[2024-01-24 15:01:23,205] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:01:23,207] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:01:23,207] [INFO] DQC Reference Directory: /var/lib/cwl/stged75a78f-caf2-40c7-b421-935a1a13edaf/dqc_reference
[2024-01-24 15:01:24,624] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:01:24,625] [INFO] Task started: Prodigal
[2024-01-24 15:01:24,625] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb188356-38ac-4dc3-8734-ab4e1a505308/GCF_013358405.1_ASM1335840v1_genomic.fna.gz | prodigal -d GCF_013358405.1_ASM1335840v1_genomic.fna/cds.fna -a GCF_013358405.1_ASM1335840v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:01:37,365] [INFO] Task succeeded: Prodigal
[2024-01-24 15:01:37,366] [INFO] Task started: HMMsearch
[2024-01-24 15:01:37,366] [INFO] Running command: hmmsearch --tblout GCF_013358405.1_ASM1335840v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged75a78f-caf2-40c7-b421-935a1a13edaf/dqc_reference/reference_markers.hmm GCF_013358405.1_ASM1335840v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:01:37,737] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:01:37,738] [INFO] Found 6/6 markers.
[2024-01-24 15:01:37,779] [INFO] Query marker FASTA was written to GCF_013358405.1_ASM1335840v1_genomic.fna/markers.fasta
[2024-01-24 15:01:37,780] [INFO] Task started: Blastn
[2024-01-24 15:01:37,780] [INFO] Running command: blastn -query GCF_013358405.1_ASM1335840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged75a78f-caf2-40c7-b421-935a1a13edaf/dqc_reference/reference_markers.fasta -out GCF_013358405.1_ASM1335840v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:01:38,986] [INFO] Task succeeded: Blastn
[2024-01-24 15:01:38,990] [INFO] Selected 22 target genomes.
[2024-01-24 15:01:38,990] [INFO] Target genome list was writen to GCF_013358405.1_ASM1335840v1_genomic.fna/target_genomes.txt
[2024-01-24 15:01:39,003] [INFO] Task started: fastANI
[2024-01-24 15:01:39,004] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb188356-38ac-4dc3-8734-ab4e1a505308/GCF_013358405.1_ASM1335840v1_genomic.fna.gz --refList GCF_013358405.1_ASM1335840v1_genomic.fna/target_genomes.txt --output GCF_013358405.1_ASM1335840v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:01,192] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:01,193] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged75a78f-caf2-40c7-b421-935a1a13edaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:01,193] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged75a78f-caf2-40c7-b421-935a1a13edaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:01,213] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:01,213] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:01,213] [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
Oricola thermophila	strain=MEBiC13590	GCA_013358405.1	2742145	2742145	type	True	100.0	1331	1332	95	conclusive
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	80.2872	707	1332	95	below_threshold
Oricola cellulosilytica	strain=JCM 19534	GCA_019966575.1	1429082	1429082	type	True	79.0534	442	1332	95	below_threshold
Zhengella mangrovi	strain=X9-2-2	GCA_002727065.1	1982044	1982044	type	True	78.5687	425	1332	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.4921	402	1332	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	78.4277	397	1332	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	78.3902	392	1332	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	78.3305	374	1332	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	78.157	369	1332	95	below_threshold
Mesorhizobium sediminum	strain=KCTC 42205	GCA_013240295.1	1849104	1849104	type	True	78.1482	359	1332	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	78.1297	368	1332	95	below_threshold
Chelativorans xinjiangense	strain=lm93	GCA_009812055.1	2681485	2681485	type	True	78.1159	369	1332	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	78.0863	393	1332	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	77.9429	318	1332	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.9019	319	1332	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	77.891	320	1332	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	77.882	331	1332	95	below_threshold
Rhizobium ecuadorense	strain=CNPSO 671	GCA_001187535.1	1671795	1671795	type	True	77.8709	296	1332	95	below_threshold
Phyllobacterium salinisoli	strain=LLAN61	GCA_003335045.1	1899321	1899321	type	True	77.8496	270	1332	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	77.8141	339	1332	95	below_threshold
Ciceribacter lividus	strain=DSM 25528	GCA_003337715.1	1197950	1197950	type	True	77.7374	296	1332	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	77.1244	193	1332	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:01,215] [INFO] DFAST Taxonomy check result was written to GCF_013358405.1_ASM1335840v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:01,216] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:01,216] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:01,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged75a78f-caf2-40c7-b421-935a1a13edaf/dqc_reference/checkm_data
[2024-01-24 15:02:01,217] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:01,262] [INFO] Task started: CheckM
[2024-01-24 15:02:01,262] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013358405.1_ASM1335840v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013358405.1_ASM1335840v1_genomic.fna/checkm_input GCF_013358405.1_ASM1335840v1_genomic.fna/checkm_result
[2024-01-24 15:02:41,116] [INFO] Task succeeded: CheckM
[2024-01-24 15:02:41,117] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:02:41,139] [INFO] ===== Completeness check finished =====
[2024-01-24 15:02:41,139] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:02:41,140] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013358405.1_ASM1335840v1_genomic.fna/markers.fasta)
[2024-01-24 15:02:41,140] [INFO] Task started: Blastn
[2024-01-24 15:02:41,140] [INFO] Running command: blastn -query GCF_013358405.1_ASM1335840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged75a78f-caf2-40c7-b421-935a1a13edaf/dqc_reference/reference_markers_gtdb.fasta -out GCF_013358405.1_ASM1335840v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:43,202] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:43,206] [INFO] Selected 10 target genomes.
[2024-01-24 15:02:43,206] [INFO] Target genome list was writen to GCF_013358405.1_ASM1335840v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:02:43,225] [INFO] Task started: fastANI
[2024-01-24 15:02:43,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb188356-38ac-4dc3-8734-ab4e1a505308/GCF_013358405.1_ASM1335840v1_genomic.fna.gz --refList GCF_013358405.1_ASM1335840v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013358405.1_ASM1335840v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:02:54,536] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:54,550] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:02:54,550] [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_013358405.1	s__Oricola thermophila	100.0	1331	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014904745.1	s__Oricola sp014904745	81.2678	778	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698425.1	s__Oricola sp002698425	80.7638	747	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706335.1	s__Oricola sp002706335	80.2192	685	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331745.1	s__Oricola cellulosilytica	79.0187	441	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860725.1	s__Aquamicrobium_A sp014860725	78.4246	254	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007922615.2	s__Nitratireductor_D sp007922615	78.3487	405	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823835.1	s__RCIZ01 sp018823835	78.3347	383	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIZ01	95.0	99.96	99.89	0.99	0.96	11	-
GCF_004010325.2	s__Mesorhizobium sp004010325	78.004	358	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.05	98.94	0.91	0.90	4	-
GCF_003934165.1	s__Pseudaminobacter arsenicus	77.8813	297	1332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:02:54,552] [INFO] GTDB search result was written to GCF_013358405.1_ASM1335840v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:02:54,553] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:02:54,557] [INFO] DFAST_QC result json was written to GCF_013358405.1_ASM1335840v1_genomic.fna/dqc_result.json
[2024-01-24 15:02:54,557] [INFO] DFAST_QC completed!
[2024-01-24 15:02:54,557] [INFO] Total running time: 0h1m31s