[2024-01-25 20:03:35,569] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:35,570] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:35,570] [INFO] DQC Reference Directory: /var/lib/cwl/stg70c520b0-a177-49c0-ae34-b1b8b16f6e19/dqc_reference
[2024-01-25 20:03:36,816] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:36,821] [INFO] Task started: Prodigal
[2024-01-25 20:03:36,821] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc598a34-235e-4c35-8283-aaeade5f59c0/GCF_002014985.1_ASM201498v1_genomic.fna.gz | prodigal -d GCF_002014985.1_ASM201498v1_genomic.fna/cds.fna -a GCF_002014985.1_ASM201498v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:43,356] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:43,356] [INFO] Task started: HMMsearch
[2024-01-25 20:03:43,356] [INFO] Running command: hmmsearch --tblout GCF_002014985.1_ASM201498v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70c520b0-a177-49c0-ae34-b1b8b16f6e19/dqc_reference/reference_markers.hmm GCF_002014985.1_ASM201498v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:43,542] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:43,543] [INFO] Found 6/6 markers.
[2024-01-25 20:03:43,565] [INFO] Query marker FASTA was written to GCF_002014985.1_ASM201498v1_genomic.fna/markers.fasta
[2024-01-25 20:03:43,565] [INFO] Task started: Blastn
[2024-01-25 20:03:43,565] [INFO] Running command: blastn -query GCF_002014985.1_ASM201498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70c520b0-a177-49c0-ae34-b1b8b16f6e19/dqc_reference/reference_markers.fasta -out GCF_002014985.1_ASM201498v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:44,198] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:44,200] [INFO] Selected 18 target genomes.
[2024-01-25 20:03:44,201] [INFO] Target genome list was writen to GCF_002014985.1_ASM201498v1_genomic.fna/target_genomes.txt
[2024-01-25 20:03:44,221] [INFO] Task started: fastANI
[2024-01-25 20:03:44,222] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc598a34-235e-4c35-8283-aaeade5f59c0/GCF_002014985.1_ASM201498v1_genomic.fna.gz --refList GCF_002014985.1_ASM201498v1_genomic.fna/target_genomes.txt --output GCF_002014985.1_ASM201498v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:52,512] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:52,512] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70c520b0-a177-49c0-ae34-b1b8b16f6e19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:52,512] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70c520b0-a177-49c0-ae34-b1b8b16f6e19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:52,526] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:03:52,526] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:03:52,526] [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=CCUG 355	GCA_002014985.1	34060	34060	type	True	100.0	772	778	95	conclusive
Moraxella caviae	strain=NCTC10293	GCA_900453175.1	34060	34060	type	True	99.9916	778	778	95	conclusive
Moraxella ovis	strain=NCTC11227	GCA_900453105.1	29433	29433	type	True	78.5002	240	778	95	below_threshold
Moraxella bovoculi	strain=237	GCA_000696305.2	386891	386891	type	True	78.4845	226	778	95	below_threshold
Moraxella ovis	strain=199/55	GCA_001636015.1	29433	29433	type	True	78.3999	249	778	95	below_threshold
Moraxella pluranimalium	strain=CCUG 54913	GCA_002014825.1	470453	470453	type	True	78.2568	247	778	95	below_threshold
Moraxella nasovis	strain=ZY201115	GCA_022701215.1	2904121	2904121	type	True	78.1831	208	778	95	below_threshold
Moraxella canis	strain=CCUG 8415A	GCA_002014965.1	90239	90239	type	True	78.1091	186	778	95	below_threshold
Moraxella porci	strain=CCUG 54912	GCA_002014855.1	1288392	1288392	type	True	78.0736	218	778	95	below_threshold
Moraxella lacunata	strain=CCUG 4441	GCA_002027545.1	477	477	suspected-type	True	78.0048	232	778	95	below_threshold
Moraxella caprae	strain=DSM 19149	GCA_000426885.1	90240	90240	type	True	77.9875	240	778	95	below_threshold
Moraxella lacunata	strain=NBRC 102154	GCA_001591245.1	477	477	suspected-type	True	77.8941	209	778	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	76.4007	60	778	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:52,528] [INFO] DFAST Taxonomy check result was written to GCF_002014985.1_ASM201498v1_genomic.fna/tc_result.tsv
[2024-01-25 20:03:52,528] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:52,529] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:52,529] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70c520b0-a177-49c0-ae34-b1b8b16f6e19/dqc_reference/checkm_data
[2024-01-25 20:03:52,530] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:52,557] [INFO] Task started: CheckM
[2024-01-25 20:03:52,557] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002014985.1_ASM201498v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002014985.1_ASM201498v1_genomic.fna/checkm_input GCF_002014985.1_ASM201498v1_genomic.fna/checkm_result
[2024-01-25 20:04:16,309] [INFO] Task succeeded: CheckM
[2024-01-25 20:04:16,310] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:04:16,326] [INFO] ===== Completeness check finished =====
[2024-01-25 20:04:16,326] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:04:16,327] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002014985.1_ASM201498v1_genomic.fna/markers.fasta)
[2024-01-25 20:04:16,327] [INFO] Task started: Blastn
[2024-01-25 20:04:16,327] [INFO] Running command: blastn -query GCF_002014985.1_ASM201498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70c520b0-a177-49c0-ae34-b1b8b16f6e19/dqc_reference/reference_markers_gtdb.fasta -out GCF_002014985.1_ASM201498v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:17,391] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:17,394] [INFO] Selected 16 target genomes.
[2024-01-25 20:04:17,395] [INFO] Target genome list was writen to GCF_002014985.1_ASM201498v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:17,409] [INFO] Task started: fastANI
[2024-01-25 20:04:17,409] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc598a34-235e-4c35-8283-aaeade5f59c0/GCF_002014985.1_ASM201498v1_genomic.fna.gz --refList GCF_002014985.1_ASM201498v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002014985.1_ASM201498v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:04:25,098] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:25,107] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:04:25,107] [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	100.0	772	778	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_000696305.2	s__Moraxella bovoculi	78.5021	225	778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.978	98.49	98.41	0.96	0.96	5	-
GCF_001636015.1	s__Moraxella ovis	78.3999	249	778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.978	97.95	96.93	0.90	0.85	8	-
GCF_002014825.1	s__Moraxella pluranimalium	78.2568	247	778	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	78.1718	230	778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002014965.1	s__Moraxella canis	78.1158	185	778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	97.14	96.86	0.93	0.92	4	-
GCF_002014855.1	s__Moraxella porci	78.0736	218	778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	96.21	96.21	0.92	0.92	2	-
GCF_900156515.1	s__Moraxella cuniculi	78.0361	207	778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.10	98.21	0.93	0.87	3	-
GCF_002027545.1	s__Moraxella lacunata	78.0206	231	778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	96.28	95.16	0.88	0.84	9	-
GCF_002014975.1	s__Moraxella bovis	77.9967	242	778	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	77.9875	240	778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.6695	99.99	99.99	1.00	1.00	2	-
GCF_904846055.1	s__Psychrobacter ciconiae_A	76.9512	84	778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012847335.1	s__Psychrobacter sp012847335	76.6074	79	778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.15	96.31	0.98	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:04:25,108] [INFO] GTDB search result was written to GCF_002014985.1_ASM201498v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:04:25,109] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:04:25,112] [INFO] DFAST_QC result json was written to GCF_002014985.1_ASM201498v1_genomic.fna/dqc_result.json
[2024-01-25 20:04:25,112] [INFO] DFAST_QC completed!
[2024-01-25 20:04:25,112] [INFO] Total running time: 0h0m50s