[2024-01-24 11:09:50,717] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:09:50,795] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:09:50,796] [INFO] DQC Reference Directory: /var/lib/cwl/stg19fcb116-6bd9-4aa5-ba05-90d1ec55ffef/dqc_reference
[2024-01-24 11:09:53,303] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:09:53,304] [INFO] Task started: Prodigal
[2024-01-24 11:09:53,304] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b845467-db5a-4be3-a6a6-097dbb91f5c9/GCF_023283765.1_ASM2328376v1_genomic.fna.gz | prodigal -d GCF_023283765.1_ASM2328376v1_genomic.fna/cds.fna -a GCF_023283765.1_ASM2328376v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:10:03,849] [INFO] Task succeeded: Prodigal
[2024-01-24 11:10:03,849] [INFO] Task started: HMMsearch
[2024-01-24 11:10:03,850] [INFO] Running command: hmmsearch --tblout GCF_023283765.1_ASM2328376v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19fcb116-6bd9-4aa5-ba05-90d1ec55ffef/dqc_reference/reference_markers.hmm GCF_023283765.1_ASM2328376v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:10:04,142] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:10:04,144] [INFO] Found 6/6 markers.
[2024-01-24 11:10:04,182] [INFO] Query marker FASTA was written to GCF_023283765.1_ASM2328376v1_genomic.fna/markers.fasta
[2024-01-24 11:10:04,183] [INFO] Task started: Blastn
[2024-01-24 11:10:04,183] [INFO] Running command: blastn -query GCF_023283765.1_ASM2328376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19fcb116-6bd9-4aa5-ba05-90d1ec55ffef/dqc_reference/reference_markers.fasta -out GCF_023283765.1_ASM2328376v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:10:04,973] [INFO] Task succeeded: Blastn
[2024-01-24 11:10:04,977] [INFO] Selected 11 target genomes.
[2024-01-24 11:10:04,978] [INFO] Target genome list was writen to GCF_023283765.1_ASM2328376v1_genomic.fna/target_genomes.txt
[2024-01-24 11:10:05,022] [INFO] Task started: fastANI
[2024-01-24 11:10:05,022] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b845467-db5a-4be3-a6a6-097dbb91f5c9/GCF_023283765.1_ASM2328376v1_genomic.fna.gz --refList GCF_023283765.1_ASM2328376v1_genomic.fna/target_genomes.txt --output GCF_023283765.1_ASM2328376v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:10:17,469] [INFO] Task succeeded: fastANI
[2024-01-24 11:10:17,470] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19fcb116-6bd9-4aa5-ba05-90d1ec55ffef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:10:17,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19fcb116-6bd9-4aa5-ba05-90d1ec55ffef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:10:17,486] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:10:17,487] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:10:17,487] [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 profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	100.0	1513	1518	95	conclusive
Shewanella putrefaciens	strain=JCM 20190	GCA_014647555.1	24	24	type	True	89.6826	1194	1518	95	below_threshold
Shewanella putrefaciens	strain=ATCC 8071	GCA_016406325.1	24	24	type	True	89.6618	1224	1518	95	below_threshold
Shewanella putrefaciens	strain=NBRC 3908	GCA_001591325.1	24	24	type	True	89.6273	1179	1518	95	below_threshold
Shewanella oncorhynchi	strain=S-1	GCA_012584455.1	2726434	2726434	type	True	85.4006	1091	1518	95	below_threshold
Shewanella hafniensis	strain=ATCC BAA-1207	GCA_019655335.1	365590	365590	type	True	84.8315	1068	1518	95	below_threshold
Shewanella baltica	strain=NCTC10735	GCA_900456975.1	62322	62322	type	True	84.7673	1105	1518	95	below_threshold
Shewanella glacialipiscicola	strain=LMG 23744	GCA_023283485.1	614069	614069	type	True	82.7741	904	1518	95	below_threshold
Shewanella oneidensis	strain=MR-1	GCA_013267215.1	70863	70863	type	True	81.6058	890	1518	95	below_threshold
Shewanella seohaensis	strain=CCUG 60900	GCA_023283775.1	755175	755175	type	True	81.5108	915	1518	95	below_threshold
Shewanella seohaensis	strain=KCTC 23556	GCA_025449215.1	755175	755175	type	True	81.1463	912	1518	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:10:17,488] [INFO] DFAST Taxonomy check result was written to GCF_023283765.1_ASM2328376v1_genomic.fna/tc_result.tsv
[2024-01-24 11:10:17,489] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:10:17,489] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:10:17,489] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19fcb116-6bd9-4aa5-ba05-90d1ec55ffef/dqc_reference/checkm_data
[2024-01-24 11:10:17,490] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:10:17,534] [INFO] Task started: CheckM
[2024-01-24 11:10:17,535] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023283765.1_ASM2328376v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023283765.1_ASM2328376v1_genomic.fna/checkm_input GCF_023283765.1_ASM2328376v1_genomic.fna/checkm_result
[2024-01-24 11:10:52,832] [INFO] Task succeeded: CheckM
[2024-01-24 11:10:52,834] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:10:52,853] [INFO] ===== Completeness check finished =====
[2024-01-24 11:10:52,854] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:10:52,854] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023283765.1_ASM2328376v1_genomic.fna/markers.fasta)
[2024-01-24 11:10:52,855] [INFO] Task started: Blastn
[2024-01-24 11:10:52,855] [INFO] Running command: blastn -query GCF_023283765.1_ASM2328376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19fcb116-6bd9-4aa5-ba05-90d1ec55ffef/dqc_reference/reference_markers_gtdb.fasta -out GCF_023283765.1_ASM2328376v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:10:54,003] [INFO] Task succeeded: Blastn
[2024-01-24 11:10:54,006] [INFO] Selected 9 target genomes.
[2024-01-24 11:10:54,006] [INFO] Target genome list was writen to GCF_023283765.1_ASM2328376v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:10:54,023] [INFO] Task started: fastANI
[2024-01-24 11:10:54,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b845467-db5a-4be3-a6a6-097dbb91f5c9/GCF_023283765.1_ASM2328376v1_genomic.fna.gz --refList GCF_023283765.1_ASM2328376v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023283765.1_ASM2328376v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:11:04,199] [INFO] Task succeeded: fastANI
[2024-01-24 11:11:04,215] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:11:04,216] [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_016406325.1	s__Shewanella putrefaciens	89.7044	1220	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.29	98.60	0.96	0.93	12	-
GCF_002966515.1	s__Shewanella sp002966515	85.3638	1134	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.53	97.30	0.89	0.86	10	-
GCF_900456975.1	s__Shewanella baltica	84.7409	1109	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.88	96.32	0.89	0.85	16	-
GCF_002838165.1	s__Shewanella sp002838165	84.6724	1075	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.37	97.32	0.89	0.88	8	-
GCF_016406305.1	s__Shewanella putrefaciens_C	84.2187	1067	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002783505.1	s__Shewanella sp002783505	83.8896	1021	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000217915.1	s__Shewanella sp000217915	83.6915	1011	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203935.1	s__Shewanella sp000203935	81.7744	920	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.76	95.76	0.86	0.86	2	-
GCF_000146165.2	s__Shewanella oneidensis	81.5976	904	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:11:04,218] [INFO] GTDB search result was written to GCF_023283765.1_ASM2328376v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:11:04,218] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:11:04,223] [INFO] DFAST_QC result json was written to GCF_023283765.1_ASM2328376v1_genomic.fna/dqc_result.json
[2024-01-24 11:11:04,223] [INFO] DFAST_QC completed!
[2024-01-24 11:11:04,223] [INFO] Total running time: 0h1m14s