[2024-01-25 17:48:50,473] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:48:50,476] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:48:50,476] [INFO] DQC Reference Directory: /var/lib/cwl/stgd08e98d4-83a7-419e-9a85-5ff353cf104c/dqc_reference
[2024-01-25 17:48:51,612] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:48:51,613] [INFO] Task started: Prodigal
[2024-01-25 17:48:51,613] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e700255-53af-44fb-8780-7a5ebe4e3cb3/GCF_013409875.1_ASM1340987v1_genomic.fna.gz | prodigal -d GCF_013409875.1_ASM1340987v1_genomic.fna/cds.fna -a GCF_013409875.1_ASM1340987v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:49:02,006] [INFO] Task succeeded: Prodigal
[2024-01-25 17:49:02,007] [INFO] Task started: HMMsearch
[2024-01-25 17:49:02,007] [INFO] Running command: hmmsearch --tblout GCF_013409875.1_ASM1340987v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd08e98d4-83a7-419e-9a85-5ff353cf104c/dqc_reference/reference_markers.hmm GCF_013409875.1_ASM1340987v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:49:02,231] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:49:02,232] [INFO] Found 6/6 markers.
[2024-01-25 17:49:02,270] [INFO] Query marker FASTA was written to GCF_013409875.1_ASM1340987v1_genomic.fna/markers.fasta
[2024-01-25 17:49:02,270] [INFO] Task started: Blastn
[2024-01-25 17:49:02,270] [INFO] Running command: blastn -query GCF_013409875.1_ASM1340987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd08e98d4-83a7-419e-9a85-5ff353cf104c/dqc_reference/reference_markers.fasta -out GCF_013409875.1_ASM1340987v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:03,563] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:03,566] [INFO] Selected 13 target genomes.
[2024-01-25 17:49:03,566] [INFO] Target genome list was writen to GCF_013409875.1_ASM1340987v1_genomic.fna/target_genomes.txt
[2024-01-25 17:49:03,589] [INFO] Task started: fastANI
[2024-01-25 17:49:03,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e700255-53af-44fb-8780-7a5ebe4e3cb3/GCF_013409875.1_ASM1340987v1_genomic.fna.gz --refList GCF_013409875.1_ASM1340987v1_genomic.fna/target_genomes.txt --output GCF_013409875.1_ASM1340987v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:49:19,047] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:19,048] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd08e98d4-83a7-419e-9a85-5ff353cf104c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:49:19,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd08e98d4-83a7-419e-9a85-5ff353cf104c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:49:19,061] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:49:19,062] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:49:19,062] [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 oligotrophica	strain=DSM 24482	GCA_013409875.1	931536	931536	type	True	100.0	1383	1383	95	conclusive
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	82.9763	828	1383	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	82.6674	880	1383	95	below_threshold
Cellulomonas shaoxiangyii	strain=Z28	GCA_004798685.1	2566013	2566013	type	True	82.4188	860	1383	95	below_threshold
Cellulomonas flavigena	strain=DSM 20109	GCA_000092865.1	1711	1711	type	True	82.2383	871	1383	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	82.1953	849	1383	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	81.2954	753	1383	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	81.1557	747	1383	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	81.1145	859	1383	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	81.0963	849	1383	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	80.3775	739	1383	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.0734	702	1383	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	78.8831	625	1383	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:49:19,064] [INFO] DFAST Taxonomy check result was written to GCF_013409875.1_ASM1340987v1_genomic.fna/tc_result.tsv
[2024-01-25 17:49:19,064] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:49:19,065] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:49:19,065] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd08e98d4-83a7-419e-9a85-5ff353cf104c/dqc_reference/checkm_data
[2024-01-25 17:49:19,066] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:49:19,112] [INFO] Task started: CheckM
[2024-01-25 17:49:19,112] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013409875.1_ASM1340987v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013409875.1_ASM1340987v1_genomic.fna/checkm_input GCF_013409875.1_ASM1340987v1_genomic.fna/checkm_result
[2024-01-25 17:50:59,003] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:59,004] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:59,025] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:59,025] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:59,026] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013409875.1_ASM1340987v1_genomic.fna/markers.fasta)
[2024-01-25 17:50:59,027] [INFO] Task started: Blastn
[2024-01-25 17:50:59,027] [INFO] Running command: blastn -query GCF_013409875.1_ASM1340987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd08e98d4-83a7-419e-9a85-5ff353cf104c/dqc_reference/reference_markers_gtdb.fasta -out GCF_013409875.1_ASM1340987v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:01,176] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:01,179] [INFO] Selected 10 target genomes.
[2024-01-25 17:51:01,179] [INFO] Target genome list was writen to GCF_013409875.1_ASM1340987v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:51:01,187] [INFO] Task started: fastANI
[2024-01-25 17:51:01,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e700255-53af-44fb-8780-7a5ebe4e3cb3/GCF_013409875.1_ASM1340987v1_genomic.fna.gz --refList GCF_013409875.1_ASM1340987v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013409875.1_ASM1340987v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:51:13,279] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:13,286] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:51:13,286] [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_006386485.1	s__Cellulomonas oligotrophica	99.9923	1377	1383	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_006715865.1	s__Cellulomonas sp006715865	94.9417	1261	1383	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	82.9648	829	1383	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.21	97.89	0.91	0.88	6	-
GCF_001462455.1	s__Cellulomonas sp001462455	82.7929	830	1383	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720485.1	s__Cellulomonas sp009720485	82.6615	894	1383	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	82.6559	881	1383	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004798685.1	s__Cellulomonas shaoxiangyii	82.5154	852	1383	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_018388445.1	s__Cellulomonas sp018388445	82.083	877	1383	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.55	99.30	0.98	0.97	4	-
GCF_004306155.1	s__Cellulomonas biazotea	81.2777	756	1383	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000212695.1	s__Cellulomonas fimi	81.107	861	1383	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:51:13,288] [INFO] GTDB search result was written to GCF_013409875.1_ASM1340987v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:51:13,289] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:51:13,292] [INFO] DFAST_QC result json was written to GCF_013409875.1_ASM1340987v1_genomic.fna/dqc_result.json
[2024-01-25 17:51:13,292] [INFO] DFAST_QC completed!
[2024-01-25 17:51:13,292] [INFO] Total running time: 0h2m23s