[2024-01-24 13:49:28,096] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:28,098] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:28,098] [INFO] DQC Reference Directory: /var/lib/cwl/stg17cf6495-ed12-4caf-b2dd-75784b1cc0f8/dqc_reference
[2024-01-24 13:49:29,322] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:29,323] [INFO] Task started: Prodigal
[2024-01-24 13:49:29,323] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ad84bdc-a4cc-45a4-b8dd-5e80997abca1/GCF_025643275.1_ASM2564327v1_genomic.fna.gz | prodigal -d GCF_025643275.1_ASM2564327v1_genomic.fna/cds.fna -a GCF_025643275.1_ASM2564327v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:36,173] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:36,174] [INFO] Task started: HMMsearch
[2024-01-24 13:49:36,174] [INFO] Running command: hmmsearch --tblout GCF_025643275.1_ASM2564327v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17cf6495-ed12-4caf-b2dd-75784b1cc0f8/dqc_reference/reference_markers.hmm GCF_025643275.1_ASM2564327v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:36,435] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:36,436] [INFO] Found 6/6 markers.
[2024-01-24 13:49:36,457] [INFO] Query marker FASTA was written to GCF_025643275.1_ASM2564327v1_genomic.fna/markers.fasta
[2024-01-24 13:49:36,457] [INFO] Task started: Blastn
[2024-01-24 13:49:36,458] [INFO] Running command: blastn -query GCF_025643275.1_ASM2564327v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17cf6495-ed12-4caf-b2dd-75784b1cc0f8/dqc_reference/reference_markers.fasta -out GCF_025643275.1_ASM2564327v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:37,148] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:37,152] [INFO] Selected 25 target genomes.
[2024-01-24 13:49:37,152] [INFO] Target genome list was writen to GCF_025643275.1_ASM2564327v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:37,164] [INFO] Task started: fastANI
[2024-01-24 13:49:37,164] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ad84bdc-a4cc-45a4-b8dd-5e80997abca1/GCF_025643275.1_ASM2564327v1_genomic.fna.gz --refList GCF_025643275.1_ASM2564327v1_genomic.fna/target_genomes.txt --output GCF_025643275.1_ASM2564327v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:47,713] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:47,713] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17cf6495-ed12-4caf-b2dd-75784b1cc0f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:47,713] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17cf6495-ed12-4caf-b2dd-75784b1cc0f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:47,730] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:49:47,730] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:49:47,731] [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 oblonga	strain=NBRC 102422	GCA_001598275.1	200413	200413	type	True	80.8171	248	702	95	below_threshold
Moraxella caprae	strain=NCTC12877	GCA_900453285.1	90240	90240	type	True	79.7926	237	702	95	below_threshold
Moraxella caprae	strain=DSM 19149	GCA_000426885.1	90240	90240	type	True	79.2659	214	702	95	below_threshold
Moraxella equi	strain=NCTC11012	GCA_900453335.1	60442	60442	type	True	79.2252	233	702	95	below_threshold
Moraxella ovis	strain=199/55	GCA_001636015.1	29433	29433	type	True	79.0689	203	702	95	below_threshold
Moraxella ovis	strain=NCTC11227	GCA_900453105.1	29433	29433	type	True	78.9748	206	702	95	below_threshold
Moraxella cuniculi	strain=NCTC10297	GCA_900637105.1	34061	34061	type	True	78.9244	253	702	95	below_threshold
Moraxella cuniculi	strain=CCUG 2154	GCA_002015175.1	34061	34061	type	True	78.8479	248	702	95	below_threshold
Moraxella catarrhalis	strain=NCTC11020	GCA_900476075.1	480	480	type	True	78.8117	182	702	95	below_threshold
Moraxella cuniculi	strain=DSM 21768	GCA_900156515.1	34061	34061	type	True	78.8103	257	702	95	below_threshold
Moraxella equi	strain=CCUG 4950	GCA_002027555.1	60442	60442	type	True	78.7886	220	702	95	below_threshold
Moraxella caviae	strain=NCTC10293	GCA_900453175.1	34060	34060	type	True	78.7856	237	702	95	below_threshold
Moraxella nasovis	strain=ZY201115	GCA_022701215.1	2904121	2904121	type	True	78.7577	169	702	95	below_threshold
Moraxella pluranimalium	strain=CCUG 54913	GCA_002014825.1	470453	470453	type	True	78.7563	289	702	95	below_threshold
Moraxella porci	strain=CCUG 54912	GCA_002014855.1	1288392	1288392	type	True	78.716	251	702	95	below_threshold
Moraxella canis	strain=CCUG 8415A	GCA_002014965.1	90239	90239	type	True	78.3833	198	702	95	below_threshold
Moraxella bovis	strain=CCUG 2133	GCA_002014975.1	476	476	type	True	78.3252	231	702	95	below_threshold
Moraxella bovoculi	strain=237	GCA_000696305.2	386891	386891	type	True	78.245	199	702	95	below_threshold
Moraxella catarrhalis	strain=CCUG 353	GCA_001632285.1	480	480	type	True	78.1161	183	702	95	below_threshold
Moraxella caviae	strain=CCUG 355	GCA_002014985.1	34060	34060	type	True	78.0534	220	702	95	below_threshold
Psychrobacter celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	77.1316	50	702	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	77.1278	53	702	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:47,732] [INFO] DFAST Taxonomy check result was written to GCF_025643275.1_ASM2564327v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:47,733] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:47,733] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:47,733] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17cf6495-ed12-4caf-b2dd-75784b1cc0f8/dqc_reference/checkm_data
[2024-01-24 13:49:47,735] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:47,762] [INFO] Task started: CheckM
[2024-01-24 13:49:47,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025643275.1_ASM2564327v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025643275.1_ASM2564327v1_genomic.fna/checkm_input GCF_025643275.1_ASM2564327v1_genomic.fna/checkm_result
[2024-01-24 13:50:15,315] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:15,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:15,335] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:15,335] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:15,336] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025643275.1_ASM2564327v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:15,336] [INFO] Task started: Blastn
[2024-01-24 13:50:15,337] [INFO] Running command: blastn -query GCF_025643275.1_ASM2564327v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17cf6495-ed12-4caf-b2dd-75784b1cc0f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_025643275.1_ASM2564327v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:16,466] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:16,470] [INFO] Selected 19 target genomes.
[2024-01-24 13:50:16,470] [INFO] Target genome list was writen to GCF_025643275.1_ASM2564327v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:16,483] [INFO] Task started: fastANI
[2024-01-24 13:50:16,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ad84bdc-a4cc-45a4-b8dd-5e80997abca1/GCF_025643275.1_ASM2564327v1_genomic.fna.gz --refList GCF_025643275.1_ASM2564327v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025643275.1_ASM2564327v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:24,865] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:24,880] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:50:24,880] [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_001598275.1	s__Moraxella oblonga	80.7695	249	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900453205.1	s__Moraxella lacunata_B	80.3579	233	702	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	79.3229	214	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.6695	99.99	99.99	1.00	1.00	2	-
GCF_001656295.1	s__Moraxella catarrhalis_C	79.1214	187	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	98.44	97.90	0.94	0.92	5	-
GCF_001636015.1	s__Moraxella ovis	79.0689	203	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.978	97.95	96.93	0.90	0.85	8	-
GCF_900156515.1	s__Moraxella cuniculi	78.817	256	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.10	98.21	0.93	0.87	3	-
GCF_002027555.1	s__Moraxella equi	78.8083	219	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002014825.1	s__Moraxella pluranimalium	78.7563	289	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002014855.1	s__Moraxella porci	78.716	251	702	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	78.3748	228	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.6695	98.79	98.38	0.94	0.91	3	-
GCF_002014965.1	s__Moraxella canis	78.3631	198	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	97.14	96.86	0.93	0.92	4	-
GCF_001435295.1	s__Psychrobacter sp001435295	78.2638	55	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.4083	N/A	N/A	N/A	N/A	1	-
GCF_000696305.2	s__Moraxella bovoculi	78.245	199	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.978	98.49	98.41	0.96	0.96	5	-
GCF_001632285.1	s__Moraxella catarrhalis	78.1161	183	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	98.72	95.96	0.96	0.91	200	-
GCF_002014985.1	s__Moraxella caviae	78.0368	221	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.91	99.82	0.90	0.81	3	-
GCA_002377905.1	s__Psychrobacter sp002377905	76.1501	62	702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:24,883] [INFO] GTDB search result was written to GCF_025643275.1_ASM2564327v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:24,884] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:24,890] [INFO] DFAST_QC result json was written to GCF_025643275.1_ASM2564327v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:24,891] [INFO] DFAST_QC completed!
[2024-01-24 13:50:24,891] [INFO] Total running time: 0h0m57s