout GCF_023499985.1_ASM2349998v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b12c44a-582b-4c01-85ba-f2b54dd1b8f9/dqc_reference/reference_markers.hmm GCF_023499985.1_ASM2349998v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:50:29,062] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:50:29,063] [INFO] Found 6/6 markers.
[2024-01-25 19:50:29,091] [INFO] Query marker FASTA was written to GCF_023499985.1_ASM2349998v1_genomic.fna/markers.fasta
[2024-01-25 19:50:29,092] [INFO] Task started: Blastn
[2024-01-25 19:50:29,092] [INFO] Running command: blastn -query GCF_023499985.1_ASM2349998v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b12c44a-582b-4c01-85ba-f2b54dd1b8f9/dqc_reference/reference_markers.fasta -out GCF_023499985.1_ASM2349998v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:29,759] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:29,761] [INFO] Selected 25 target genomes.
[2024-01-25 19:50:29,762] [INFO] Target genome list was writen to GCF_023499985.1_ASM2349998v1_genomic.fna/target_genomes.txt
[2024-01-25 19:50:29,782] [INFO] Task started: fastANI
[2024-01-25 19:50:29,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg70ddc738-4e43-4523-9e09-0fd8fecfe697/GCF_023499985.1_ASM2349998v1_genomic.fna.gz --refList GCF_023499985.1_ASM2349998v1_genomic.fna/target_genomes.txt --output GCF_023499985.1_ASM2349998v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:50:46,866] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:46,866] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b12c44a-582b-4c01-85ba-f2b54dd1b8f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:50:46,866] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b12c44a-582b-4c01-85ba-f2b54dd1b8f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:50:46,880] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:50:46,881] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:50:46,881] [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 gandensis	strain=ANC 4275	GCA_001678755.1	1443941	1443941	type	True	85.4714	811	1134	95	below_threshold
Acinetobacter gandensis	strain=CCUG 68482	GCA_008802205.1	1443941	1443941	type	True	85.4295	802	1134	95	below_threshold
Acinetobacter cumulans	strain=WCHAc060092	GCA_003024525.3	2136182	2136182	type	True	82.19	644	1134	95	below_threshold
Acinetobacter chengduensis	strain=WCHAc060005	GCA_003664645.1	2420890	2420890	type	True	82.084	618	1134	95	below_threshold
Acinetobacter wanghuae	strain=dk386	GCA_009557235.1	2662362	2662362	type	True	81.0736	505	1134	95	below_threshold
Acinetobacter portensis	strain=AC 877	GCA_009372215.1	1839785	1839785	type	True	80.9576	470	1134	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	80.8729	541	1134	95	below_threshold
Acinetobacter variabilis	strain=NIPH 2171	GCA_000369625.1	70346	70346	type	True	80.8386	479	1134	95	below_threshold
Acinetobacter johnsonii	strain=FDAARGOS_910	GCA_016027055.1	40214	40214	suspected-type	True	80.816	547	1134	95	below_threshold
Acinetobacter johnsonii	strain=DSM 6963	GCA_000949655.1	40214	40214	suspected-type	True	80.7143	517	1134	95	below_threshold
Acinetobacter pragensis	strain=ANC 4149	GCA_001605895.1	1806892	1806892	type	True	80.6608	525	1134	95	below_threshold
Acinetobacter seohaensis	strain=DSM 16313	GCA_018403785.1	281376	281376	type	True	80.5928	461	1134	95	below_threshold
Acinetobacter pseudolwoffii	strain=ANC 5044	GCA_002803605.1	2053287	2053287	type	True	80.5655	493	1134	95	below_threshold
Acinetobacter schindleri	strain=CIP 107287	GCA_000368625.1	108981	108981	type	True	80.5438	482	1134	95	below_threshold
Acinetobacter lwoffii	strain=FDAARGOS 1393	GCA_019048305.1	28090	28090	type	True	80.5165	489	1134	95	below_threshold
Acinetobacter lwoffii	strain=NCTC5866	GCA_900699155.1	28090	28090	type	True	80.4927	486	1134	95	below_threshold
Acinetobacter towneri	strain=DSM 14962	GCA_000688495.1	202956	202956	type	True	80.4847	489	1134	95	below_threshold
Acinetobacter towneri	strain=CIP 107472	GCA_000368785.1	202956	202956	type	True	80.4588	494	1134	95	below_threshold
Acinetobacter equi	strain=114	GCA_001307195.1	1324350	1324350	type	True	80.4489	429	1134	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	80.3498	460	1134	95	below_threshold
Acinetobacter wuhouensis	strain=WCHA60	GCA_001696605.3	1879050	1879050	type	True	80.1152	507	1134	95	below_threshold
Acinetobacter sichuanensis	strain=WCHAc060041	GCA_003024515.2	2136183	2136183	type	True	79.9444	478	1134	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	79.5484	422	1134	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	79.3613	357	1134	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	79.2719	331	1134	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:50:46,882] [INFO] DFAST Taxonomy check result was written to GCF_023499985.1_ASM2349998v1_genomic.fna/tc_result.tsv
[2024-01-25 19:50:46,882] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:50:46,882] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:50:46,883] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b12c44a-582b-4c01-85ba-f2b54dd1b8f9/dqc_reference/checkm_data
[2024-01-25 19:50:46,883] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:50:46,919] [INFO] Task started: CheckM
[2024-01-25 19:50:46,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023499985.1_ASM2349998v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023499985.1_ASM2349998v1_genomic.fna/checkm_input GCF_023499985.1_ASM2349998v1_genomic.fna/checkm_result
[2024-01-25 19:51:13,315] [INFO] Task succeeded: CheckM
[2024-01-25 19:51:13,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 19:51:13,337] [INFO] ===== Completeness check finished =====
[2024-01-25 19:51:13,337] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:51:13,337] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023499985.1_ASM2349998v1_genomic.fna/markers.fasta)
[2024-01-25 19:51:13,337] [INFO] Task started: Blastn
[2024-01-25 19:51:13,337] [INFO] Running command: blastn -query GCF_023499985.1_ASM2349998v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b12c44a-582b-4c01-85ba-f2b54dd1b8f9/dqc_reference/reference_markers_gtdb.fasta -out GCF_023499985.1_ASM2349998v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:14,400] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:14,403] [INFO] Selected 18 target genomes.
[2024-01-25 19:51:14,403] [INFO] Target genome list was writen to GCF_023499985.1_ASM2349998v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:51:14,421] [INFO] Task started: fastANI
[2024-01-25 19:51:14,421] [INFO] Running command: fastANI --query /var/lib/cwl/stg70ddc738-4e43-4523-9e09-0fd8fecfe697/GCF_023499985.1_ASM2349998v1_genomic.fna.gz --refList GCF_023499985.1_ASM2349998v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023499985.1_ASM2349998v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:51:27,182] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:27,193] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:51:27,194] [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_002018365.1	s__Acinetobacter sp002018365	95.4543	1001	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.65	95.34	0.86	0.83	71	conclusive
GCF_001678755.1	s__Acinetobacter gandensis	85.4499	813	1134	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	84.6794	836	1134	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	82.2213	639	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	97.84	0.86	0.82	9	-
GCF_003664645.1	s__Acinetobacter chengduensis	82.084	618	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.56	99.34	0.91	0.89	3	-
GCF_001647675.1	s__Acinetobacter sp001647675	81.4785	516	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902753875.1	s__Acinetobacter bouvetii_A	81.4422	541	1134	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	81.225	590	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009557235.1	s__Acinetobacter wanghuae	81.0867	504	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.95	99.95	0.94	0.94	2	-
GCF_002135315.1	s__Acinetobacter sp002135315	80.9861	540	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016599715.1	s__Acinetobacter sp002135245	80.9836	525	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.80	96.56	0.83	0.80	8	-
GCF_000368045.1	s__Acinetobacter johnsonii	80.8305	539	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.19	95.36	0.86	0.80	59	-
GCA_002365595.1	s__Acinetobacter sp002365595	80.6914	517	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.10	98.08	0.91	0.89	3	-
GCF_000773685.1	s__Acinetobacter sp000773685	80.6075	432	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000487975.1	s__Acinetobacter lwoffii	80.4822	482	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.2485	99.52	96.36	0.98	0.86	9	-
GCA_900766635.1	s__Acinetobacter sp900766635	80.0702	233	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024515.2	s__Acinetobacter sichuanensis	79.9619	476	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009912575.1	s__Acinetobacter bereziniae_A	79.2979	410	1134	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 19:51:27,195] [INFO] GTDB search result was written to GCF_023499985.1_ASM2349998v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:51:27,196] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:51:27,199] [INFO] DFAST_QC result json was written to GCF_023499985.1_ASM2349998v1_genomic.fna/dqc_result.json
[2024-01-25 19:51:27,199] [INFO] DFAST_QC completed!
[2024-01-25 19:51:27,199] [INFO] Total running time: 0h1m7s