[2024-01-25 18:33:20,527] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:33:20,528] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:33:20,528] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc04e904-168d-4e63-a888-72713438a2a5/dqc_reference
[2024-01-25 18:33:21,655] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:33:21,656] [INFO] Task started: Prodigal
[2024-01-25 18:33:21,656] [INFO] Running command: gunzip -c /var/lib/cwl/stg64370fd1-0e0e-4df9-aa3d-0864a330530e/GCF_002563715.1_ASM256371v1_genomic.fna.gz | prodigal -d GCF_002563715.1_ASM256371v1_genomic.fna/cds.fna -a GCF_002563715.1_ASM256371v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:33:32,063] [INFO] Task succeeded: Prodigal
[2024-01-25 18:33:32,064] [INFO] Task started: HMMsearch
[2024-01-25 18:33:32,064] [INFO] Running command: hmmsearch --tblout GCF_002563715.1_ASM256371v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc04e904-168d-4e63-a888-72713438a2a5/dqc_reference/reference_markers.hmm GCF_002563715.1_ASM256371v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:33:32,267] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:33:32,268] [INFO] Found 6/6 markers.
[2024-01-25 18:33:32,306] [INFO] Query marker FASTA was written to GCF_002563715.1_ASM256371v1_genomic.fna/markers.fasta
[2024-01-25 18:33:32,306] [INFO] Task started: Blastn
[2024-01-25 18:33:32,306] [INFO] Running command: blastn -query GCF_002563715.1_ASM256371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc04e904-168d-4e63-a888-72713438a2a5/dqc_reference/reference_markers.fasta -out GCF_002563715.1_ASM256371v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:33:33,541] [INFO] Task succeeded: Blastn
[2024-01-25 18:33:33,544] [INFO] Selected 17 target genomes.
[2024-01-25 18:33:33,544] [INFO] Target genome list was writen to GCF_002563715.1_ASM256371v1_genomic.fna/target_genomes.txt
[2024-01-25 18:33:33,608] [INFO] Task started: fastANI
[2024-01-25 18:33:33,608] [INFO] Running command: fastANI --query /var/lib/cwl/stg64370fd1-0e0e-4df9-aa3d-0864a330530e/GCF_002563715.1_ASM256371v1_genomic.fna.gz --refList GCF_002563715.1_ASM256371v1_genomic.fna/target_genomes.txt --output GCF_002563715.1_ASM256371v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:33:50,409] [INFO] Task succeeded: fastANI
[2024-01-25 18:33:50,410] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc04e904-168d-4e63-a888-72713438a2a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:33:50,410] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc04e904-168d-4e63-a888-72713438a2a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:33:50,420] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:33:50,420] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:33:50,421] [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
Isoptericola jiangsuensis	strain=DSM 21863	GCA_002563715.1	548579	548579	type	True	100.0	1344	1347	95	conclusive
Isoptericola dokdonensis	strain=DS-3	GCA_001636295.1	372663	372663	type	True	88.5158	1097	1347	95	below_threshold
Isoptericola chiayiensis	strain=KCTC 19740	GCA_013149805.1	579446	579446	type	True	83.0972	886	1347	95	below_threshold
Isoptericola sediminis	strain=JC619	GCA_013085345.1	2733572	2733572	type	True	82.4633	763	1347	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	80.1374	690	1347	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	80.1241	701	1347	95	below_threshold
Promicromonospora citrea	strain=JCM 3051	GCA_014647735.1	43677	43677	type	True	80.0433	730	1347	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	80.028	730	1347	95	below_threshold
Promicromonospora sukumoe	strain=DSM 44121	GCA_014137995.1	88382	88382	type	True	79.9752	751	1347	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	79.5502	595	1347	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	79.4384	616	1347	95	below_threshold
Myceligenerans indicum	strain=I2	GCA_016742955.1	2593663	2593663	type	True	79.2263	585	1347	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	79.209	605	1347	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.0017	610	1347	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	78.8909	619	1347	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	78.8329	591	1347	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	78.3072	588	1347	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:33:50,427] [INFO] DFAST Taxonomy check result was written to GCF_002563715.1_ASM256371v1_genomic.fna/tc_result.tsv
[2024-01-25 18:33:50,430] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:33:50,430] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:33:50,430] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc04e904-168d-4e63-a888-72713438a2a5/dqc_reference/checkm_data
[2024-01-25 18:33:50,431] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:33:50,480] [INFO] Task started: CheckM
[2024-01-25 18:33:50,480] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002563715.1_ASM256371v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002563715.1_ASM256371v1_genomic.fna/checkm_input GCF_002563715.1_ASM256371v1_genomic.fna/checkm_result
[2024-01-25 18:35:24,845] [INFO] Task succeeded: CheckM
[2024-01-25 18:35:24,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:35:24,869] [INFO] ===== Completeness check finished =====
[2024-01-25 18:35:24,869] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:35:24,870] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002563715.1_ASM256371v1_genomic.fna/markers.fasta)
[2024-01-25 18:35:24,870] [INFO] Task started: Blastn
[2024-01-25 18:35:24,870] [INFO] Running command: blastn -query GCF_002563715.1_ASM256371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc04e904-168d-4e63-a888-72713438a2a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_002563715.1_ASM256371v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:35:26,923] [INFO] Task succeeded: Blastn
[2024-01-25 18:35:26,925] [INFO] Selected 13 target genomes.
[2024-01-25 18:35:26,925] [INFO] Target genome list was writen to GCF_002563715.1_ASM256371v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:35:26,973] [INFO] Task started: fastANI
[2024-01-25 18:35:26,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg64370fd1-0e0e-4df9-aa3d-0864a330530e/GCF_002563715.1_ASM256371v1_genomic.fna.gz --refList GCF_002563715.1_ASM256371v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002563715.1_ASM256371v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:35:41,437] [INFO] Task succeeded: fastANI
[2024-01-25 18:35:41,445] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:35:41,446] [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_002563715.1	s__Isoptericola jiangsuensis	100.0	1344	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001636295.1	s__Isoptericola dokdonensis	88.5298	1096	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013149805.1	s__Isoptericola chiayiensis	83.0971	886	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003075.1	s__Isoptericola halotolerans_A	82.4861	894	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013085345.1	s__Isoptericola sediminis	82.4578	763	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215105.1	s__Isoptericola variabilis_A	82.2279	761	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	99.96	99.96	0.98	0.98	2	-
GCF_013149785.1	s__Isoptericola halotolerans	82.0593	870	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167525.1	s__Isoptericola flava	81.6466	866	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011634835.1	s__Isoptericola sp011634835	81.5957	863	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635665.1	s__Isoptericola cucumis	81.5024	829	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004695.1	s__Promicromonospora citrea	80.2036	682	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	99.97	99.97	0.99	0.99	2	-
GCF_016907755.1	s__Cellulosimicrobium cellulans_D	80.0859	758	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	99.18	99.18	0.97	0.97	2	-
GCF_003550025.1	s__Promicromonospora thailandica	79.9151	739	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:35:41,449] [INFO] GTDB search result was written to GCF_002563715.1_ASM256371v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:35:41,449] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:35:41,452] [INFO] DFAST_QC result json was written to GCF_002563715.1_ASM256371v1_genomic.fna/dqc_result.json
[2024-01-25 18:35:41,453] [INFO] DFAST_QC completed!
[2024-01-25 18:35:41,453] [INFO] Total running time: 0h2m21s