[2024-01-25 19:48:35,621] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:48:35,624] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:48:35,624] [INFO] DQC Reference Directory: /var/lib/cwl/stgd03bb28c-53c7-4bb9-ba5f-2503171bbf2c/dqc_reference
[2024-01-25 19:48:36,791] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:48:36,792] [INFO] Task started: Prodigal
[2024-01-25 19:48:36,792] [INFO] Running command: gunzip -c /var/lib/cwl/stgeabf8576-9a92-4b65-9bea-b17a164d3fd2/GCF_000162295.1_ASM16229v1_genomic.fna.gz | prodigal -d GCF_000162295.1_ASM16229v1_genomic.fna/cds.fna -a GCF_000162295.1_ASM16229v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:48:44,064] [INFO] Task succeeded: Prodigal
[2024-01-25 19:48:44,064] [INFO] Task started: HMMsearch
[2024-01-25 19:48:44,064] [INFO] Running command: hmmsearch --tblout GCF_000162295.1_ASM16229v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd03bb28c-53c7-4bb9-ba5f-2503171bbf2c/dqc_reference/reference_markers.hmm GCF_000162295.1_ASM16229v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:48:44,281] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:48:44,282] [INFO] Found 6/6 markers.
[2024-01-25 19:48:44,314] [INFO] Query marker FASTA was written to GCF_000162295.1_ASM16229v1_genomic.fna/markers.fasta
[2024-01-25 19:48:44,315] [INFO] Task started: Blastn
[2024-01-25 19:48:44,315] [INFO] Running command: blastn -query GCF_000162295.1_ASM16229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd03bb28c-53c7-4bb9-ba5f-2503171bbf2c/dqc_reference/reference_markers.fasta -out GCF_000162295.1_ASM16229v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:44,902] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:44,905] [INFO] Selected 8 target genomes.
[2024-01-25 19:48:44,905] [INFO] Target genome list was writen to GCF_000162295.1_ASM16229v1_genomic.fna/target_genomes.txt
[2024-01-25 19:48:44,906] [INFO] Task started: fastANI
[2024-01-25 19:48:44,906] [INFO] Running command: fastANI --query /var/lib/cwl/stgeabf8576-9a92-4b65-9bea-b17a164d3fd2/GCF_000162295.1_ASM16229v1_genomic.fna.gz --refList GCF_000162295.1_ASM16229v1_genomic.fna/target_genomes.txt --output GCF_000162295.1_ASM16229v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:48:51,909] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:51,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd03bb28c-53c7-4bb9-ba5f-2503171bbf2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:48:51,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd03bb28c-53c7-4bb9-ba5f-2503171bbf2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:48:51,917] [INFO] Found 8 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 19:48:51,917] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:48:51,917] [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 baumannii	strain=ATCC 19606	GCA_014116795.1	470	470	type	True	99.9624	1292	1312	95	conclusive
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	99.9593	1298	1312	95	conclusive
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	99.9581	1302	1312	95	conclusive
Acinetobacter baumannii	strain=ATCC 19606	GCA_009035845.1	470	470	type	True	99.9533	1309	1312	95	conclusive
Acinetobacter baumannii	strain=ATCC 19606	GCA_000737145.1	470	470	type	True	99.9501	1304	1312	95	conclusive
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	89.1961	1034	1312	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	80.256	475	1312	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	78.7771	299	1312	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:48:51,924] [INFO] DFAST Taxonomy check result was written to GCF_000162295.1_ASM16229v1_genomic.fna/tc_result.tsv
[2024-01-25 19:48:51,925] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:48:51,925] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:48:51,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd03bb28c-53c7-4bb9-ba5f-2503171bbf2c/dqc_reference/checkm_data
[2024-01-25 19:48:51,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:48:51,966] [INFO] Task started: CheckM
[2024-01-25 19:48:51,966] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000162295.1_ASM16229v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000162295.1_ASM16229v1_genomic.fna/checkm_input GCF_000162295.1_ASM16229v1_genomic.fna/checkm_result
[2024-01-25 19:49:17,663] [INFO] Task succeeded: CheckM
[2024-01-25 19:49:17,664] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:49:17,679] [INFO] ===== Completeness check finished =====
[2024-01-25 19:49:17,680] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:49:17,680] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000162295.1_ASM16229v1_genomic.fna/markers.fasta)
[2024-01-25 19:49:17,680] [INFO] Task started: Blastn
[2024-01-25 19:49:17,680] [INFO] Running command: blastn -query GCF_000162295.1_ASM16229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd03bb28c-53c7-4bb9-ba5f-2503171bbf2c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000162295.1_ASM16229v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:18,474] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:18,476] [INFO] Selected 11 target genomes.
[2024-01-25 19:49:18,476] [INFO] Target genome list was writen to GCF_000162295.1_ASM16229v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:49:18,480] [INFO] Task started: fastANI
[2024-01-25 19:49:18,480] [INFO] Running command: fastANI --query /var/lib/cwl/stgeabf8576-9a92-4b65-9bea-b17a164d3fd2/GCF_000162295.1_ASM16229v1_genomic.fna.gz --refList GCF_000162295.1_ASM16229v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000162295.1_ASM16229v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:49:28,599] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:28,608] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:49:28,609] [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_009759685.1	s__Acinetobacter baumannii	99.957	1301	1312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.86	96.67	0.89	0.80	5417	conclusive
GCF_000368085.1	s__Acinetobacter nosocomialis	91.9119	1087	1312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.94	97.50	0.90	0.85	250	-
GCF_000368065.1	s__Acinetobacter seifertii	90.1922	1049	1312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.88	96.48	0.87	0.81	81	-
GCF_002928115.1	s__Acinetobacter pittii_H	89.1771	1066	1312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.46	96.15	0.91	0.87	9	-
GCF_001605885.1	s__Acinetobacter lactucae	88.5169	1061	1312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.34	96.55	0.91	0.85	16	-
GCF_013344765.1	s__Acinetobacter lactucae_A	88.4605	864	1312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.51	97.14	0.90	0.87	4	-
GCF_000399685.1	s__Acinetobacter pittii_E	88.3583	1038	1312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196795.1	s__Acinetobacter oleivorans	88.0714	1077	1312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.22	95.12	0.90	0.85	40	-
GCF_000313935.1	s__Acinetobacter sp000313935	88.014	1055	1312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.37	99.37	0.94	0.94	2	-
GCF_000399665.1	s__Acinetobacter calcoaceticus_B	87.6832	1033	1312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016508255.1	s__Acinetobacter calcoaceticus_E	87.2924	1022	1312	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 19:49:28,610] [INFO] GTDB search result was written to GCF_000162295.1_ASM16229v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:49:28,611] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:49:28,613] [INFO] DFAST_QC result json was written to GCF_000162295.1_ASM16229v1_genomic.fna/dqc_result.json
[2024-01-25 19:49:28,614] [INFO] DFAST_QC completed!
[2024-01-25 19:49:28,614] [INFO] Total running time: 0h0m53s