[2024-01-25 18:59:05,550] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:59:05,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:59:05,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg0cb1b6c0-e938-4508-8e21-63c78f66dbb6/dqc_reference
[2024-01-25 18:59:06,662] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:59:06,662] [INFO] Task started: Prodigal
[2024-01-25 18:59:06,663] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d0c4bdc-1a90-4d9f-bf92-bc84c22ba454/GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna.gz | prodigal -d GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna/cds.fna -a GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:59:13,923] [INFO] Task succeeded: Prodigal
[2024-01-25 18:59:13,923] [INFO] Task started: HMMsearch
[2024-01-25 18:59:13,923] [INFO] Running command: hmmsearch --tblout GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0cb1b6c0-e938-4508-8e21-63c78f66dbb6/dqc_reference/reference_markers.hmm GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:59:14,136] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:59:14,137] [INFO] Found 6/6 markers.
[2024-01-25 18:59:14,170] [INFO] Query marker FASTA was written to GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna/markers.fasta
[2024-01-25 18:59:14,170] [INFO] Task started: Blastn
[2024-01-25 18:59:14,170] [INFO] Running command: blastn -query GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0cb1b6c0-e938-4508-8e21-63c78f66dbb6/dqc_reference/reference_markers.fasta -out GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:14,798] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:14,801] [INFO] Selected 11 target genomes.
[2024-01-25 18:59:14,801] [INFO] Target genome list was writen to GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna/target_genomes.txt
[2024-01-25 18:59:14,808] [INFO] Task started: fastANI
[2024-01-25 18:59:14,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d0c4bdc-1a90-4d9f-bf92-bc84c22ba454/GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna.gz --refList GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna/target_genomes.txt --output GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:59:24,910] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:24,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0cb1b6c0-e938-4508-8e21-63c78f66dbb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:59:24,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0cb1b6c0-e938-4508-8e21-63c78f66dbb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:59:24,918] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:59:24,919] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:59:24,919] [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 calcoaceticus	strain=CIP 81.8	GCA_000368965.1	471	471	type	True	100.0	1305	1307	95	conclusive
Acinetobacter calcoaceticus	strain=NCTC12983	GCA_900444805.1	471	471	type	True	99.9948	1304	1307	95	conclusive
Acinetobacter oleivorans	strain=DR1	GCA_000196795.1	1148157	1148157	suspected-type	True	91.9162	1147	1307	95	below_threshold
Acinetobacter oleivorans	strain=KCTC 23045	GCA_000836035.1	1148157	1148157	suspected-type	True	91.8425	1136	1307	95	below_threshold
Acinetobacter lactucae	strain=NRRL B-41902	GCA_001605885.1	1785128	1785128	type	True	90.1432	1108	1307	95	below_threshold
Acinetobacter pittii	strain=FDAARGOS 1399	GCA_019047205.1	48296	48296	type	True	90.099	1092	1307	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	90.0198	1061	1307	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	87.331	1048	1307	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	87.2885	1069	1307	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	80.4895	486	1307	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	80.465	471	1307	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:59:24,921] [INFO] DFAST Taxonomy check result was written to GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna/tc_result.tsv
[2024-01-25 18:59:24,921] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:59:24,921] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:59:24,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0cb1b6c0-e938-4508-8e21-63c78f66dbb6/dqc_reference/checkm_data
[2024-01-25 18:59:24,922] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:59:24,962] [INFO] Task started: CheckM
[2024-01-25 18:59:24,962] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna/checkm_input GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna/checkm_result
[2024-01-25 18:59:51,306] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:51,307] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:51,328] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:51,328] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:51,328] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna/markers.fasta)
[2024-01-25 18:59:51,328] [INFO] Task started: Blastn
[2024-01-25 18:59:51,328] [INFO] Running command: blastn -query GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0cb1b6c0-e938-4508-8e21-63c78f66dbb6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:52,348] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:52,351] [INFO] Selected 6 target genomes.
[2024-01-25 18:59:52,352] [INFO] Target genome list was writen to GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:59:52,365] [INFO] Task started: fastANI
[2024-01-25 18:59:52,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d0c4bdc-1a90-4d9f-bf92-bc84c22ba454/GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna.gz --refList GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:59:58,954] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:58,959] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:59:58,960] [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_000368965.1	s__Acinetobacter calcoaceticus	100.0	1304	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.00	95.80	0.92	0.85	26	conclusive
GCF_900520355.1	s__Acinetobacter calcoaceticus_C	93.827	1161	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.76	96.36	0.92	0.90	4	-
GCF_000399665.1	s__Acinetobacter calcoaceticus_B	92.3601	1142	1307	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	91.9329	1145	1307	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	91.7214	1072	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.37	99.37	0.94	0.94	2	-
GCF_016508255.1	s__Acinetobacter calcoaceticus_E	91.2412	1092	1307	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 18:59:58,961] [INFO] GTDB search result was written to GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:59:58,961] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:59:58,964] [INFO] DFAST_QC result json was written to GCF_000368965.1_Acin_calc_CIP_81_8_V1_genomic.fna/dqc_result.json
[2024-01-25 18:59:58,964] [INFO] DFAST_QC completed!
[2024-01-25 18:59:58,964] [INFO] Total running time: 0h0m53s