[2024-01-24 10:48:09,572] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,574] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,574] [INFO] DQC Reference Directory: /var/lib/cwl/stgd90481a7-1e50-4213-ae2a-b1e8f2132f5a/dqc_reference
[2024-01-24 10:48:23,956] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,957] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,958] [INFO] Running command: gunzip -c /var/lib/cwl/stg37ad15c7-e2c0-439b-b1b4-6cae99a1b34f/GCF_008802205.1_ASM880220v1_genomic.fna.gz | prodigal -d GCF_008802205.1_ASM880220v1_genomic.fna/cds.fna -a GCF_008802205.1_ASM880220v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:31,207] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:31,207] [INFO] Task started: HMMsearch
[2024-01-24 10:48:31,207] [INFO] Running command: hmmsearch --tblout GCF_008802205.1_ASM880220v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd90481a7-1e50-4213-ae2a-b1e8f2132f5a/dqc_reference/reference_markers.hmm GCF_008802205.1_ASM880220v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:31,482] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:31,484] [INFO] Found 6/6 markers.
[2024-01-24 10:48:31,514] [INFO] Query marker FASTA was written to GCF_008802205.1_ASM880220v1_genomic.fna/markers.fasta
[2024-01-24 10:48:31,515] [INFO] Task started: Blastn
[2024-01-24 10:48:31,515] [INFO] Running command: blastn -query GCF_008802205.1_ASM880220v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd90481a7-1e50-4213-ae2a-b1e8f2132f5a/dqc_reference/reference_markers.fasta -out GCF_008802205.1_ASM880220v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:32,209] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:32,214] [INFO] Selected 17 target genomes.
[2024-01-24 10:48:32,215] [INFO] Target genome list was writen to GCF_008802205.1_ASM880220v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:32,228] [INFO] Task started: fastANI
[2024-01-24 10:48:32,228] [INFO] Running command: fastANI --query /var/lib/cwl/stg37ad15c7-e2c0-439b-b1b4-6cae99a1b34f/GCF_008802205.1_ASM880220v1_genomic.fna.gz --refList GCF_008802205.1_ASM880220v1_genomic.fna/target_genomes.txt --output GCF_008802205.1_ASM880220v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:43,854] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:43,855] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd90481a7-1e50-4213-ae2a-b1e8f2132f5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:43,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd90481a7-1e50-4213-ae2a-b1e8f2132f5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:43,869] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:48:43,869] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:43,869] [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=CCUG 68482	GCA_008802205.1	1443941	1443941	type	True	100.0	1033	1035	95	conclusive
Acinetobacter gandensis	strain=ANC 4275	GCA_001678755.1	1443941	1443941	type	True	99.9974	1025	1035	95	conclusive
Acinetobacter cumulans	strain=WCHAc060092	GCA_003024525.3	2136182	2136182	type	True	81.6891	599	1035	95	below_threshold
Acinetobacter chengduensis	strain=WCHAc060005	GCA_003664645.1	2420890	2420890	type	True	81.6114	576	1035	95	below_threshold
Acinetobacter wanghuae	strain=dk386	GCA_009557235.1	2662362	2662362	type	True	81.2409	484	1035	95	below_threshold
Acinetobacter tianfuensis	strain=WCHAc060012	GCA_003611465.1	2419603	2419603	type	True	81.1478	501	1035	95	below_threshold
Acinetobacter celticus	strain=ANC 4603	GCA_001707755.1	1891224	1891224	type	True	80.9096	530	1035	95	below_threshold
Acinetobacter portensis	strain=AC 877	GCA_009372215.1	1839785	1839785	type	True	80.883	481	1035	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	80.7511	535	1035	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	80.7475	461	1035	95	below_threshold
Acinetobacter terrae	strain=ANC 4282	GCA_013004375.1	2731247	2731247	type	True	80.5855	535	1035	95	below_threshold
Acinetobacter equi	strain=114	GCA_001307195.1	1324350	1324350	type	True	80.3926	429	1035	95	below_threshold
Acinetobacter pragensis	strain=ANC 4149	GCA_001605895.1	1806892	1806892	type	True	80.3403	499	1035	95	below_threshold
Acinetobacter wuhouensis	strain=WCHA60	GCA_001696605.3	1879050	1879050	type	True	80.2724	471	1035	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	79.7464	434	1035	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	79.1837	369	1035	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	78.5418	334	1035	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:43,871] [INFO] DFAST Taxonomy check result was written to GCF_008802205.1_ASM880220v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:43,872] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:43,872] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:43,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd90481a7-1e50-4213-ae2a-b1e8f2132f5a/dqc_reference/checkm_data
[2024-01-24 10:48:43,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:43,914] [INFO] Task started: CheckM
[2024-01-24 10:48:43,915] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008802205.1_ASM880220v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008802205.1_ASM880220v1_genomic.fna/checkm_input GCF_008802205.1_ASM880220v1_genomic.fna/checkm_result
[2024-01-24 10:49:14,181] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:14,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:14,207] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:14,208] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:14,208] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008802205.1_ASM880220v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:14,209] [INFO] Task started: Blastn
[2024-01-24 10:49:14,209] [INFO] Running command: blastn -query GCF_008802205.1_ASM880220v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd90481a7-1e50-4213-ae2a-b1e8f2132f5a/dqc_reference/reference_markers_gtdb.fasta -out GCF_008802205.1_ASM880220v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:15,360] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:15,367] [INFO] Selected 16 target genomes.
[2024-01-24 10:49:15,367] [INFO] Target genome list was writen to GCF_008802205.1_ASM880220v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:15,416] [INFO] Task started: fastANI
[2024-01-24 10:49:15,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg37ad15c7-e2c0-439b-b1b4-6cae99a1b34f/GCF_008802205.1_ASM880220v1_genomic.fna.gz --refList GCF_008802205.1_ASM880220v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008802205.1_ASM880220v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:29,098] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:29,120] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:29,120] [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_001678755.1	s__Acinetobacter gandensis	99.9974	1025	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.74	98.30	0.89	0.84	6	conclusive
GCF_002018365.1	s__Acinetobacter sp002018365	84.8526	811	1035	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	84.4609	781	1035	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	81.6798	594	1035	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	81.599	577	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.56	99.34	0.91	0.89	3	-
GCF_009557235.1	s__Acinetobacter wanghuae	81.2551	483	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.95	99.95	0.94	0.94	2	-
GCF_009707625.1	s__Acinetobacter sp009707625	81.0241	475	1035	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	80.9247	501	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.80	96.56	0.83	0.80	8	-
GCF_001707755.1	s__Acinetobacter celticus	80.9239	528	1035	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	80.8966	480	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.69	98.69	0.93	0.93	2	-
GCF_004336635.1	s__Acinetobacter sp004336635	80.7685	527	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.82	95.73	0.86	0.83	3	-
GCF_012371325.1	s__Acinetobacter sp012371325	80.5864	467	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.91	97.28	0.89	0.84	6	-
GCF_013004375.1	s__Acinetobacter terrae	80.569	537	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.86	96.05	0.92	0.88	8	-
GCF_001307195.1	s__Acinetobacter equi	80.4255	429	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001605895.1	s__Acinetobacter pragensis	80.3403	499	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001696605.3	s__Acinetobacter wuhouensis	80.2709	471	1035	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.82	96.71	0.87	0.86	6	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:29,122] [INFO] GTDB search result was written to GCF_008802205.1_ASM880220v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:29,123] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:29,127] [INFO] DFAST_QC result json was written to GCF_008802205.1_ASM880220v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:29,127] [INFO] DFAST_QC completed!
[2024-01-24 10:49:29,127] [INFO] Total running time: 0h1m20s