[2024-01-24 12:06:10,642] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:10,645] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:10,645] [INFO] DQC Reference Directory: /var/lib/cwl/stg168813a3-2329-4177-9655-d54897b5d8da/dqc_reference
[2024-01-24 12:06:13,061] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:13,062] [INFO] Task started: Prodigal
[2024-01-24 12:06:13,062] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5414ef5-9066-4704-8478-4f23e8cc57cd/GCF_012584455.1_ASM1258445v1_genomic.fna.gz | prodigal -d GCF_012584455.1_ASM1258445v1_genomic.fna/cds.fna -a GCF_012584455.1_ASM1258445v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:25,287] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:25,287] [INFO] Task started: HMMsearch
[2024-01-24 12:06:25,287] [INFO] Running command: hmmsearch --tblout GCF_012584455.1_ASM1258445v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg168813a3-2329-4177-9655-d54897b5d8da/dqc_reference/reference_markers.hmm GCF_012584455.1_ASM1258445v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:25,694] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:25,695] [INFO] Found 6/6 markers.
[2024-01-24 12:06:25,745] [INFO] Query marker FASTA was written to GCF_012584455.1_ASM1258445v1_genomic.fna/markers.fasta
[2024-01-24 12:06:25,745] [INFO] Task started: Blastn
[2024-01-24 12:06:25,746] [INFO] Running command: blastn -query GCF_012584455.1_ASM1258445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg168813a3-2329-4177-9655-d54897b5d8da/dqc_reference/reference_markers.fasta -out GCF_012584455.1_ASM1258445v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:26,556] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:26,562] [INFO] Selected 11 target genomes.
[2024-01-24 12:06:26,562] [INFO] Target genome list was writen to GCF_012584455.1_ASM1258445v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:26,566] [INFO] Task started: fastANI
[2024-01-24 12:06:26,567] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5414ef5-9066-4704-8478-4f23e8cc57cd/GCF_012584455.1_ASM1258445v1_genomic.fna.gz --refList GCF_012584455.1_ASM1258445v1_genomic.fna/target_genomes.txt --output GCF_012584455.1_ASM1258445v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:40,053] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:40,053] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg168813a3-2329-4177-9655-d54897b5d8da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:40,054] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg168813a3-2329-4177-9655-d54897b5d8da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:40,063] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:40,064] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:40,064] [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 oncorhynchi	strain=S-1	GCA_012584455.1	2726434	2726434	type	True	100.0	1663	1667	95	conclusive
Shewanella hafniensis	strain=ATCC BAA-1207	GCA_019655335.1	365590	365590	type	True	91.6437	1305	1667	95	below_threshold
Shewanella baltica	strain=NCTC10735	GCA_900456975.1	62322	62322	type	True	91.0597	1413	1667	95	below_threshold
Shewanella putrefaciens	strain=ATCC 8071	GCA_016406325.1	24	24	type	True	86.3287	1149	1667	95	below_threshold
Shewanella putrefaciens	strain=NBRC 3908	GCA_001591325.1	24	24	type	True	86.2864	1124	1667	95	below_threshold
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	85.1904	1089	1667	95	below_threshold
Shewanella glacialipiscicola	strain=T147	GCA_019655235.1	614069	614069	type	True	85.1755	989	1667	95	below_threshold
Shewanella glacialipiscicola	strain=LMG 23744	GCA_023283485.1	614069	614069	type	True	85.0483	1107	1667	95	below_threshold
Shewanella morhuae	strain=ATCC BAA-1205	GCA_900156405.1	365591	365591	type	True	84.63	1128	1667	95	below_threshold
Shewanella seohaensis	strain=CCUG 60900	GCA_023283775.1	755175	755175	type	True	81.4279	964	1667	95	below_threshold
Shewanella seohaensis	strain=KCTC 23556	GCA_025449215.1	755175	755175	type	True	81.0519	982	1667	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:40,065] [INFO] DFAST Taxonomy check result was written to GCF_012584455.1_ASM1258445v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:40,066] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:40,066] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:40,066] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg168813a3-2329-4177-9655-d54897b5d8da/dqc_reference/checkm_data
[2024-01-24 12:06:40,067] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:40,116] [INFO] Task started: CheckM
[2024-01-24 12:06:40,116] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012584455.1_ASM1258445v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012584455.1_ASM1258445v1_genomic.fna/checkm_input GCF_012584455.1_ASM1258445v1_genomic.fna/checkm_result
[2024-01-24 12:07:19,605] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:19,606] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:19,627] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:19,627] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:19,628] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012584455.1_ASM1258445v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:19,628] [INFO] Task started: Blastn
[2024-01-24 12:07:19,629] [INFO] Running command: blastn -query GCF_012584455.1_ASM1258445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg168813a3-2329-4177-9655-d54897b5d8da/dqc_reference/reference_markers_gtdb.fasta -out GCF_012584455.1_ASM1258445v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:20,819] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:20,829] [INFO] Selected 8 target genomes.
[2024-01-24 12:07:20,829] [INFO] Target genome list was writen to GCF_012584455.1_ASM1258445v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:20,835] [INFO] Task started: fastANI
[2024-01-24 12:07:20,835] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5414ef5-9066-4704-8478-4f23e8cc57cd/GCF_012584455.1_ASM1258445v1_genomic.fna.gz --refList GCF_012584455.1_ASM1258445v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012584455.1_ASM1258445v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:30,528] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:30,536] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:30,536] [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_002966515.1	s__Shewanella sp002966515	97.5033	1500	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.53	97.30	0.89	0.86	10	conclusive
GCF_002838165.1	s__Shewanella sp002838165	91.4372	1378	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.37	97.32	0.89	0.88	8	-
GCF_900456975.1	s__Shewanella baltica	91.0679	1412	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.88	96.32	0.89	0.85	16	-
GCF_016406325.1	s__Shewanella putrefaciens	86.3287	1149	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.29	98.60	0.96	0.93	12	-
GCA_002783505.1	s__Shewanella sp002783505	84.9226	1123	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016406305.1	s__Shewanella putrefaciens_C	84.8239	1165	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156405.1	s__Shewanella morhuae	84.6369	1127	1667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.45	98.44	0.93	0.93	3	-
GCF_000014665.1	s__Shewanella sp000014665	81.4823	961	1667	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 12:07:30,538] [INFO] GTDB search result was written to GCF_012584455.1_ASM1258445v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:30,538] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:30,542] [INFO] DFAST_QC result json was written to GCF_012584455.1_ASM1258445v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:30,542] [INFO] DFAST_QC completed!
[2024-01-24 12:07:30,542] [INFO] Total running time: 0h1m20s