[2024-01-24 13:57:44,023] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:44,025] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:44,025] [INFO] DQC Reference Directory: /var/lib/cwl/stg6333b44b-5c6c-47fd-8672-bd2b66c9b9a9/dqc_reference
[2024-01-24 13:57:45,213] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:45,213] [INFO] Task started: Prodigal
[2024-01-24 13:57:45,214] [INFO] Running command: gunzip -c /var/lib/cwl/stg3423d58d-124a-4e41-babf-6f7133e503ef/GCF_014647015.1_ASM1464701v1_genomic.fna.gz | prodigal -d GCF_014647015.1_ASM1464701v1_genomic.fna/cds.fna -a GCF_014647015.1_ASM1464701v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:55,795] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:55,796] [INFO] Task started: HMMsearch
[2024-01-24 13:57:55,796] [INFO] Running command: hmmsearch --tblout GCF_014647015.1_ASM1464701v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6333b44b-5c6c-47fd-8672-bd2b66c9b9a9/dqc_reference/reference_markers.hmm GCF_014647015.1_ASM1464701v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:56,085] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:56,086] [INFO] Found 6/6 markers.
[2024-01-24 13:57:56,128] [INFO] Query marker FASTA was written to GCF_014647015.1_ASM1464701v1_genomic.fna/markers.fasta
[2024-01-24 13:57:56,129] [INFO] Task started: Blastn
[2024-01-24 13:57:56,130] [INFO] Running command: blastn -query GCF_014647015.1_ASM1464701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6333b44b-5c6c-47fd-8672-bd2b66c9b9a9/dqc_reference/reference_markers.fasta -out GCF_014647015.1_ASM1464701v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:57,484] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:57,487] [INFO] Selected 11 target genomes.
[2024-01-24 13:57:57,488] [INFO] Target genome list was writen to GCF_014647015.1_ASM1464701v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:57,510] [INFO] Task started: fastANI
[2024-01-24 13:57:57,511] [INFO] Running command: fastANI --query /var/lib/cwl/stg3423d58d-124a-4e41-babf-6f7133e503ef/GCF_014647015.1_ASM1464701v1_genomic.fna.gz --refList GCF_014647015.1_ASM1464701v1_genomic.fna/target_genomes.txt --output GCF_014647015.1_ASM1464701v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:09,234] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:09,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6333b44b-5c6c-47fd-8672-bd2b66c9b9a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:09,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6333b44b-5c6c-47fd-8672-bd2b66c9b9a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:09,246] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:09,246] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:09,246] [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
Cellulomonas gelida	strain=JCM 1490	GCA_014647015.1	1712	1712	type	True	100.0	1253	1253	95	conclusive
Cellulomonas gelida	strain=NBRC 3748	GCA_006538725.1	1712	1712	type	True	99.9597	1195	1253	95	conclusive
Cellulomonas persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	88.4397	1071	1253	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	85.6537	980	1253	95	below_threshold
Cellulomonas uda	strain=NBRC 3747	GCA_006538705.1	1714	1714	type	True	85.6205	892	1253	95	below_threshold
Cellulomonas gilvus	strain=ATCC 13127	GCA_000218545.1	11	11	type	True	84.0508	871	1253	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	83.8181	911	1253	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	81.4157	733	1253	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	80.9256	746	1253	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.4473	654	1253	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	79.1574	606	1253	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:09,248] [INFO] DFAST Taxonomy check result was written to GCF_014647015.1_ASM1464701v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:09,248] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:09,248] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:09,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6333b44b-5c6c-47fd-8672-bd2b66c9b9a9/dqc_reference/checkm_data
[2024-01-24 13:58:09,250] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:09,290] [INFO] Task started: CheckM
[2024-01-24 13:58:09,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647015.1_ASM1464701v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647015.1_ASM1464701v1_genomic.fna/checkm_input GCF_014647015.1_ASM1464701v1_genomic.fna/checkm_result
[2024-01-24 13:59:14,319] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:14,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:14,360] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:14,360] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:14,361] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647015.1_ASM1464701v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:14,361] [INFO] Task started: Blastn
[2024-01-24 13:59:14,361] [INFO] Running command: blastn -query GCF_014647015.1_ASM1464701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6333b44b-5c6c-47fd-8672-bd2b66c9b9a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647015.1_ASM1464701v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:16,550] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:16,554] [INFO] Selected 10 target genomes.
[2024-01-24 13:59:16,555] [INFO] Target genome list was writen to GCF_014647015.1_ASM1464701v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:16,589] [INFO] Task started: fastANI
[2024-01-24 13:59:16,589] [INFO] Running command: fastANI --query /var/lib/cwl/stg3423d58d-124a-4e41-babf-6f7133e503ef/GCF_014647015.1_ASM1464701v1_genomic.fna.gz --refList GCF_014647015.1_ASM1464701v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647015.1_ASM1464701v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:26,774] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:26,783] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:26,783] [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_006538725.1	s__Cellulomonas gelida	99.9597	1195	1253	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.61	99.23	0.96	0.91	3	conclusive
GCF_007989825.1	s__Cellulomonas persica	88.463	1069	1253	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538705.1	s__Cellulomonas uda	85.6003	893	1253	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.69	98.01	0.94	0.90	4	-
GCF_000218545.1	s__Cellulomonas gilvus	84.0234	873	1253	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531375.1	s__Cellulomonas sp018531375	83.8394	909	1253	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990245.1	s__Cellulomonas composti	82.9309	794	1253	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396155.1	s__Cellulomonas septica	82.2409	514	1253	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003851725.1	s__Cellulomonas algicola	82.084	726	1253	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.47	95.68	0.95	0.94	3	-
GCA_017744555.1	s__Cellulomonas sp017744555	81.5097	764	1253	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552375.1	s__Cellulomonas iranensis	81.4451	730	1253	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.21	97.89	0.91	0.88	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:26,785] [INFO] GTDB search result was written to GCF_014647015.1_ASM1464701v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:26,786] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:26,791] [INFO] DFAST_QC result json was written to GCF_014647015.1_ASM1464701v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:26,791] [INFO] DFAST_QC completed!
[2024-01-24 13:59:26,791] [INFO] Total running time: 0h1m43s