[2024-01-24 10:47:06,548] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,553] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,553] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1fa01ca-715b-40d9-a5c8-7e25171fb7ca/dqc_reference
[2024-01-24 10:47:12,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,102] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,103] [INFO] Running command: gunzip -c /var/lib/cwl/stg8379be7d-7ec8-4de7-8433-3cc7d161b7d7/GCF_000696305.2_MBO_237_genomic.fna.gz | prodigal -d GCF_000696305.2_MBO_237_genomic.fna/cds.fna -a GCF_000696305.2_MBO_237_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:17,514] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:17,515] [INFO] Task started: HMMsearch
[2024-01-24 10:47:17,515] [INFO] Running command: hmmsearch --tblout GCF_000696305.2_MBO_237_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1fa01ca-715b-40d9-a5c8-7e25171fb7ca/dqc_reference/reference_markers.hmm GCF_000696305.2_MBO_237_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:17,769] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:17,771] [INFO] Found 6/6 markers.
[2024-01-24 10:47:17,801] [INFO] Query marker FASTA was written to GCF_000696305.2_MBO_237_genomic.fna/markers.fasta
[2024-01-24 10:47:17,801] [INFO] Task started: Blastn
[2024-01-24 10:47:17,802] [INFO] Running command: blastn -query GCF_000696305.2_MBO_237_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1fa01ca-715b-40d9-a5c8-7e25171fb7ca/dqc_reference/reference_markers.fasta -out GCF_000696305.2_MBO_237_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:19,698] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:19,701] [INFO] Selected 19 target genomes.
[2024-01-24 10:47:19,701] [INFO] Target genome list was writen to GCF_000696305.2_MBO_237_genomic.fna/target_genomes.txt
[2024-01-24 10:47:19,812] [INFO] Task started: fastANI
[2024-01-24 10:47:19,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg8379be7d-7ec8-4de7-8433-3cc7d161b7d7/GCF_000696305.2_MBO_237_genomic.fna.gz --refList GCF_000696305.2_MBO_237_genomic.fna/target_genomes.txt --output GCF_000696305.2_MBO_237_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:30,839] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:30,840] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1fa01ca-715b-40d9-a5c8-7e25171fb7ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:30,840] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1fa01ca-715b-40d9-a5c8-7e25171fb7ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:30,851] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:47:30,851] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 10:47:30,851] [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 bovoculi	strain=237	GCA_000696305.2	386891	386891	type	True	100.0	665	666	95	inconclusive
Moraxella ovis	strain=NCTC11227	GCA_900453105.1	29433	29433	type	True	96.0858	604	666	95	inconclusive
Moraxella ovis	strain=199/55	GCA_001636015.1	29433	29433	type	True	95.978	614	666	95	inconclusive
Moraxella bovis	strain=CCUG 2133	GCA_002014975.1	476	476	type	True	85.3651	269	666	95	below_threshold
Moraxella caprae	strain=DSM 19149	GCA_000426885.1	90240	90240	type	True	84.4733	259	666	95	below_threshold
Moraxella caprae	strain=NCTC12877	GCA_900453285.1	90240	90240	type	True	84.4197	272	666	95	below_threshold
Moraxella porci	strain=CCUG 54912	GCA_002014855.1	1288392	1288392	type	True	78.3268	192	666	95	below_threshold
Moraxella nasovis	strain=ZY201115	GCA_022701215.1	2904121	2904121	type	True	78.2672	175	666	95	below_threshold
Moraxella caviae	strain=CCUG 355	GCA_002014985.1	34060	34060	type	True	78.1819	244	666	95	below_threshold
Moraxella caviae	strain=NCTC10293	GCA_900453175.1	34060	34060	type	True	78.1685	244	666	95	below_threshold
Moraxella pluranimalium	strain=CCUG 54913	GCA_002014825.1	470453	470453	type	True	77.9339	203	666	95	below_threshold
Moraxella cuniculi	strain=DSM 21768	GCA_900156515.1	34061	34061	type	True	77.7851	146	666	95	below_threshold
Moraxella cuniculi	strain=CCUG 2154	GCA_002015175.1	34061	34061	type	True	77.6176	150	666	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:30,853] [INFO] DFAST Taxonomy check result was written to GCF_000696305.2_MBO_237_genomic.fna/tc_result.tsv
[2024-01-24 10:47:30,854] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:30,854] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:30,854] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1fa01ca-715b-40d9-a5c8-7e25171fb7ca/dqc_reference/checkm_data
[2024-01-24 10:47:30,855] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:30,921] [INFO] Task started: CheckM
[2024-01-24 10:47:30,921] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000696305.2_MBO_237_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000696305.2_MBO_237_genomic.fna/checkm_input GCF_000696305.2_MBO_237_genomic.fna/checkm_result
[2024-01-24 10:47:53,924] [INFO] Task succeeded: CheckM
[2024-01-24 10:47:53,926] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:47:53,939] [INFO] ===== Completeness check finished =====
[2024-01-24 10:47:53,940] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:47:53,940] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000696305.2_MBO_237_genomic.fna/markers.fasta)
[2024-01-24 10:47:53,940] [INFO] Task started: Blastn
[2024-01-24 10:47:53,940] [INFO] Running command: blastn -query GCF_000696305.2_MBO_237_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1fa01ca-715b-40d9-a5c8-7e25171fb7ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_000696305.2_MBO_237_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:55,194] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:55,197] [INFO] Selected 18 target genomes.
[2024-01-24 10:47:55,197] [INFO] Target genome list was writen to GCF_000696305.2_MBO_237_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:47:55,229] [INFO] Task started: fastANI
[2024-01-24 10:47:55,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg8379be7d-7ec8-4de7-8433-3cc7d161b7d7/GCF_000696305.2_MBO_237_genomic.fna.gz --refList GCF_000696305.2_MBO_237_genomic.fna/target_genomes_gtdb.txt --output GCF_000696305.2_MBO_237_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:06,353] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:06,364] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:06,365] [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_000696305.2	s__Moraxella bovoculi	100.0	665	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.978	98.49	98.41	0.96	0.96	5	conclusive
GCF_001636015.1	s__Moraxella ovis	95.978	614	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.978	97.95	96.93	0.90	0.85	8	conclusive
GCF_002014975.1	s__Moraxella bovis	85.2996	271	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.6695	98.79	98.38	0.94	0.91	3	-
GCF_000426885.1	s__Moraxella caprae	84.4774	258	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.6695	99.99	99.99	1.00	1.00	2	-
GCF_900453205.1	s__Moraxella lacunata_B	83.5144	276	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001679005.1	s__Moraxella nonliquefaciens	79.9672	213	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.13	98.18	0.96	0.92	5	-
GCF_002014855.1	s__Moraxella porci	78.3268	192	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	96.21	96.21	0.92	0.92	2	-
GCF_002014985.1	s__Moraxella caviae	78.1678	245	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.91	99.82	0.90	0.81	3	-
GCF_002014825.1	s__Moraxella pluranimalium	77.9503	202	666	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	77.7538	145	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.10	98.21	0.93	0.87	3	-
GCF_016464015.1	s__Psychrobacter sp016464015	77.4202	56	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900162815.1	s__Psychrobacter pasteurii	77.3333	58	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107555.1	s__Psychrobacter celer	76.4333	62	666	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.12	95.68	0.88	0.85	9	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:06,369] [INFO] GTDB search result was written to GCF_000696305.2_MBO_237_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:06,370] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:06,374] [INFO] DFAST_QC result json was written to GCF_000696305.2_MBO_237_genomic.fna/dqc_result.json
[2024-01-24 10:48:06,374] [INFO] DFAST_QC completed!
[2024-01-24 10:48:06,374] [INFO] Total running time: 0h0m60s