[2024-01-24 10:47:40,957] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,964] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,964] [INFO] DQC Reference Directory: /var/lib/cwl/stg85bde003-4595-4679-bb1a-b5f51e665ec9/dqc_reference
[2024-01-24 10:47:44,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,789] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,790] [INFO] Running command: gunzip -c /var/lib/cwl/stg81cf2aa8-2059-4802-a2b6-d1cf469c3623/GCF_023283535.1_ASM2328353v1_genomic.fna.gz | prodigal -d GCF_023283535.1_ASM2328353v1_genomic.fna/cds.fna -a GCF_023283535.1_ASM2328353v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:55,657] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:55,657] [INFO] Task started: HMMsearch
[2024-01-24 10:47:55,658] [INFO] Running command: hmmsearch --tblout GCF_023283535.1_ASM2328353v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85bde003-4595-4679-bb1a-b5f51e665ec9/dqc_reference/reference_markers.hmm GCF_023283535.1_ASM2328353v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:56,004] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:56,005] [INFO] Found 6/6 markers.
[2024-01-24 10:47:56,048] [INFO] Query marker FASTA was written to GCF_023283535.1_ASM2328353v1_genomic.fna/markers.fasta
[2024-01-24 10:47:56,048] [INFO] Task started: Blastn
[2024-01-24 10:47:56,048] [INFO] Running command: blastn -query GCF_023283535.1_ASM2328353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85bde003-4595-4679-bb1a-b5f51e665ec9/dqc_reference/reference_markers.fasta -out GCF_023283535.1_ASM2328353v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:56,829] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:56,833] [INFO] Selected 10 target genomes.
[2024-01-24 10:47:56,833] [INFO] Target genome list was writen to GCF_023283535.1_ASM2328353v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:56,839] [INFO] Task started: fastANI
[2024-01-24 10:47:56,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg81cf2aa8-2059-4802-a2b6-d1cf469c3623/GCF_023283535.1_ASM2328353v1_genomic.fna.gz --refList GCF_023283535.1_ASM2328353v1_genomic.fna/target_genomes.txt --output GCF_023283535.1_ASM2328353v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:07,910] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:07,911] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85bde003-4595-4679-bb1a-b5f51e665ec9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:07,911] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85bde003-4595-4679-bb1a-b5f51e665ec9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:07,924] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:48:07,924] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:07,924] [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 sairae	strain=LMG 21408	GCA_023283535.1	190310	190310	type	True	100.0	1679	1686	95	conclusive
Shewanella sairae	strain=JCM 11563	GCA_019655015.1	190310	190310	type	True	99.9283	1614	1686	95	conclusive
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	88.1583	1215	1686	95	below_threshold
Shewanella fidelis	strain=ATCC BAA-318	GCA_000518605.1	173509	173509	type	True	83.037	1042	1686	95	below_threshold
Shewanella pealeana	strain=ATCC 700345	GCA_000018285.1	70864	70864	type	True	82.6406	979	1686	95	below_threshold
Shewanella schlegeliana	strain=JCM 11561	GCA_016765635.1	190308	190308	type	True	82.0559	893	1686	95	below_threshold
Shewanella schlegeliana	strain=LMG 21406	GCA_023283605.1	190308	190308	type	True	82.0092	881	1686	95	below_threshold
Shewanella gelidimarina	strain=ATCC 700752	GCA_023283945.1	56813	56813	type	True	79.6522	592	1686	95	below_threshold
Shewanella abyssi	strain=DSM 17171	GCA_023284025.1	311789	311789	type	True	79.51	577	1686	95	below_threshold
Shewanella algidipiscicola	strain=LMG 23746	GCA_003605125.1	614070	614070	type	True	78.8458	307	1686	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:07,926] [INFO] DFAST Taxonomy check result was written to GCF_023283535.1_ASM2328353v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:07,928] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:07,929] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:07,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85bde003-4595-4679-bb1a-b5f51e665ec9/dqc_reference/checkm_data
[2024-01-24 10:48:07,930] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:07,982] [INFO] Task started: CheckM
[2024-01-24 10:48:07,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023283535.1_ASM2328353v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023283535.1_ASM2328353v1_genomic.fna/checkm_input GCF_023283535.1_ASM2328353v1_genomic.fna/checkm_result
[2024-01-24 10:48:44,255] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:44,256] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:44,276] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:44,276] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:44,277] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023283535.1_ASM2328353v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:44,277] [INFO] Task started: Blastn
[2024-01-24 10:48:44,277] [INFO] Running command: blastn -query GCF_023283535.1_ASM2328353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85bde003-4595-4679-bb1a-b5f51e665ec9/dqc_reference/reference_markers_gtdb.fasta -out GCF_023283535.1_ASM2328353v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:45,463] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:45,466] [INFO] Selected 12 target genomes.
[2024-01-24 10:48:45,467] [INFO] Target genome list was writen to GCF_023283535.1_ASM2328353v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:45,474] [INFO] Task started: fastANI
[2024-01-24 10:48:45,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg81cf2aa8-2059-4802-a2b6-d1cf469c3623/GCF_023283535.1_ASM2328353v1_genomic.fna.gz --refList GCF_023283535.1_ASM2328353v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023283535.1_ASM2328353v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:57,434] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:57,455] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:48:57,455] [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_000518605.1	s__Shewanella fidelis	83.0205	1045	1686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.11	97.11	0.90	0.90	2	-
GCF_000018285.1	s__Shewanella pealeana	82.6454	979	1686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019185.1	s__Shewanella halifaxensis	82.1692	914	1686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765635.1	s__Shewanella schlegeliana	82.0631	893	1686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014885.1	s__Shewanella piezotolerans	80.0289	618	1686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836205.1	s__Shewanella sp002836205	79.6324	605	1686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.46	99.13	0.96	0.92	4	-
GCF_016757755.1	s__Shewanella sp016757755	79.5919	594	1686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018025.1	s__Shewanella sediminis	78.8971	326	1686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605125.1	s__Shewanella algidipiscicola	78.8433	303	1686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.64	98.64	0.92	0.92	2	-
GCF_001957125.1	s__Shewanella sp001957125	78.7378	380	1686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648295.1	s__Shewanella saliphila	77.9633	272	1686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_009828585.1	s__Shewanella litoralis	77.8916	260	1686	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 10:48:57,457] [INFO] GTDB search result was written to GCF_023283535.1_ASM2328353v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:57,458] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:57,461] [INFO] DFAST_QC result json was written to GCF_023283535.1_ASM2328353v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:57,462] [INFO] DFAST_QC completed!
[2024-01-24 10:48:57,462] [INFO] Total running time: 0h1m17s