[2024-01-24 11:44:23,867] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,872] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,873] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5ac0c2c-44b4-43cc-b011-67decccc8baa/dqc_reference
[2024-01-24 11:44:26,341] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,342] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,342] [INFO] Running command: gunzip -c /var/lib/cwl/stg4204e0fb-7efa-4f2e-9fb1-9ff5d6a56182/GCF_019654995.1_ASM1965499v1_genomic.fna.gz | prodigal -d GCF_019654995.1_ASM1965499v1_genomic.fna/cds.fna -a GCF_019654995.1_ASM1965499v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:36,853] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:36,853] [INFO] Task started: HMMsearch
[2024-01-24 11:44:36,853] [INFO] Running command: hmmsearch --tblout GCF_019654995.1_ASM1965499v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5ac0c2c-44b4-43cc-b011-67decccc8baa/dqc_reference/reference_markers.hmm GCF_019654995.1_ASM1965499v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:37,164] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:37,166] [INFO] Found 6/6 markers.
[2024-01-24 11:44:37,207] [INFO] Query marker FASTA was written to GCF_019654995.1_ASM1965499v1_genomic.fna/markers.fasta
[2024-01-24 11:44:37,207] [INFO] Task started: Blastn
[2024-01-24 11:44:37,208] [INFO] Running command: blastn -query GCF_019654995.1_ASM1965499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5ac0c2c-44b4-43cc-b011-67decccc8baa/dqc_reference/reference_markers.fasta -out GCF_019654995.1_ASM1965499v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:37,991] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:37,995] [INFO] Selected 11 target genomes.
[2024-01-24 11:44:37,996] [INFO] Target genome list was writen to GCF_019654995.1_ASM1965499v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:38,023] [INFO] Task started: fastANI
[2024-01-24 11:44:38,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg4204e0fb-7efa-4f2e-9fb1-9ff5d6a56182/GCF_019654995.1_ASM1965499v1_genomic.fna.gz --refList GCF_019654995.1_ASM1965499v1_genomic.fna/target_genomes.txt --output GCF_019654995.1_ASM1965499v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:50,515] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:50,516] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5ac0c2c-44b4-43cc-b011-67decccc8baa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:50,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5ac0c2c-44b4-43cc-b011-67decccc8baa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:50,531] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:44:50,532] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:50,532] [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 schlegeliana	strain=JCM 11561	GCA_019654995.1	190308	190308	type	True	100.0	1581	1586	95	conclusive
Shewanella schlegeliana	strain=JCM 11561	GCA_016765635.1	190308	190308	type	True	99.9974	1582	1586	95	conclusive
Shewanella schlegeliana	strain=LMG 21406	GCA_023283605.1	190308	190308	type	True	99.9955	1576	1586	95	conclusive
Shewanella halifaxensis	strain=HAW-EB4	GCA_000019185.1	271098	271098	type	True	86.1988	1291	1586	95	below_threshold
Shewanella pealeana	strain=ATCC 700345	GCA_000018285.1	70864	70864	type	True	83.9716	1225	1586	95	below_threshold
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	82.0384	939	1586	95	below_threshold
Shewanella sairae	strain=LMG 21408	GCA_023283535.1	190310	190310	type	True	81.9559	877	1586	95	below_threshold
Shewanella sairae	strain=JCM 11563	GCA_019655015.1	190310	190310	type	True	81.9537	901	1586	95	below_threshold
Shewanella fidelis	strain=ATCC BAA-318	GCA_000518605.1	173509	173509	type	True	81.555	835	1586	95	below_threshold
Shewanella abyssi	strain=DSM 17171	GCA_023284025.1	311789	311789	type	True	79.5931	611	1586	95	below_threshold
Shewanella surugensis	strain=DSM 17177	GCA_023284005.1	212020	212020	type	True	78.2218	188	1586	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:50,535] [INFO] DFAST Taxonomy check result was written to GCF_019654995.1_ASM1965499v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:50,536] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:50,536] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:50,536] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5ac0c2c-44b4-43cc-b011-67decccc8baa/dqc_reference/checkm_data
[2024-01-24 11:44:50,538] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:50,586] [INFO] Task started: CheckM
[2024-01-24 11:44:50,586] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019654995.1_ASM1965499v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019654995.1_ASM1965499v1_genomic.fna/checkm_input GCF_019654995.1_ASM1965499v1_genomic.fna/checkm_result
[2024-01-24 11:45:25,945] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:25,946] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:25,965] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:25,966] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:25,966] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019654995.1_ASM1965499v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:25,966] [INFO] Task started: Blastn
[2024-01-24 11:45:25,967] [INFO] Running command: blastn -query GCF_019654995.1_ASM1965499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5ac0c2c-44b4-43cc-b011-67decccc8baa/dqc_reference/reference_markers_gtdb.fasta -out GCF_019654995.1_ASM1965499v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:27,107] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:27,111] [INFO] Selected 9 target genomes.
[2024-01-24 11:45:27,112] [INFO] Target genome list was writen to GCF_019654995.1_ASM1965499v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:27,120] [INFO] Task started: fastANI
[2024-01-24 11:45:27,120] [INFO] Running command: fastANI --query /var/lib/cwl/stg4204e0fb-7efa-4f2e-9fb1-9ff5d6a56182/GCF_019654995.1_ASM1965499v1_genomic.fna.gz --refList GCF_019654995.1_ASM1965499v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019654995.1_ASM1965499v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:37,413] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:37,430] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:37,430] [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_016765635.1	s__Shewanella schlegeliana	99.9974	1582	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000019185.1	s__Shewanella halifaxensis	86.195	1291	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018285.1	s__Shewanella pealeana	83.9652	1226	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518605.1	s__Shewanella fidelis	81.5574	834	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.11	97.11	0.90	0.90	2	-
GCF_000014885.1	s__Shewanella piezotolerans	80.1255	633	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757755.1	s__Shewanella sp016757755	79.8143	640	1586	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	79.6097	617	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.46	99.13	0.96	0.92	4	-
GCF_000016065.1	s__Shewanella loihica	78.4716	300	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.22	95.22	0.91	0.91	2	-
GCF_004358445.1	s__Parashewanella tropica	78.0522	131	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:37,432] [INFO] GTDB search result was written to GCF_019654995.1_ASM1965499v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:37,433] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:37,437] [INFO] DFAST_QC result json was written to GCF_019654995.1_ASM1965499v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:37,437] [INFO] DFAST_QC completed!
[2024-01-24 11:45:37,437] [INFO] Total running time: 0h1m14s