[2024-01-24 13:58:41,087] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:41,089] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:41,089] [INFO] DQC Reference Directory: /var/lib/cwl/stg72b5c576-c54f-42a7-8bed-9998ae082480/dqc_reference
[2024-01-24 13:58:42,469] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:42,470] [INFO] Task started: Prodigal
[2024-01-24 13:58:42,471] [INFO] Running command: gunzip -c /var/lib/cwl/stgf50ba7e5-592e-4fe1-81d6-16a41cc8c4fa/GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna.gz | prodigal -d GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna/cds.fna -a GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:54,119] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:54,119] [INFO] Task started: HMMsearch
[2024-01-24 13:58:54,119] [INFO] Running command: hmmsearch --tblout GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72b5c576-c54f-42a7-8bed-9998ae082480/dqc_reference/reference_markers.hmm GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:54,462] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:54,464] [INFO] Found 6/6 markers.
[2024-01-24 13:58:54,505] [INFO] Query marker FASTA was written to GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna/markers.fasta
[2024-01-24 13:58:54,505] [INFO] Task started: Blastn
[2024-01-24 13:58:54,505] [INFO] Running command: blastn -query GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72b5c576-c54f-42a7-8bed-9998ae082480/dqc_reference/reference_markers.fasta -out GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:55,280] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:55,285] [INFO] Selected 13 target genomes.
[2024-01-24 13:58:55,286] [INFO] Target genome list was writen to GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:55,294] [INFO] Task started: fastANI
[2024-01-24 13:58:55,295] [INFO] Running command: fastANI --query /var/lib/cwl/stgf50ba7e5-592e-4fe1-81d6-16a41cc8c4fa/GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna.gz --refList GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna/target_genomes.txt --output GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:06,676] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:06,677] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72b5c576-c54f-42a7-8bed-9998ae082480/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:06,677] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72b5c576-c54f-42a7-8bed-9998ae082480/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:06,695] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:06,695] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:06,696] [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 proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	99.994	1416	1437	95	conclusive
Acinetobacter gyllenbergii	strain=CIP 110306	GCA_000413855.1	134534	134534	type	True	91.7868	1154	1437	95	below_threshold
Acinetobacter gyllenbergii	strain=MTCC 11365	GCA_000414075.1	134534	134534	type	True	91.7501	1173	1437	95	below_threshold
Acinetobacter colistiniresistens	strain=NIPH 2036	GCA_000413935.1	280145	280145	type	True	88.2005	1029	1437	95	below_threshold
Acinetobacter courvalinii	strain=CCUG 67960	GCA_008802255.1	280147	280147	type	True	86.0956	1003	1437	95	below_threshold
Acinetobacter vivianii	strain=CCM 8642	GCA_014635885.1	1776742	1776742	type	True	85.6303	995	1437	95	below_threshold
Acinetobacter modestus	strain=CCM 8639	GCA_014636095.1	1776740	1776740	type	True	84.3575	828	1437	95	below_threshold
Acinetobacter venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	83.5815	778	1437	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	82.9002	718	1437	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	82.6776	754	1437	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	80.1741	522	1437	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	80.1335	527	1437	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	79.4549	425	1437	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:06,697] [INFO] DFAST Taxonomy check result was written to GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:06,698] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:06,698] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:06,698] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72b5c576-c54f-42a7-8bed-9998ae082480/dqc_reference/checkm_data
[2024-01-24 13:59:06,700] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:06,742] [INFO] Task started: CheckM
[2024-01-24 13:59:06,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna/checkm_input GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna/checkm_result
[2024-01-24 13:59:46,693] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:46,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:46,716] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:46,717] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:46,717] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna/markers.fasta)
[2024-01-24 13:59:46,718] [INFO] Task started: Blastn
[2024-01-24 13:59:46,718] [INFO] Running command: blastn -query GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72b5c576-c54f-42a7-8bed-9998ae082480/dqc_reference/reference_markers_gtdb.fasta -out GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:47,791] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:47,794] [INFO] Selected 11 target genomes.
[2024-01-24 13:59:47,795] [INFO] Target genome list was writen to GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:47,801] [INFO] Task started: fastANI
[2024-01-24 13:59:47,801] [INFO] Running command: fastANI --query /var/lib/cwl/stgf50ba7e5-592e-4fe1-81d6-16a41cc8c4fa/GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna.gz --refList GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:58,485] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:58,498] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:58,498] [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_000367945.1	s__Acinetobacter proteolyticus	99.994	1417	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.84	97.76	0.89	0.87	5	conclusive
GCF_000413855.1	s__Acinetobacter gyllenbergii	91.7697	1156	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.05	97.97	0.95	0.91	6	-
GCF_000369525.1	s__Acinetobacter sp000369525	91.6185	1198	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.13	96.00	0.90	0.87	7	-
GCF_000400715.1	s__Acinetobacter sp000400715	91.4606	1145	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013072695.1	s__Acinetobacter sp013072695	90.6931	1185	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009884975.1	s__Acinetobacter dispersus	89.3912	1106	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.44	95.54	0.90	0.89	4	-
GCF_011753255.1	s__Acinetobacter sp011753255	89.3805	1086	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000369645.1	s__Acinetobacter sp000369645	88.2916	1061	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.86	98.16	0.89	0.84	9	-
GCF_000413935.1	s__Acinetobacter colistiniresistens	88.1889	1030	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.98	96.69	0.90	0.86	10	-
GCF_014636095.1	s__Acinetobacter modestus	84.3631	827	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.76	96.94	0.90	0.86	5	-
GCF_002165255.2	s__Acinetobacter sp002165255	84.2448	722	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.92	96.70	0.85	0.83	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:58,500] [INFO] GTDB search result was written to GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:58,500] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:58,504] [INFO] DFAST_QC result json was written to GCF_000367945.1_Acin_sp_NIPH_809_V1_genomic.fna/dqc_result.json
[2024-01-24 13:59:58,504] [INFO] DFAST_QC completed!
[2024-01-24 13:59:58,504] [INFO] Total running time: 0h1m17s