[2023-06-28 07:57:02,207] [INFO] DFAST_QC pipeline started.
[2023-06-28 07:57:02,210] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 07:57:02,210] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0f697a9-2576-416e-982c-935b3d8590ab/dqc_reference
[2023-06-28 07:57:06,188] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 07:57:06,189] [INFO] Task started: Prodigal
[2023-06-28 07:57:06,189] [INFO] Running command: gunzip -c /var/lib/cwl/stgbacf6adc-0269-452c-98d0-b79fc9cb5cc7/GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna.gz | prodigal -d GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna/cds.fna -a GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 07:57:49,580] [INFO] Task succeeded: Prodigal
[2023-06-28 07:57:49,581] [INFO] Task started: HMMsearch
[2023-06-28 07:57:49,581] [INFO] Running command: hmmsearch --tblout GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0f697a9-2576-416e-982c-935b3d8590ab/dqc_reference/reference_markers.hmm GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna/protein.faa > /dev/null
[2023-06-28 07:57:50,105] [INFO] Task succeeded: HMMsearch
[2023-06-28 07:57:50,107] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbacf6adc-0269-452c-98d0-b79fc9cb5cc7/GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna.gz]
[2023-06-28 07:57:50,262] [INFO] Query marker FASTA was written to GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna/markers.fasta
[2023-06-28 07:57:50,263] [INFO] Task started: Blastn
[2023-06-28 07:57:50,263] [INFO] Running command: blastn -query GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0f697a9-2576-416e-982c-935b3d8590ab/dqc_reference/reference_markers.fasta -out GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:57:50,867] [INFO] Task succeeded: Blastn
[2023-06-28 07:57:50,870] [INFO] Selected 26 target genomes.
[2023-06-28 07:57:50,870] [INFO] Target genome list was writen to GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna/target_genomes.txt
[2023-06-28 07:57:50,873] [INFO] Task started: fastANI
[2023-06-28 07:57:50,873] [INFO] Running command: fastANI --query /var/lib/cwl/stgbacf6adc-0269-452c-98d0-b79fc9cb5cc7/GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna.gz --refList GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna/target_genomes.txt --output GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 07:58:05,883] [INFO] Task succeeded: fastANI
[2023-06-28 07:58:05,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0f697a9-2576-416e-982c-935b3d8590ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 07:58:05,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0f697a9-2576-416e-982c-935b3d8590ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 07:58:05,897] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-06-28 07:58:05,897] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 07:58:05,897] [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 soli	strain=KCTC 22184	GCA_000760595.1	487316	487316	type	True	98.3864	523	934	95	conclusive
Acinetobacter baylyi	strain=DSM 14961	GCA_000621045.1	202950	202950	type	True	83.3317	383	934	95	below_threshold
Acinetobacter baylyi	strain=CIP 107474	GCA_000368685.1	202950	202950	type	True	83.2937	388	934	95	below_threshold
Acinetobacter guerrae	strain=AC 1271	GCA_009372255.1	1843371	1843371	type	True	80.0042	245	934	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	79.9525	264	934	95	below_threshold
Acinetobacter ursingii	strain=CIP 107286	GCA_000368825.1	108980	108980	type	True	79.8594	256	934	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	79.8056	208	934	95	below_threshold
Acinetobacter septicus	strain=FDAARGOS_1401	GCA_019355975.1	465797	465797	type	True	79.7933	252	934	95	below_threshold
Acinetobacter ursingii	strain=FDAARGOS_1095	GCA_016726205.1	108980	108980	type	True	79.7608	256	934	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	79.5609	160	934	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	79.51	217	934	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	79.495	219	934	95	below_threshold
Acinetobacter vivianii	strain=CCM 8642	GCA_014635885.1	1776742	1776742	type	True	78.9559	219	934	95	below_threshold
Acinetobacter venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	78.8585	197	934	95	below_threshold
Acinetobacter piscicola	strain=LW15	GCA_002233755.1	2006115	2006115	type	True	78.6647	167	934	95	below_threshold
Acinetobacter stercoris	strain=KPC-SM-21	GCA_900323515.1	2126983	2126983	type	True	78.6636	161	934	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 07:58:05,899] [INFO] DFAST Taxonomy check result was written to GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna/tc_result.tsv
[2023-06-28 07:58:05,899] [INFO] ===== Taxonomy check completed =====
[2023-06-28 07:58:05,899] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 07:58:05,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0f697a9-2576-416e-982c-935b3d8590ab/dqc_reference/checkm_data
[2023-06-28 07:58:05,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 07:58:06,113] [INFO] Task started: CheckM
[2023-06-28 07:58:06,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna/checkm_input GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna/checkm_result
[2023-06-28 08:00:08,577] [INFO] Task succeeded: CheckM
[2023-06-28 08:00:08,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.68%
Contamintation: 15.86%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 08:00:08,607] [INFO] ===== Completeness check finished =====
[2023-06-28 08:00:08,608] [INFO] ===== Start GTDB Search =====
[2023-06-28 08:00:08,608] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna/markers.fasta)
[2023-06-28 08:00:08,608] [INFO] Task started: Blastn
[2023-06-28 08:00:08,608] [INFO] Running command: blastn -query GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0f697a9-2576-416e-982c-935b3d8590ab/dqc_reference/reference_markers_gtdb.fasta -out GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:00:09,412] [INFO] Task succeeded: Blastn
[2023-06-28 08:00:09,423] [INFO] Selected 28 target genomes.
[2023-06-28 08:00:09,423] [INFO] Target genome list was writen to GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 08:00:09,428] [INFO] Task started: fastANI
[2023-06-28 08:00:09,428] [INFO] Running command: fastANI --query /var/lib/cwl/stgbacf6adc-0269-452c-98d0-b79fc9cb5cc7/GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna.gz --refList GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna/target_genomes_gtdb.txt --output GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 08:00:25,722] [INFO] Task succeeded: fastANI
[2023-06-28 08:00:25,738] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 08:00:25,738] [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_000760595.1	s__Acinetobacter soli	98.3864	523	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.45	98.17	0.92	0.88	38	conclusive
GCF_000368685.1	s__Acinetobacter baylyi	83.3162	387	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.85	98.65	0.98	0.93	13	-
GCF_009372255.1	s__Acinetobacter guerrae	80.0042	245	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	98.41	0.90	0.89	3	-
GCF_016624945.1	s__Acinetobacter sp016624945	79.965	230	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.57	99.14	0.97	0.94	3	-
GCF_900625095.1	s__Acinetobacter sp900625095	79.9404	265	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368825.1	s__Acinetobacter ursingii	79.8796	255	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.69	96.95	0.88	0.80	69	-
GCF_000368085.1	s__Acinetobacter nosocomialis	79.7093	204	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.94	97.50	0.90	0.85	250	-
GCF_000369045.1	s__Acinetobacter pittii	79.672	213	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.31	95.52	0.91	0.84	337	-
GCF_000399685.1	s__Acinetobacter pittii_E	79.6143	215	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013344765.1	s__Acinetobacter lactucae_A	79.5183	198	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.51	97.14	0.90	0.87	4	-
GCF_001605885.1	s__Acinetobacter lactucae	79.3845	220	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.34	96.55	0.91	0.85	16	-
GCF_002928115.1	s__Acinetobacter pittii_H	79.303	227	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.46	96.15	0.91	0.87	9	-
GCF_900406815.1	s__Acinetobacter haemolyticus_A	79.2733	178	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635545.1	s__Acinetobacter courvalinii	79.25	205	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.40	96.40	0.91	0.86	14	-
GCA_003987695.1	s__Acinetobacter sp003987695	79.0319	179	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.01	98.01	0.75	0.75	2	-
GCF_014635885.1	s__Acinetobacter vivianii	78.9509	218	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.48	96.89	0.92	0.86	8	-
GCF_003711395.1	s__Acinetobacter sp003711395	78.8085	153	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.62	98.61	0.92	0.90	3	-
GCF_000368585.1	s__Acinetobacter venetianus	78.7346	204	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.49	96.30	0.89	0.81	21	-
GCF_002233755.1	s__Acinetobacter piscicola	78.6896	166	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900323515.1	s__Acinetobacter stercoris	78.6517	160	934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.59	98.59	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-06-28 08:00:25,740] [INFO] GTDB search result was written to GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna/result_gtdb.tsv
[2023-06-28 08:00:25,740] [INFO] ===== GTDB Search completed =====
[2023-06-28 08:00:25,744] [INFO] DFAST_QC result json was written to GCA_913773785.1_maxbin_SP184_3.002_sub_cleaned_genomic.fna/dqc_result.json
[2023-06-28 08:00:25,744] [INFO] DFAST_QC completed!
[2023-06-28 08:00:25,744] [INFO] Total running time: 0h3m24s