[2024-01-24 13:49:19,423] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:19,426] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:19,426] [INFO] DQC Reference Directory: /var/lib/cwl/stg3cf3fd76-5a31-4613-bf9b-e5f1a861a261/dqc_reference
[2024-01-24 13:49:20,805] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:20,806] [INFO] Task started: Prodigal
[2024-01-24 13:49:20,806] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c6b592e-d7bc-46e0-b701-f118fa09b150/GCF_007830495.1_ASM783049v1_genomic.fna.gz | prodigal -d GCF_007830495.1_ASM783049v1_genomic.fna/cds.fna -a GCF_007830495.1_ASM783049v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:47,686] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:47,686] [INFO] Task started: HMMsearch
[2024-01-24 13:49:47,686] [INFO] Running command: hmmsearch --tblout GCF_007830495.1_ASM783049v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3cf3fd76-5a31-4613-bf9b-e5f1a861a261/dqc_reference/reference_markers.hmm GCF_007830495.1_ASM783049v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:48,076] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:48,077] [INFO] Found 6/6 markers.
[2024-01-24 13:49:48,133] [INFO] Query marker FASTA was written to GCF_007830495.1_ASM783049v1_genomic.fna/markers.fasta
[2024-01-24 13:49:48,133] [INFO] Task started: Blastn
[2024-01-24 13:49:48,133] [INFO] Running command: blastn -query GCF_007830495.1_ASM783049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3cf3fd76-5a31-4613-bf9b-e5f1a861a261/dqc_reference/reference_markers.fasta -out GCF_007830495.1_ASM783049v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:49,208] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:49,212] [INFO] Selected 16 target genomes.
[2024-01-24 13:49:49,213] [INFO] Target genome list was writen to GCF_007830495.1_ASM783049v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:49,220] [INFO] Task started: fastANI
[2024-01-24 13:49:49,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c6b592e-d7bc-46e0-b701-f118fa09b150/GCF_007830495.1_ASM783049v1_genomic.fna.gz --refList GCF_007830495.1_ASM783049v1_genomic.fna/target_genomes.txt --output GCF_007830495.1_ASM783049v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:18,495] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:18,495] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3cf3fd76-5a31-4613-bf9b-e5f1a861a261/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:18,495] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3cf3fd76-5a31-4613-bf9b-e5f1a861a261/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:18,509] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:18,509] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:18,510] [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
Pseudoduganella flava	strain=CGMCC 1.10685	GCA_007830495.1	871742	871742	type	True	100.0	2275	2276	95	conclusive
Pseudoduganella dura	strain=DSM 17513	GCA_009727155.1	321982	321982	type	True	85.255	1562	2276	95	below_threshold
Pseudoduganella dura	strain=KCTC 12342	GCA_014651395.1	321982	321982	type	True	85.1588	1526	2276	95	below_threshold
Pseudoduganella lurida	strain=CGMCC 1.10822	GCA_007830455.1	1036180	1036180	type	True	85.1011	1428	2276	95	below_threshold
Pseudoduganella umbonata	strain=CECT 7753	GCA_014192225.1	864828	864828	type	True	85.0605	1578	2276	95	below_threshold
Pseudoduganella albidiflava	strain=KCTC 12343	GCA_014651415.1	321983	321983	type	True	84.9682	1609	2276	95	below_threshold
Pseudoduganella albidiflava	strain=DSM 17472	GCA_004322755.1	321983	321983	type	True	84.8595	1637	2276	95	below_threshold
Pseudoduganella lutea	strain=DSM 17473	GCA_004209755.1	321985	321985	type	True	84.6393	1575	2276	95	below_threshold
Pseudoduganella armeniaca	strain=ZMN-3	GCA_003028855.1	2072590	2072590	type	True	84.2636	1510	2276	95	below_threshold
Pseudoduganella plicata	strain=KCTC 12344	GCA_014651435.1	321984	321984	type	True	83.7396	1410	2276	95	below_threshold
Pseudoduganella plicata	strain=DSM 17505	GCA_004421005.1	321984	321984	type	True	83.6503	1431	2276	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	81.2527	1018	2276	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	81.1295	1000	2276	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	80.9525	1212	2276	95	below_threshold
Pseudoduganella guangdongensis	strain=DS3	GCA_009857475.1	2692179	2692179	type	True	80.6707	993	2276	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	80.4965	898	2276	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:18,511] [INFO] DFAST Taxonomy check result was written to GCF_007830495.1_ASM783049v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:18,512] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:18,512] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:18,512] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3cf3fd76-5a31-4613-bf9b-e5f1a861a261/dqc_reference/checkm_data
[2024-01-24 13:50:18,513] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:18,580] [INFO] Task started: CheckM
[2024-01-24 13:50:18,580] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830495.1_ASM783049v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830495.1_ASM783049v1_genomic.fna/checkm_input GCF_007830495.1_ASM783049v1_genomic.fna/checkm_result
[2024-01-24 13:51:33,884] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:33,886] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:33,910] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:33,910] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:33,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830495.1_ASM783049v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:33,911] [INFO] Task started: Blastn
[2024-01-24 13:51:33,911] [INFO] Running command: blastn -query GCF_007830495.1_ASM783049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3cf3fd76-5a31-4613-bf9b-e5f1a861a261/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830495.1_ASM783049v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:35,897] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:35,905] [INFO] Selected 10 target genomes.
[2024-01-24 13:51:35,905] [INFO] Target genome list was writen to GCF_007830495.1_ASM783049v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:35,934] [INFO] Task started: fastANI
[2024-01-24 13:51:35,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c6b592e-d7bc-46e0-b701-f118fa09b150/GCF_007830495.1_ASM783049v1_genomic.fna.gz --refList GCF_007830495.1_ASM783049v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830495.1_ASM783049v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:53,900] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:53,913] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:53,913] [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_007830495.1	s__Pseudoduganella flava	100.0	2275	2276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_009727155.1	s__Pseudoduganella dura	85.2981	1555	2276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002454505.1	s__Pseudoduganella sp002454505	85.24	1377	2276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830455.1	s__Pseudoduganella lurida	85.1049	1429	2276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192225.1	s__Pseudoduganella umbonata	85.0221	1584	2276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004322755.1	s__Pseudoduganella albidiflava	84.8811	1630	2276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004209755.1	s__Pseudoduganella lutea	84.5936	1584	2276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008011715.1	s__Pseudoduganella haloabium	84.303	1471	2276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	98.13	98.13	0.91	0.91	2	-
GCF_003028855.1	s__Pseudoduganella armeniaca	84.2421	1514	2276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004421005.1	s__Pseudoduganella plicata	83.6183	1437	2276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:53,915] [INFO] GTDB search result was written to GCF_007830495.1_ASM783049v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:53,915] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:53,929] [INFO] DFAST_QC result json was written to GCF_007830495.1_ASM783049v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:53,930] [INFO] DFAST_QC completed!
[2024-01-24 13:51:53,930] [INFO] Total running time: 0h2m35s