[2024-01-25 17:58:50,556] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:58:50,558] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:58:50,558] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c8da4d0-373e-4500-b9f6-0ef074bf7bca/dqc_reference
[2024-01-25 17:58:51,670] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:58:51,671] [INFO] Task started: Prodigal
[2024-01-25 17:58:51,671] [INFO] Running command: gunzip -c /var/lib/cwl/stgbbe05cba-b25a-402d-a195-9102de15b6cc/GCF_016862715.1_ASM1686271v1_genomic.fna.gz | prodigal -d GCF_016862715.1_ASM1686271v1_genomic.fna/cds.fna -a GCF_016862715.1_ASM1686271v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:59:00,611] [INFO] Task succeeded: Prodigal
[2024-01-25 17:59:00,611] [INFO] Task started: HMMsearch
[2024-01-25 17:59:00,611] [INFO] Running command: hmmsearch --tblout GCF_016862715.1_ASM1686271v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c8da4d0-373e-4500-b9f6-0ef074bf7bca/dqc_reference/reference_markers.hmm GCF_016862715.1_ASM1686271v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:59:00,817] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:59:00,818] [INFO] Found 6/6 markers.
[2024-01-25 17:59:00,851] [INFO] Query marker FASTA was written to GCF_016862715.1_ASM1686271v1_genomic.fna/markers.fasta
[2024-01-25 17:59:00,851] [INFO] Task started: Blastn
[2024-01-25 17:59:00,851] [INFO] Running command: blastn -query GCF_016862715.1_ASM1686271v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c8da4d0-373e-4500-b9f6-0ef074bf7bca/dqc_reference/reference_markers.fasta -out GCF_016862715.1_ASM1686271v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:59:02,137] [INFO] Task succeeded: Blastn
[2024-01-25 17:59:02,139] [INFO] Selected 16 target genomes.
[2024-01-25 17:59:02,140] [INFO] Target genome list was writen to GCF_016862715.1_ASM1686271v1_genomic.fna/target_genomes.txt
[2024-01-25 17:59:02,149] [INFO] Task started: fastANI
[2024-01-25 17:59:02,149] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbe05cba-b25a-402d-a195-9102de15b6cc/GCF_016862715.1_ASM1686271v1_genomic.fna.gz --refList GCF_016862715.1_ASM1686271v1_genomic.fna/target_genomes.txt --output GCF_016862715.1_ASM1686271v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:59:17,411] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:17,411] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c8da4d0-373e-4500-b9f6-0ef074bf7bca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:59:17,412] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c8da4d0-373e-4500-b9f6-0ef074bf7bca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:59:17,421] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:59:17,421] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:59:17,422] [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 marina	strain=CGMCC 4.6945	GCA_900111925.1	988821	988821	type	True	99.9876	1281	1284	95	conclusive
Cellulomonas endophytica	strain=SYSUP0004	GCA_004123805.1	2494735	2494735	type	True	82.7848	836	1284	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	80.1979	634	1284	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	80.1275	706	1284	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	80.1254	698	1284	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	80.0648	703	1284	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	80.0433	624	1284	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	80.001	623	1284	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	79.92	615	1284	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	79.9049	653	1284	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	79.7362	627	1284	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	79.6032	644	1284	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	79.5492	627	1284	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.0891	631	1284	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	78.7803	577	1284	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	78.6443	582	1284	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:59:17,423] [INFO] DFAST Taxonomy check result was written to GCF_016862715.1_ASM1686271v1_genomic.fna/tc_result.tsv
[2024-01-25 17:59:17,423] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:59:17,423] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:59:17,424] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c8da4d0-373e-4500-b9f6-0ef074bf7bca/dqc_reference/checkm_data
[2024-01-25 17:59:17,424] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:59:17,463] [INFO] Task started: CheckM
[2024-01-25 17:59:17,463] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862715.1_ASM1686271v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862715.1_ASM1686271v1_genomic.fna/checkm_input GCF_016862715.1_ASM1686271v1_genomic.fna/checkm_result
[2024-01-25 18:00:11,810] [INFO] Task succeeded: CheckM
[2024-01-25 18:00:11,811] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:00:11,827] [INFO] ===== Completeness check finished =====
[2024-01-25 18:00:11,827] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:00:11,828] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862715.1_ASM1686271v1_genomic.fna/markers.fasta)
[2024-01-25 18:00:11,828] [INFO] Task started: Blastn
[2024-01-25 18:00:11,829] [INFO] Running command: blastn -query GCF_016862715.1_ASM1686271v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c8da4d0-373e-4500-b9f6-0ef074bf7bca/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862715.1_ASM1686271v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:14,131] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:14,134] [INFO] Selected 17 target genomes.
[2024-01-25 18:00:14,134] [INFO] Target genome list was writen to GCF_016862715.1_ASM1686271v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:00:14,145] [INFO] Task started: fastANI
[2024-01-25 18:00:14,145] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbe05cba-b25a-402d-a195-9102de15b6cc/GCF_016862715.1_ASM1686271v1_genomic.fna.gz --refList GCF_016862715.1_ASM1686271v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862715.1_ASM1686271v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:00:30,533] [INFO] Task succeeded: fastANI
[2024-01-25 18:00:30,543] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:00:30,544] [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_900111925.1	s__Cellulomonas marina	99.9876	1281	1284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_004123805.1	s__Cellulomonas endophytica	82.7556	839	1284	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	80.3044	607	1284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.47	95.68	0.95	0.94	3	-
GCF_000312005.1	s__Cellulomonas massiliensis	80.2423	629	1284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000212695.1	s__Cellulomonas fimi	80.0831	712	1284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	99.99	1.00	1.00	3	-
GCF_009720485.1	s__Cellulomonas sp009720485	80.0655	683	1284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004886325.1	s__Cellulomonas telluris	80.0417	707	1284	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	79.9388	612	1284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001462455.1	s__Cellulomonas sp001462455	79.9317	645	1284	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	79.9043	653	1284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.21	97.89	0.91	0.88	6	-
GCF_018531375.1	s__Cellulomonas sp018531375	79.7249	628	1284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018623035.1	s__Cellulomonas sp018623035	79.6555	655	1284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.51	99.03	0.98	0.95	3	-
GCF_018388465.1	s__Cellulomonas sp018388465	79.6373	609	1284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.65	99.29	0.98	0.97	3	-
GCF_014837175.1	s__Cellulomonas sp014837175	79.576	604	1284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990265.1	s__Cellulomonas terrae	79.5571	627	1284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011603975.1	s__Cellulomonas sp011603975	79.5193	613	1284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001019615.1	s__Cellulosimicrobium cellulans_E	78.4265	604	1284	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.64	98.58	0.94	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:00:30,545] [INFO] GTDB search result was written to GCF_016862715.1_ASM1686271v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:00:30,546] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:00:30,549] [INFO] DFAST_QC result json was written to GCF_016862715.1_ASM1686271v1_genomic.fna/dqc_result.json
[2024-01-25 18:00:30,549] [INFO] DFAST_QC completed!
[2024-01-25 18:00:30,549] [INFO] Total running time: 0h1m40s