[2023-03-18 06:15:37,955] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:15:37,955] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:15:37,955] [INFO] DQC Reference Directory: /var/lib/cwl/stg2272a5db-6a52-44f2-a5ea-eff6b924cf9c/dqc_reference
[2023-03-18 06:15:39,082] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:15:39,083] [INFO] Task started: Prodigal
[2023-03-18 06:15:39,083] [INFO] Running command: cat /var/lib/cwl/stg91a23d31-ee51-466c-afbf-46d475040f28/OceanDNA-b38574.fa | prodigal -d OceanDNA-b38574/cds.fna -a OceanDNA-b38574/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:15:58,617] [INFO] Task succeeded: Prodigal
[2023-03-18 06:15:58,618] [INFO] Task started: HMMsearch
[2023-03-18 06:15:58,618] [INFO] Running command: hmmsearch --tblout OceanDNA-b38574/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2272a5db-6a52-44f2-a5ea-eff6b924cf9c/dqc_reference/reference_markers.hmm OceanDNA-b38574/protein.faa > /dev/null
[2023-03-18 06:15:58,822] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:15:58,823] [INFO] Found 6/6 markers.
[2023-03-18 06:15:58,845] [INFO] Query marker FASTA was written to OceanDNA-b38574/markers.fasta
[2023-03-18 06:15:58,847] [INFO] Task started: Blastn
[2023-03-18 06:15:58,847] [INFO] Running command: blastn -query OceanDNA-b38574/markers.fasta -db /var/lib/cwl/stg2272a5db-6a52-44f2-a5ea-eff6b924cf9c/dqc_reference/reference_markers.fasta -out OceanDNA-b38574/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:15:59,474] [INFO] Task succeeded: Blastn
[2023-03-18 06:15:59,475] [INFO] Selected 11 target genomes.
[2023-03-18 06:15:59,475] [INFO] Target genome list was writen to OceanDNA-b38574/target_genomes.txt
[2023-03-18 06:15:59,484] [INFO] Task started: fastANI
[2023-03-18 06:15:59,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg91a23d31-ee51-466c-afbf-46d475040f28/OceanDNA-b38574.fa --refList OceanDNA-b38574/target_genomes.txt --output OceanDNA-b38574/fastani_result.tsv --threads 1
[2023-03-18 06:16:09,019] [INFO] Task succeeded: fastANI
[2023-03-18 06:16:09,020] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2272a5db-6a52-44f2-a5ea-eff6b924cf9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:16:09,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2272a5db-6a52-44f2-a5ea-eff6b924cf9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:16:09,027] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2023-03-18 06:16:09,027] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 06:16:09,027] [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 oleivorans	strain=KCTC 23045	GCA_000836035.1	1148157	1148157	suspected-type	True	95.0698	1058	1201	95	conclusive
Acinetobacter oleivorans	strain=DR1	GCA_000196795.1	1148157	1148157	suspected-type	True	95.051	1069	1201	95	conclusive
Acinetobacter calcoaceticus	strain=NCTC12983	GCA_900444805.1	471	471	type	True	91.4736	1012	1201	95	below_threshold
Acinetobacter calcoaceticus	strain=CIP 81.8	GCA_000368965.1	471	471	type	True	91.4711	1001	1201	95	below_threshold
Acinetobacter lactucae	strain=NRRL B-41902	GCA_001605885.1	1785128	1785128	type	True	91.3642	993	1201	95	below_threshold
Acinetobacter pittii	strain=FDAARGOS 1399	GCA_019047205.1	48296	48296	type	True	91.2952	1010	1201	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	91.2768	950	1201	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	87.8684	971	1201	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	87.8075	978	1201	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	79.8771	425	1201	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 06:16:09,027] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38574/tc_result.tsv
[2023-03-18 06:16:09,028] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:16:09,028] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:16:09,028] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2272a5db-6a52-44f2-a5ea-eff6b924cf9c/dqc_reference/checkm_data
[2023-03-18 06:16:09,029] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:16:09,141] [INFO] Task started: CheckM
[2023-03-18 06:16:09,142] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38574/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38574/checkm_input OceanDNA-b38574/checkm_result
[2023-03-18 06:16:59,286] [INFO] Task succeeded: CheckM
[2023-03-18 06:16:59,287] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 06:16:59,289] [INFO] ===== Completeness check finished =====
[2023-03-18 06:16:59,290] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:16:59,290] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38574/markers.fasta)
[2023-03-18 06:16:59,291] [INFO] Task started: Blastn
[2023-03-18 06:16:59,291] [INFO] Running command: blastn -query OceanDNA-b38574/markers.fasta -db /var/lib/cwl/stg2272a5db-6a52-44f2-a5ea-eff6b924cf9c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38574/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:17:00,325] [INFO] Task succeeded: Blastn
[2023-03-18 06:17:00,327] [INFO] Selected 7 target genomes.
[2023-03-18 06:17:00,328] [INFO] Target genome list was writen to OceanDNA-b38574/target_genomes_gtdb.txt
[2023-03-18 06:17:00,335] [INFO] Task started: fastANI
[2023-03-18 06:17:00,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg91a23d31-ee51-466c-afbf-46d475040f28/OceanDNA-b38574.fa --refList OceanDNA-b38574/target_genomes_gtdb.txt --output OceanDNA-b38574/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:17:06,824] [INFO] Task succeeded: fastANI
[2023-03-18 06:17:06,830] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 06:17:06,830] [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_000196795.1	s__Acinetobacter oleivorans	95.051	1069	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.22	95.12	0.90	0.85	40	conclusive
GCF_000399665.1	s__Acinetobacter calcoaceticus_B	93.7362	1011	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000313935.1	s__Acinetobacter sp000313935	92.472	988	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.37	99.37	0.94	0.94	2	-
GCF_000399685.1	s__Acinetobacter pittii_E	91.7065	1003	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368965.1	s__Acinetobacter calcoaceticus	91.4766	1000	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.00	95.80	0.92	0.85	26	-
GCF_016508255.1	s__Acinetobacter calcoaceticus_E	90.9621	972	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900520355.1	s__Acinetobacter calcoaceticus_C	90.8318	1015	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.76	96.36	0.92	0.90	4	-
--------------------------------------------------------------------------------
[2023-03-18 06:17:06,830] [INFO] GTDB search result was written to OceanDNA-b38574/result_gtdb.tsv
[2023-03-18 06:17:06,830] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:17:06,831] [INFO] DFAST_QC result json was written to OceanDNA-b38574/dqc_result.json
[2023-03-18 06:17:06,831] [INFO] DFAST_QC completed!
[2023-03-18 06:17:06,831] [INFO] Total running time: 0h1m29s