[2024-01-25 19:12:50,939] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:12:50,940] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:12:50,940] [INFO] DQC Reference Directory: /var/lib/cwl/stge6c23006-c046-42b0-9e9a-25cbda28afad/dqc_reference
[2024-01-25 19:12:52,106] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:12:52,107] [INFO] Task started: Prodigal
[2024-01-25 19:12:52,107] [INFO] Running command: gunzip -c /var/lib/cwl/stg638b1d95-30c3-49b4-bdf4-f5e38f04280e/GCF_003351745.1_ASM335174v1_genomic.fna.gz | prodigal -d GCF_003351745.1_ASM335174v1_genomic.fna/cds.fna -a GCF_003351745.1_ASM335174v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:13:01,284] [INFO] Task succeeded: Prodigal
[2024-01-25 19:13:01,284] [INFO] Task started: HMMsearch
[2024-01-25 19:13:01,285] [INFO] Running command: hmmsearch --tblout GCF_003351745.1_ASM335174v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6c23006-c046-42b0-9e9a-25cbda28afad/dqc_reference/reference_markers.hmm GCF_003351745.1_ASM335174v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:13:01,491] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:13:01,492] [INFO] Found 6/6 markers.
[2024-01-25 19:13:01,521] [INFO] Query marker FASTA was written to GCF_003351745.1_ASM335174v1_genomic.fna/markers.fasta
[2024-01-25 19:13:01,522] [INFO] Task started: Blastn
[2024-01-25 19:13:01,522] [INFO] Running command: blastn -query GCF_003351745.1_ASM335174v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6c23006-c046-42b0-9e9a-25cbda28afad/dqc_reference/reference_markers.fasta -out GCF_003351745.1_ASM335174v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:13:02,141] [INFO] Task succeeded: Blastn
[2024-01-25 19:13:02,144] [INFO] Selected 29 target genomes.
[2024-01-25 19:13:02,144] [INFO] Target genome list was writen to GCF_003351745.1_ASM335174v1_genomic.fna/target_genomes.txt
[2024-01-25 19:13:02,157] [INFO] Task started: fastANI
[2024-01-25 19:13:02,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg638b1d95-30c3-49b4-bdf4-f5e38f04280e/GCF_003351745.1_ASM335174v1_genomic.fna.gz --refList GCF_003351745.1_ASM335174v1_genomic.fna/target_genomes.txt --output GCF_003351745.1_ASM335174v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:13:18,987] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:18,987] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6c23006-c046-42b0-9e9a-25cbda28afad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:13:18,988] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6c23006-c046-42b0-9e9a-25cbda28afad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:13:18,999] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:13:19,000] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:13:19,000] [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
Aquirhabdus parva	strain=HYN0046	GCA_003351745.1	2283318	2283318	type	True	100.0	1253	1259	95	conclusive
Acinetobacter pullicarnis	strain=S23	GCA_006352475.1	2576829	2576829	type	True	78.3356	66	1259	95	below_threshold
Acinetobacter bohemicus	strain=ANC 3994	GCA_000367925.1	1435036	1435036	type	True	78.318	75	1259	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	78.1522	68	1259	95	below_threshold
Acinetobacter johnsonii	strain=CIP 64.6	GCA_000368045.1	40214	40214	suspected-type	True	78.1188	72	1259	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	77.9411	68	1259	95	below_threshold
Acinetobacter johnsonii	strain=FDAARGOS_910	GCA_016027055.1	40214	40214	suspected-type	True	77.7693	68	1259	95	below_threshold
Acinetobacter septicus	strain=FDAARGOS_1401	GCA_019355975.1	465797	465797	type	True	77.7322	77	1259	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	77.6796	69	1259	95	below_threshold
Acinetobacter baylyi	strain=CIP 107474	GCA_000368685.1	202950	202950	type	True	77.4759	62	1259	95	below_threshold
Acinetobacter proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	77.4183	79	1259	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	77.1892	65	1259	95	below_threshold
Acinetobacter harbinensis	strain=HITLi 7	GCA_000816495.1	1353941	1353941	type	True	77.1714	78	1259	95	below_threshold
Acinetobacter kanungonis	strain=PS-1	GCA_009939195.1	2699469	2699469	type	True	77.0443	63	1259	95	below_threshold
Acinetobacter haemolyticus	strain=CIP 64.3	GCA_000369065.1	29430	29430	type	True	76.9683	69	1259	95	below_threshold
Acinetobacter halotolerans	strain=JCM 31009	GCA_004208515.1	1752076	1752076	type	True	76.7652	65	1259	95	below_threshold
Acinetobacter vivianii	strain=CCM 8642	GCA_014635885.1	1776742	1776742	type	True	76.7348	74	1259	95	below_threshold
Acinetobacter baylyi	strain=DSM 14961	GCA_000621045.1	202950	202950	type	True	76.4384	59	1259	95	below_threshold
Acinetobacter johnsonii	strain=DSM 6963	GCA_000949655.1	40214	40214	suspected-type	True	75.9726	60	1259	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:13:19,010] [INFO] DFAST Taxonomy check result was written to GCF_003351745.1_ASM335174v1_genomic.fna/tc_result.tsv
[2024-01-25 19:13:19,011] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:13:19,011] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:13:19,012] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6c23006-c046-42b0-9e9a-25cbda28afad/dqc_reference/checkm_data
[2024-01-25 19:13:19,013] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:13:19,055] [INFO] Task started: CheckM
[2024-01-25 19:13:19,055] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003351745.1_ASM335174v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003351745.1_ASM335174v1_genomic.fna/checkm_input GCF_003351745.1_ASM335174v1_genomic.fna/checkm_result
[2024-01-25 19:13:50,808] [INFO] Task succeeded: CheckM
[2024-01-25 19:13:50,809] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:13:50,867] [INFO] ===== Completeness check finished =====
[2024-01-25 19:13:50,867] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:13:50,868] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003351745.1_ASM335174v1_genomic.fna/markers.fasta)
[2024-01-25 19:13:50,868] [INFO] Task started: Blastn
[2024-01-25 19:13:50,868] [INFO] Running command: blastn -query GCF_003351745.1_ASM335174v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6c23006-c046-42b0-9e9a-25cbda28afad/dqc_reference/reference_markers_gtdb.fasta -out GCF_003351745.1_ASM335174v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:13:51,886] [INFO] Task succeeded: Blastn
[2024-01-25 19:13:51,890] [INFO] Selected 26 target genomes.
[2024-01-25 19:13:51,891] [INFO] Target genome list was writen to GCF_003351745.1_ASM335174v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:13:51,929] [INFO] Task started: fastANI
[2024-01-25 19:13:51,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg638b1d95-30c3-49b4-bdf4-f5e38f04280e/GCF_003351745.1_ASM335174v1_genomic.fna.gz --refList GCF_003351745.1_ASM335174v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003351745.1_ASM335174v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:14:07,290] [INFO] Task succeeded: fastANI
[2024-01-25 19:14:07,302] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:14:07,303] [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_003351745.1	s__Aquirhabdus parva	100.0	1253	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Aquirhabdus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013343215.1	s__Acinetobacter lwoffii_C	78.4692	59	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	97.90	0.93	0.91	5	-
GCA_014378805.1	s__Aquirhabdus sp014378805	78.3201	197	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Aquirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000367925.1	s__Acinetobacter bohemicus	78.0407	74	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.89	95.82	0.83	0.82	4	-
GCF_000368045.1	s__Acinetobacter johnsonii	77.6416	72	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.19	95.36	0.86	0.80	59	-
GCF_000369405.1	s__Acinetobacter sp000369405	77.6355	73	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368685.1	s__Acinetobacter baylyi	77.46	61	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.85	98.65	0.98	0.93	13	-
GCF_000816495.1	s__Acinetobacter harbinensis	77.4371	80	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.59	98.59	0.98	0.98	2	-
GCF_000369525.1	s__Acinetobacter sp000369525	77.418	70	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.13	96.00	0.90	0.87	7	-
GCF_000369505.1	s__Acinetobacter sp000369505	77.204	82	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.55	96.55	0.85	0.85	2	-
GCF_014635885.1	s__Acinetobacter vivianii	76.7655	73	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.48	96.89	0.92	0.86	8	-
GCF_004208515.1	s__Acinetobacter halotolerans	76.7652	65	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.44	95.44	0.89	0.89	2	-
GCA_004173455.1	s__Alkanindiges sp004173455	76.6967	74	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Alkanindiges	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107285.1	s__Acinetobacter kyonggiensis	76.6171	64	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.53	95.22	0.88	0.86	3	-
GCF_004345325.1	s__Acinetobacter calcoaceticus_D	76.5203	65	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902753875.1	s__Acinetobacter bouvetii_A	76.519	68	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011753255.1	s__Acinetobacter sp011753255	76.4672	75	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000773685.1	s__Acinetobacter sp000773685	76.4553	56	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009912575.1	s__Acinetobacter bereziniae_A	76.1135	58	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003987695.1	s__Acinetobacter sp003987695	75.8976	64	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.01	98.01	0.75	0.75	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:14:07,304] [INFO] GTDB search result was written to GCF_003351745.1_ASM335174v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:14:07,305] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:14:07,312] [INFO] DFAST_QC result json was written to GCF_003351745.1_ASM335174v1_genomic.fna/dqc_result.json
[2024-01-25 19:14:07,312] [INFO] DFAST_QC completed!
[2024-01-25 19:14:07,312] [INFO] Total running time: 0h1m16s