[2024-01-24 11:58:55,608] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:55,611] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:55,611] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c7e944d-9cf2-474f-9806-91b59ed1158e/dqc_reference
[2024-01-24 11:58:56,863] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:56,865] [INFO] Task started: Prodigal
[2024-01-24 11:58:56,865] [INFO] Running command: gunzip -c /var/lib/cwl/stg5447274d-22d6-4dff-ba48-a60855eb2247/GCF_023283665.1_ASM2328366v1_genomic.fna.gz | prodigal -d GCF_023283665.1_ASM2328366v1_genomic.fna/cds.fna -a GCF_023283665.1_ASM2328366v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:07,534] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:07,535] [INFO] Task started: HMMsearch
[2024-01-24 11:59:07,535] [INFO] Running command: hmmsearch --tblout GCF_023283665.1_ASM2328366v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c7e944d-9cf2-474f-9806-91b59ed1158e/dqc_reference/reference_markers.hmm GCF_023283665.1_ASM2328366v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:07,867] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:07,868] [INFO] Found 6/6 markers.
[2024-01-24 11:59:07,907] [INFO] Query marker FASTA was written to GCF_023283665.1_ASM2328366v1_genomic.fna/markers.fasta
[2024-01-24 11:59:07,908] [INFO] Task started: Blastn
[2024-01-24 11:59:07,908] [INFO] Running command: blastn -query GCF_023283665.1_ASM2328366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c7e944d-9cf2-474f-9806-91b59ed1158e/dqc_reference/reference_markers.fasta -out GCF_023283665.1_ASM2328366v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:08,759] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:08,762] [INFO] Selected 9 target genomes.
[2024-01-24 11:59:08,762] [INFO] Target genome list was writen to GCF_023283665.1_ASM2328366v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:08,768] [INFO] Task started: fastANI
[2024-01-24 11:59:08,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg5447274d-22d6-4dff-ba48-a60855eb2247/GCF_023283665.1_ASM2328366v1_genomic.fna.gz --refList GCF_023283665.1_ASM2328366v1_genomic.fna/target_genomes.txt --output GCF_023283665.1_ASM2328366v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:19,406] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:19,407] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c7e944d-9cf2-474f-9806-91b59ed1158e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:19,407] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c7e944d-9cf2-474f-9806-91b59ed1158e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:19,415] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:19,416] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:19,416] [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
Shewanella xiamenensis	strain=JCM 16212	GCA_014647135.1	332186	332186	type	True	99.9949	1493	1505	95	conclusive
Shewanella decolorationis	strain=S12	GCA_000485795.1	256839	256839	type	True	89.7896	1313	1505	95	below_threshold
Shewanella seohaensis	strain=CCUG 60900	GCA_023283775.1	755175	755175	type	True	89.2895	1268	1505	95	below_threshold
Shewanella oneidensis	strain=MR-1	GCA_000146165.2	70863	70863	type	True	89.2831	1319	1505	95	below_threshold
Shewanella oneidensis	strain=MR-1	GCA_013267215.1	70863	70863	type	True	89.2605	1301	1505	95	below_threshold
Shewanella seohaensis	strain=KCTC 23556	GCA_025449215.1	755175	755175	type	True	89.1159	1265	1505	95	below_threshold
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	81.764	885	1505	95	below_threshold
Shewanella oncorhynchi	strain=S-1	GCA_012584455.1	2726434	2726434	type	True	81.6539	959	1505	95	below_threshold
Shewanella kaireitica	strain=DSM 17170	GCA_023284045.1	212021	212021	type	True	77.8155	229	1505	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:19,418] [INFO] DFAST Taxonomy check result was written to GCF_023283665.1_ASM2328366v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:19,418] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:19,418] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:19,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c7e944d-9cf2-474f-9806-91b59ed1158e/dqc_reference/checkm_data
[2024-01-24 11:59:19,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:19,462] [INFO] Task started: CheckM
[2024-01-24 11:59:19,462] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023283665.1_ASM2328366v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023283665.1_ASM2328366v1_genomic.fna/checkm_input GCF_023283665.1_ASM2328366v1_genomic.fna/checkm_result
[2024-01-24 11:59:56,536] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:56,537] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:56,555] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:56,555] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:56,555] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023283665.1_ASM2328366v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:56,556] [INFO] Task started: Blastn
[2024-01-24 11:59:56,556] [INFO] Running command: blastn -query GCF_023283665.1_ASM2328366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c7e944d-9cf2-474f-9806-91b59ed1158e/dqc_reference/reference_markers_gtdb.fasta -out GCF_023283665.1_ASM2328366v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:57,752] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:57,755] [INFO] Selected 6 target genomes.
[2024-01-24 11:59:57,755] [INFO] Target genome list was writen to GCF_023283665.1_ASM2328366v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:57,760] [INFO] Task started: fastANI
[2024-01-24 11:59:57,760] [INFO] Running command: fastANI --query /var/lib/cwl/stg5447274d-22d6-4dff-ba48-a60855eb2247/GCF_023283665.1_ASM2328366v1_genomic.fna.gz --refList GCF_023283665.1_ASM2328366v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023283665.1_ASM2328366v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:05,753] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:05,760] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:05,761] [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_014647135.1	s__Shewanella xiamenensis	99.9949	1493	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.56	97.34	0.92	0.88	25	conclusive
GCF_000485795.1	s__Shewanella decolorationis	89.7896	1313	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.60	97.51	0.93	0.92	3	-
GCF_002216875.1	s__Shewanella bicestrii	89.425	1278	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.51	96.32	0.89	0.87	4	-
GCF_000146165.2	s__Shewanella oneidensis	89.2928	1318	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000203935.1	s__Shewanella sp000203935	89.2764	1292	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.76	95.76	0.86	0.86	2	-
GCF_000014665.1	s__Shewanella sp000014665	89.2367	1272	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.13	97.13	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:05,762] [INFO] GTDB search result was written to GCF_023283665.1_ASM2328366v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:05,763] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:05,766] [INFO] DFAST_QC result json was written to GCF_023283665.1_ASM2328366v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:05,766] [INFO] DFAST_QC completed!
[2024-01-24 12:00:05,766] [INFO] Total running time: 0h1m10s