[2024-01-25 19:31:51,340] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:31:51,343] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:31:51,343] [INFO] DQC Reference Directory: /var/lib/cwl/stg9241ef4d-407a-4f08-9a10-cb7f09538507/dqc_reference
[2024-01-25 19:31:52,537] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:31:52,538] [INFO] Task started: Prodigal
[2024-01-25 19:31:52,538] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f13f942-bf66-4d75-bde1-309c9b13cf5e/GCF_002014965.1_ASM201496v1_genomic.fna.gz | prodigal -d GCF_002014965.1_ASM201496v1_genomic.fna/cds.fna -a GCF_002014965.1_ASM201496v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:31:57,656] [INFO] Task succeeded: Prodigal
[2024-01-25 19:31:57,657] [INFO] Task started: HMMsearch
[2024-01-25 19:31:57,657] [INFO] Running command: hmmsearch --tblout GCF_002014965.1_ASM201496v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9241ef4d-407a-4f08-9a10-cb7f09538507/dqc_reference/reference_markers.hmm GCF_002014965.1_ASM201496v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:31:57,842] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:31:57,843] [INFO] Found 6/6 markers.
[2024-01-25 19:31:57,868] [INFO] Query marker FASTA was written to GCF_002014965.1_ASM201496v1_genomic.fna/markers.fasta
[2024-01-25 19:31:57,869] [INFO] Task started: Blastn
[2024-01-25 19:31:57,869] [INFO] Running command: blastn -query GCF_002014965.1_ASM201496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9241ef4d-407a-4f08-9a10-cb7f09538507/dqc_reference/reference_markers.fasta -out GCF_002014965.1_ASM201496v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:31:58,469] [INFO] Task succeeded: Blastn
[2024-01-25 19:31:58,473] [INFO] Selected 12 target genomes.
[2024-01-25 19:31:58,473] [INFO] Target genome list was writen to GCF_002014965.1_ASM201496v1_genomic.fna/target_genomes.txt
[2024-01-25 19:31:58,479] [INFO] Task started: fastANI
[2024-01-25 19:31:58,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f13f942-bf66-4d75-bde1-309c9b13cf5e/GCF_002014965.1_ASM201496v1_genomic.fna.gz --refList GCF_002014965.1_ASM201496v1_genomic.fna/target_genomes.txt --output GCF_002014965.1_ASM201496v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:32:03,881] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:03,881] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9241ef4d-407a-4f08-9a10-cb7f09538507/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:32:03,881] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9241ef4d-407a-4f08-9a10-cb7f09538507/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:32:03,888] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:32:03,888] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:32:03,888] [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 canis	strain=CCUG 8415A	GCA_002014965.1	90239	90239	type	True	100.0	703	705	95	conclusive
Moraxella catarrhalis	strain=CCUG 353	GCA_001632285.1	480	480	type	True	83.8052	491	705	95	below_threshold
Moraxella catarrhalis	strain=NCTC11020	GCA_900476075.1	480	480	type	True	83.7603	493	705	95	below_threshold
Moraxella porci	strain=CCUG 54912	GCA_002014855.1	1288392	1288392	type	True	79.2697	344	705	95	below_threshold
Moraxella pluranimalium	strain=CCUG 54913	GCA_002014825.1	470453	470453	type	True	78.5433	321	705	95	below_threshold
Moraxella caviae	strain=NCTC10293	GCA_900453175.1	34060	34060	type	True	78.4002	200	705	95	below_threshold
Moraxella caviae	strain=CCUG 355	GCA_002014985.1	34060	34060	type	True	78.1486	197	705	95	below_threshold
Psychrobacter coccoides	strain=F1192	GCA_017498085.1	2818440	2818440	type	True	76.6479	66	705	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:32:03,891] [INFO] DFAST Taxonomy check result was written to GCF_002014965.1_ASM201496v1_genomic.fna/tc_result.tsv
[2024-01-25 19:32:03,892] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:32:03,892] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:32:03,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9241ef4d-407a-4f08-9a10-cb7f09538507/dqc_reference/checkm_data
[2024-01-25 19:32:03,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:32:03,918] [INFO] Task started: CheckM
[2024-01-25 19:32:03,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002014965.1_ASM201496v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002014965.1_ASM201496v1_genomic.fna/checkm_input GCF_002014965.1_ASM201496v1_genomic.fna/checkm_result
[2024-01-25 19:32:24,534] [INFO] Task succeeded: CheckM
[2024-01-25 19:32:24,535] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:32:24,549] [INFO] ===== Completeness check finished =====
[2024-01-25 19:32:24,549] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:32:24,550] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002014965.1_ASM201496v1_genomic.fna/markers.fasta)
[2024-01-25 19:32:24,550] [INFO] Task started: Blastn
[2024-01-25 19:32:24,551] [INFO] Running command: blastn -query GCF_002014965.1_ASM201496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9241ef4d-407a-4f08-9a10-cb7f09538507/dqc_reference/reference_markers_gtdb.fasta -out GCF_002014965.1_ASM201496v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:25,549] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:25,552] [INFO] Selected 7 target genomes.
[2024-01-25 19:32:25,552] [INFO] Target genome list was writen to GCF_002014965.1_ASM201496v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:32:25,554] [INFO] Task started: fastANI
[2024-01-25 19:32:25,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f13f942-bf66-4d75-bde1-309c9b13cf5e/GCF_002014965.1_ASM201496v1_genomic.fna.gz --refList GCF_002014965.1_ASM201496v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002014965.1_ASM201496v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:32:28,935] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:28,941] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:32:28,941] [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_002014965.1	s__Moraxella canis	100.0	703	705	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	97.14	96.86	0.93	0.92	4	conclusive
GCF_001656295.1	s__Moraxella catarrhalis_C	93.1244	593	705	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	98.44	97.90	0.94	0.92	5	-
GCF_001632285.1	s__Moraxella catarrhalis	83.8052	491	705	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	98.72	95.96	0.96	0.91	200	-
GCF_002014855.1	s__Moraxella porci	79.2563	345	705	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	96.21	96.21	0.92	0.92	2	-
GCF_002014825.1	s__Moraxella pluranimalium	78.5304	321	705	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002014985.1	s__Moraxella caviae	78.1486	197	705	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.91	99.82	0.90	0.81	3	-
GCF_000426885.1	s__Moraxella caprae	77.8929	127	705	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.6695	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:32:28,943] [INFO] GTDB search result was written to GCF_002014965.1_ASM201496v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:32:28,945] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:32:28,951] [INFO] DFAST_QC result json was written to GCF_002014965.1_ASM201496v1_genomic.fna/dqc_result.json
[2024-01-25 19:32:28,951] [INFO] DFAST_QC completed!
[2024-01-25 19:32:28,951] [INFO] Total running time: 0h0m38s