[2024-01-24 10:57:50,259] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:50,261] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:50,261] [INFO] DQC Reference Directory: /var/lib/cwl/stg309207b3-b459-409f-9b17-1f4c2b568d68/dqc_reference
[2024-01-24 10:57:52,641] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:52,642] [INFO] Task started: Prodigal
[2024-01-24 10:57:52,643] [INFO] Running command: gunzip -c /var/lib/cwl/stgca6845a4-dbe0-42e3-9551-54cb9dfa8d75/GCF_016862675.1_ASM1686267v1_genomic.fna.gz | prodigal -d GCF_016862675.1_ASM1686267v1_genomic.fna/cds.fna -a GCF_016862675.1_ASM1686267v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:05,945] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:05,946] [INFO] Task started: HMMsearch
[2024-01-24 10:58:05,946] [INFO] Running command: hmmsearch --tblout GCF_016862675.1_ASM1686267v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg309207b3-b459-409f-9b17-1f4c2b568d68/dqc_reference/reference_markers.hmm GCF_016862675.1_ASM1686267v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:06,252] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:06,254] [INFO] Found 6/6 markers.
[2024-01-24 10:58:06,303] [INFO] Query marker FASTA was written to GCF_016862675.1_ASM1686267v1_genomic.fna/markers.fasta
[2024-01-24 10:58:06,304] [INFO] Task started: Blastn
[2024-01-24 10:58:06,304] [INFO] Running command: blastn -query GCF_016862675.1_ASM1686267v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg309207b3-b459-409f-9b17-1f4c2b568d68/dqc_reference/reference_markers.fasta -out GCF_016862675.1_ASM1686267v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:07,580] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:07,584] [INFO] Selected 16 target genomes.
[2024-01-24 10:58:07,585] [INFO] Target genome list was writen to GCF_016862675.1_ASM1686267v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:07,592] [INFO] Task started: fastANI
[2024-01-24 10:58:07,593] [INFO] Running command: fastANI --query /var/lib/cwl/stgca6845a4-dbe0-42e3-9551-54cb9dfa8d75/GCF_016862675.1_ASM1686267v1_genomic.fna.gz --refList GCF_016862675.1_ASM1686267v1_genomic.fna/target_genomes.txt --output GCF_016862675.1_ASM1686267v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:23,577] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:23,578] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg309207b3-b459-409f-9b17-1f4c2b568d68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:23,578] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg309207b3-b459-409f-9b17-1f4c2b568d68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:23,602] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:58:23,602] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:58:23,602] [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 biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	83.3111	867	1611	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	82.9689	965	1611	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	82.8807	989	1611	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	82.3425	893	1611	95	below_threshold
Cellulomonas rhizosphaerae	strain=NEAU-TCZ24	GCA_003470205.1	2293719	2293719	type	True	82.1643	739	1611	95	below_threshold
Cellulomonas humilata	strain=ATCC 25174	GCA_013359775.1	144055	144055	type	True	81.9652	930	1611	95	below_threshold
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	81.8304	928	1611	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	81.556	833	1611	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	81.5374	774	1611	95	below_threshold
Cellulomonas persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	81.3284	795	1611	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	81.2212	780	1611	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	81.0632	788	1611	95	below_threshold
Cellulomonas oligotrophica	strain=DSM 24482	GCA_013409875.1	931536	931536	type	True	80.6073	808	1611	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	80.4221	764	1611	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.4187	711	1611	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	78.889	608	1611	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:23,604] [INFO] DFAST Taxonomy check result was written to GCF_016862675.1_ASM1686267v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:23,605] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:23,605] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:23,605] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg309207b3-b459-409f-9b17-1f4c2b568d68/dqc_reference/checkm_data
[2024-01-24 10:58:23,606] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:23,666] [INFO] Task started: CheckM
[2024-01-24 10:58:23,667] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862675.1_ASM1686267v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862675.1_ASM1686267v1_genomic.fna/checkm_input GCF_016862675.1_ASM1686267v1_genomic.fna/checkm_result
[2024-01-24 10:59:36,214] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:36,216] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:36,234] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:36,234] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:36,235] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862675.1_ASM1686267v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:36,235] [INFO] Task started: Blastn
[2024-01-24 10:59:36,235] [INFO] Running command: blastn -query GCF_016862675.1_ASM1686267v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg309207b3-b459-409f-9b17-1f4c2b568d68/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862675.1_ASM1686267v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:38,311] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:38,315] [INFO] Selected 14 target genomes.
[2024-01-24 10:59:38,316] [INFO] Target genome list was writen to GCF_016862675.1_ASM1686267v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:38,352] [INFO] Task started: fastANI
[2024-01-24 10:59:38,352] [INFO] Running command: fastANI --query /var/lib/cwl/stgca6845a4-dbe0-42e3-9551-54cb9dfa8d75/GCF_016862675.1_ASM1686267v1_genomic.fna.gz --refList GCF_016862675.1_ASM1686267v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862675.1_ASM1686267v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:53,461] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:53,477] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:53,478] [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_016862675.1	s__Cellulomonas chitinilytica	100.0	1611	1611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017744555.1	s__Cellulomonas sp017744555	89.0958	1127	1611	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	83.8763	580	1611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004306155.1	s__Cellulomonas biazotea	83.3806	861	1611	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	83.3209	884	1611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.47	95.68	0.95	0.94	3	-
GCF_000212695.1	s__Cellulomonas fimi	82.9504	981	1611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	99.99	1.00	1.00	3	-
GCF_007990265.1	s__Cellulomonas terrae	82.3453	893	1611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003470205.1	s__Cellulomonas rhizosphaerae	82.1569	740	1611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426705.1	s__Cellulomonas sp001426705	82.1223	964	1611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424125.1	s__Cellulomonas sp001424125	82.0314	857	1611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424195.1	s__Cellulomonas sp001424195	82.0279	937	1611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989805.1	s__Cellulomonas xylanilytica	81.8412	925	1611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426185.1	s__Cellulomonas sp000426185	81.2036	818	1611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409305.1	s__Cellulomonas soli	81.1988	783	1611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:53,479] [INFO] GTDB search result was written to GCF_016862675.1_ASM1686267v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:53,480] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:53,484] [INFO] DFAST_QC result json was written to GCF_016862675.1_ASM1686267v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:53,484] [INFO] DFAST_QC completed!
[2024-01-24 10:59:53,484] [INFO] Total running time: 0h2m3s