[2024-01-24 10:47:54,170] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:54,173] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:54,173] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bb1547c-346a-4f88-8e65-7373a1cc03d2/dqc_reference
[2024-01-24 10:48:03,342] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:03,344] [INFO] Task started: Prodigal
[2024-01-24 10:48:03,344] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb644214-bdb9-4fa4-ba1b-800cc76a44fa/GCF_900453175.1_51108_C01_genomic.fna.gz | prodigal -d GCF_900453175.1_51108_C01_genomic.fna/cds.fna -a GCF_900453175.1_51108_C01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:11,916] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:11,917] [INFO] Task started: HMMsearch
[2024-01-24 10:48:11,917] [INFO] Running command: hmmsearch --tblout GCF_900453175.1_51108_C01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bb1547c-346a-4f88-8e65-7373a1cc03d2/dqc_reference/reference_markers.hmm GCF_900453175.1_51108_C01_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:12,132] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:12,134] [INFO] Found 6/6 markers.
[2024-01-24 10:48:12,206] [INFO] Query marker FASTA was written to GCF_900453175.1_51108_C01_genomic.fna/markers.fasta
[2024-01-24 10:48:12,207] [INFO] Task started: Blastn
[2024-01-24 10:48:12,207] [INFO] Running command: blastn -query GCF_900453175.1_51108_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bb1547c-346a-4f88-8e65-7373a1cc03d2/dqc_reference/reference_markers.fasta -out GCF_900453175.1_51108_C01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:12,900] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:12,905] [INFO] Selected 18 target genomes.
[2024-01-24 10:48:12,906] [INFO] Target genome list was writen to GCF_900453175.1_51108_C01_genomic.fna/target_genomes.txt
[2024-01-24 10:48:12,917] [INFO] Task started: fastANI
[2024-01-24 10:48:12,917] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb644214-bdb9-4fa4-ba1b-800cc76a44fa/GCF_900453175.1_51108_C01_genomic.fna.gz --refList GCF_900453175.1_51108_C01_genomic.fna/target_genomes.txt --output GCF_900453175.1_51108_C01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:22,319] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:22,320] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bb1547c-346a-4f88-8e65-7373a1cc03d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:22,320] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bb1547c-346a-4f88-8e65-7373a1cc03d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:22,332] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:48:22,332] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:22,332] [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
Moraxella caviae	strain=NCTC10293	GCA_900453175.1	34060	34060	type	True	100.0	889	908	95	conclusive
Moraxella caviae	strain=CCUG 355	GCA_002014985.1	34060	34060	type	True	99.8874	767	908	95	conclusive
Moraxella ovis	strain=NCTC11227	GCA_900453105.1	29433	29433	type	True	78.9659	261	908	95	below_threshold
Moraxella nasovis	strain=ZY201115	GCA_022701215.1	2904121	2904121	type	True	78.8852	211	908	95	below_threshold
Moraxella ovis	strain=199/55	GCA_001636015.1	29433	29433	type	True	78.8217	265	908	95	below_threshold
Moraxella bovoculi	strain=237	GCA_000696305.2	386891	386891	type	True	78.3682	228	908	95	below_threshold
Moraxella canis	strain=CCUG 8415A	GCA_002014965.1	90239	90239	type	True	78.288	194	908	95	below_threshold
Moraxella pluranimalium	strain=CCUG 54913	GCA_002014825.1	470453	470453	type	True	78.2637	262	908	95	below_threshold
Moraxella caprae	strain=DSM 19149	GCA_000426885.1	90240	90240	type	True	78.2226	243	908	95	below_threshold
Moraxella porci	strain=CCUG 54912	GCA_002014855.1	1288392	1288392	type	True	78.1675	227	908	95	below_threshold
Moraxella lacunata	strain=CCUG 4441	GCA_002027545.1	477	477	suspected-type	True	77.8308	249	908	95	below_threshold
Moraxella lacunata	strain=NBRC 102154	GCA_001591245.1	477	477	suspected-type	True	77.7935	216	908	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	76.6913	56	908	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:22,334] [INFO] DFAST Taxonomy check result was written to GCF_900453175.1_51108_C01_genomic.fna/tc_result.tsv
[2024-01-24 10:48:22,335] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:22,335] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:22,335] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bb1547c-346a-4f88-8e65-7373a1cc03d2/dqc_reference/checkm_data
[2024-01-24 10:48:22,336] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:22,367] [INFO] Task started: CheckM
[2024-01-24 10:48:22,368] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900453175.1_51108_C01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900453175.1_51108_C01_genomic.fna/checkm_input GCF_900453175.1_51108_C01_genomic.fna/checkm_result
[2024-01-24 10:48:52,527] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:52,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:52,552] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:52,552] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:52,553] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900453175.1_51108_C01_genomic.fna/markers.fasta)
[2024-01-24 10:48:52,554] [INFO] Task started: Blastn
[2024-01-24 10:48:52,554] [INFO] Running command: blastn -query GCF_900453175.1_51108_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bb1547c-346a-4f88-8e65-7373a1cc03d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_900453175.1_51108_C01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:53,673] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:53,676] [INFO] Selected 16 target genomes.
[2024-01-24 10:48:53,677] [INFO] Target genome list was writen to GCF_900453175.1_51108_C01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:53,688] [INFO] Task started: fastANI
[2024-01-24 10:48:53,688] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb644214-bdb9-4fa4-ba1b-800cc76a44fa/GCF_900453175.1_51108_C01_genomic.fna.gz --refList GCF_900453175.1_51108_C01_genomic.fna/target_genomes_gtdb.txt --output GCF_900453175.1_51108_C01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:01,159] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:01,175] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:01,176] [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_002014985.1	s__Moraxella caviae	99.8874	767	908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.91	99.82	0.90	0.81	3	conclusive
GCF_001636015.1	s__Moraxella ovis	78.7867	262	908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.978	97.95	96.93	0.90	0.85	8	-
GCF_900453205.1	s__Moraxella lacunata_B	78.5446	241	908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156515.1	s__Moraxella cuniculi	78.3884	209	908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.10	98.21	0.93	0.87	3	-
GCF_000696305.2	s__Moraxella bovoculi	78.3514	229	908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.978	98.49	98.41	0.96	0.96	5	-
GCF_002014965.1	s__Moraxella canis	78.3081	193	908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	97.14	96.86	0.93	0.92	4	-
GCF_002014825.1	s__Moraxella pluranimalium	78.2808	260	908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426885.1	s__Moraxella caprae	78.2258	243	908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.6695	99.99	99.99	1.00	1.00	2	-
GCF_002014855.1	s__Moraxella porci	78.1675	227	908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	96.21	96.21	0.92	0.92	2	-
GCF_002014975.1	s__Moraxella bovis	78.0591	241	908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.6695	98.79	98.38	0.94	0.91	3	-
GCF_904846055.1	s__Psychrobacter ciconiae_A	77.9559	95	908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002027545.1	s__Moraxella lacunata	77.8529	249	908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	96.28	95.16	0.88	0.84	9	-
GCF_012847335.1	s__Psychrobacter sp012847335	76.6386	80	908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.15	96.31	0.98	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:01,178] [INFO] GTDB search result was written to GCF_900453175.1_51108_C01_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:01,179] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:01,183] [INFO] DFAST_QC result json was written to GCF_900453175.1_51108_C01_genomic.fna/dqc_result.json
[2024-01-24 10:49:01,184] [INFO] DFAST_QC completed!
[2024-01-24 10:49:01,184] [INFO] Total running time: 0h1m7s