[2024-01-24 15:02:07,441] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:07,443] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:07,443] [INFO] DQC Reference Directory: /var/lib/cwl/stge2c00c52-36f0-4dd4-9380-7f16868345e4/dqc_reference
[2024-01-24 15:02:09,605] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:09,606] [INFO] Task started: Prodigal
[2024-01-24 15:02:09,607] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a979868-9c8d-4aed-9db9-07824dfc8040/GCF_013149785.1_ASM1314978v1_genomic.fna.gz | prodigal -d GCF_013149785.1_ASM1314978v1_genomic.fna/cds.fna -a GCF_013149785.1_ASM1314978v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:20,666] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:20,666] [INFO] Task started: HMMsearch
[2024-01-24 15:02:20,667] [INFO] Running command: hmmsearch --tblout GCF_013149785.1_ASM1314978v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2c00c52-36f0-4dd4-9380-7f16868345e4/dqc_reference/reference_markers.hmm GCF_013149785.1_ASM1314978v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:20,916] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:20,917] [INFO] Found 6/6 markers.
[2024-01-24 15:02:20,955] [INFO] Query marker FASTA was written to GCF_013149785.1_ASM1314978v1_genomic.fna/markers.fasta
[2024-01-24 15:02:20,956] [INFO] Task started: Blastn
[2024-01-24 15:02:20,956] [INFO] Running command: blastn -query GCF_013149785.1_ASM1314978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2c00c52-36f0-4dd4-9380-7f16868345e4/dqc_reference/reference_markers.fasta -out GCF_013149785.1_ASM1314978v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:22,314] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:22,324] [INFO] Selected 19 target genomes.
[2024-01-24 15:02:22,324] [INFO] Target genome list was writen to GCF_013149785.1_ASM1314978v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:22,343] [INFO] Task started: fastANI
[2024-01-24 15:02:22,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a979868-9c8d-4aed-9db9-07824dfc8040/GCF_013149785.1_ASM1314978v1_genomic.fna.gz --refList GCF_013149785.1_ASM1314978v1_genomic.fna/target_genomes.txt --output GCF_013149785.1_ASM1314978v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:39,140] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:39,140] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2c00c52-36f0-4dd4-9380-7f16868345e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:39,141] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2c00c52-36f0-4dd4-9380-7f16868345e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:39,156] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:02:39,156] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:02:39,157] [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 chiayiensis	strain=KCTC 19740	GCA_013149805.1	579446	579446	type	True	82.8534	861	1320	95	below_threshold
Isoptericola sediminis	strain=JC619	GCA_013085345.1	2733572	2733572	type	True	82.3755	757	1320	95	below_threshold
Isoptericola jiangsuensis	strain=DSM 21863	GCA_002563715.1	548579	548579	type	True	82.226	851	1320	95	below_threshold
Isoptericola dokdonensis	strain=DS-3	GCA_001636295.1	372663	372663	type	True	82.1995	859	1320	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	79.5883	617	1320	95	below_threshold
Promicromonospora citrea	strain=JCM 3051	GCA_014647735.1	43677	43677	type	True	79.4732	653	1320	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	79.1972	660	1320	95	below_threshold
Myceligenerans xiligouense	strain=DSM 15700	GCA_003814695.1	253184	253184	type	True	79.1815	588	1320	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	79.1381	643	1320	95	below_threshold
Myceligenerans salitolerans	strain=XHU 5031	GCA_017349295.1	1230528	1230528	type	True	79.1355	543	1320	95	below_threshold
Promicromonospora kroppenstedtii	strain=DSM 19349	GCA_000515355.1	440482	440482	type	True	79.125	650	1320	95	below_threshold
Promicromonospora umidemergens	strain=DSM 22081	GCA_024171995.1	629679	629679	type	True	79.1182	628	1320	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	78.8286	531	1320	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	78.6585	546	1320	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	78.5815	543	1320	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	78.3056	534	1320	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.2843	506	1320	95	below_threshold
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	78.2555	448	1320	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	77.9941	501	1320	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:39,158] [INFO] DFAST Taxonomy check result was written to GCF_013149785.1_ASM1314978v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:39,159] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:39,159] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:39,159] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2c00c52-36f0-4dd4-9380-7f16868345e4/dqc_reference/checkm_data
[2024-01-24 15:02:39,161] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:39,201] [INFO] Task started: CheckM
[2024-01-24 15:02:39,201] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013149785.1_ASM1314978v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013149785.1_ASM1314978v1_genomic.fna/checkm_input GCF_013149785.1_ASM1314978v1_genomic.fna/checkm_result
[2024-01-24 15:03:44,644] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:44,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:44,663] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:44,663] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:44,663] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013149785.1_ASM1314978v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:44,664] [INFO] Task started: Blastn
[2024-01-24 15:03:44,664] [INFO] Running command: blastn -query GCF_013149785.1_ASM1314978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2c00c52-36f0-4dd4-9380-7f16868345e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_013149785.1_ASM1314978v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:46,852] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:46,861] [INFO] Selected 14 target genomes.
[2024-01-24 15:03:46,861] [INFO] Target genome list was writen to GCF_013149785.1_ASM1314978v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:46,871] [INFO] Task started: fastANI
[2024-01-24 15:03:46,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a979868-9c8d-4aed-9db9-07824dfc8040/GCF_013149785.1_ASM1314978v1_genomic.fna.gz --refList GCF_013149785.1_ASM1314978v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013149785.1_ASM1314978v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:01,163] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:01,176] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:01,176] [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_013149785.1	s__Isoptericola halotolerans	100.0	1320	1320	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_003003075.1	s__Isoptericola halotolerans_A	85.5182	1006	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013149805.1	s__Isoptericola chiayiensis	82.8156	865	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013085345.1	s__Isoptericola sediminis	82.3725	758	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636295.1	s__Isoptericola dokdonensis	82.2513	853	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563715.1	s__Isoptericola jiangsuensis	82.1729	857	1320	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	81.0322	822	1320	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	80.9869	765	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009663185.1	s__Isoptericola sp009663185	80.9498	728	1320	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	80.6945	790	1320	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	79.5869	617	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	99.97	99.97	0.99	0.99	2	-
GCA_009783295.1	s__Xylanimonas sp009783295	79.5186	583	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135345.1	s__Xylanimonas allomyrinae	79.5121	552	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014137995.1	s__Promicromonospora sukumoe	79.1561	716	1320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:01,178] [INFO] GTDB search result was written to GCF_013149785.1_ASM1314978v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:01,178] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:01,183] [INFO] DFAST_QC result json was written to GCF_013149785.1_ASM1314978v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:01,183] [INFO] DFAST_QC completed!
[2024-01-24 15:04:01,183] [INFO] Total running time: 0h1m54s