[2024-01-24 11:43:40,749] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:40,751] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:40,751] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ee50f1d-dae9-4a91-b6c2-323ce48788e8/dqc_reference
[2024-01-24 11:43:42,058] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:42,059] [INFO] Task started: Prodigal
[2024-01-24 11:43:42,059] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d82e4d8-07f3-45d3-90a7-718cffecdaaa/GCF_002836975.1_ASM283697v1_genomic.fna.gz | prodigal -d GCF_002836975.1_ASM283697v1_genomic.fna/cds.fna -a GCF_002836975.1_ASM283697v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:54,900] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:54,900] [INFO] Task started: HMMsearch
[2024-01-24 11:43:54,901] [INFO] Running command: hmmsearch --tblout GCF_002836975.1_ASM283697v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ee50f1d-dae9-4a91-b6c2-323ce48788e8/dqc_reference/reference_markers.hmm GCF_002836975.1_ASM283697v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:55,262] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:55,263] [INFO] Found 6/6 markers.
[2024-01-24 11:43:55,332] [INFO] Query marker FASTA was written to GCF_002836975.1_ASM283697v1_genomic.fna/markers.fasta
[2024-01-24 11:43:55,333] [INFO] Task started: Blastn
[2024-01-24 11:43:55,333] [INFO] Running command: blastn -query GCF_002836975.1_ASM283697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ee50f1d-dae9-4a91-b6c2-323ce48788e8/dqc_reference/reference_markers.fasta -out GCF_002836975.1_ASM283697v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:56,224] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:56,227] [INFO] Selected 15 target genomes.
[2024-01-24 11:43:56,227] [INFO] Target genome list was writen to GCF_002836975.1_ASM283697v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:56,233] [INFO] Task started: fastANI
[2024-01-24 11:43:56,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d82e4d8-07f3-45d3-90a7-718cffecdaaa/GCF_002836975.1_ASM283697v1_genomic.fna.gz --refList GCF_002836975.1_ASM283697v1_genomic.fna/target_genomes.txt --output GCF_002836975.1_ASM283697v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:12,910] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:12,911] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ee50f1d-dae9-4a91-b6c2-323ce48788e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:12,912] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ee50f1d-dae9-4a91-b6c2-323ce48788e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:12,928] [INFO] Found 15 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 11:44:12,928] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:44:12,928] [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 indica	strain=KJW27	GCA_002836975.1	768528	768528	type	True	100.0	1437	1439	95	inconclusive
Shewanella indica	strain=KCTC 23171	GCA_014652115.1	768528	768528	type	True	99.9911	1423	1439	95	inconclusive
Shewanella chilikensis	strain=JC5	GCA_003217175.1	558541	558541	type	True	95.8024	1307	1439	95	inconclusive
Shewanella chilikensis	strain=KCTC 22540	GCA_014651975.1	558541	558541	type	True	95.7851	1311	1439	95	inconclusive
Shewanella chilikensis	strain=JC5	GCA_002836945.1	558541	558541	type	True	95.7693	1308	1439	95	inconclusive
Shewanella chilikensis	strain=CCUG 57101	GCA_023283475.1	558541	558541	type	True	95.7671	1328	1439	95	inconclusive
Shewanella algae	strain=ATCC 51192	GCA_012396675.1	38313	38313	type	True	94.2549	1298	1439	95	below_threshold
Shewanella algae	strain=NBRC 103173	GCA_001598875.1	38313	38313	type	True	94.2539	1254	1439	95	below_threshold
Shewanella algae	strain=CECT 5071	GCA_009183365.2	38313	38313	type	True	94.2373	1307	1439	95	below_threshold
Shewanella carassii	strain=CGMCC 1.16033	GCA_014644375.1	1987584	1987584	type	True	93.7332	1247	1439	95	below_threshold
Shewanella carassii	strain=08MAS2251	GCA_002777975.1	1987584	1987584	type	True	93.7108	1253	1439	95	below_threshold
Shewanella litorisediminis	strain=CCUG 62411	GCA_023349165.1	1173586	1173586	type	True	78.8135	394	1439	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	78.4974	412	1439	95	below_threshold
Shewanella aquimarina	strain=JCM 12193	GCA_023349185.1	260365	260365	type	True	77.9716	384	1439	95	below_threshold
Shewanella insulae	strain=JBTF-M18	GCA_009831655.1	2681496	2681496	type	True	77.9417	388	1439	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:12,930] [INFO] DFAST Taxonomy check result was written to GCF_002836975.1_ASM283697v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:12,931] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:12,931] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:12,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ee50f1d-dae9-4a91-b6c2-323ce48788e8/dqc_reference/checkm_data
[2024-01-24 11:44:12,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:12,975] [INFO] Task started: CheckM
[2024-01-24 11:44:12,976] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002836975.1_ASM283697v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002836975.1_ASM283697v1_genomic.fna/checkm_input GCF_002836975.1_ASM283697v1_genomic.fna/checkm_result
[2024-01-24 11:44:54,832] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:54,833] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:54,854] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:54,855] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:54,855] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002836975.1_ASM283697v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:54,855] [INFO] Task started: Blastn
[2024-01-24 11:44:54,855] [INFO] Running command: blastn -query GCF_002836975.1_ASM283697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ee50f1d-dae9-4a91-b6c2-323ce48788e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002836975.1_ASM283697v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:56,221] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:56,227] [INFO] Selected 9 target genomes.
[2024-01-24 11:44:56,228] [INFO] Target genome list was writen to GCF_002836975.1_ASM283697v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:56,233] [INFO] Task started: fastANI
[2024-01-24 11:44:56,234] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d82e4d8-07f3-45d3-90a7-718cffecdaaa/GCF_002836975.1_ASM283697v1_genomic.fna.gz --refList GCF_002836975.1_ASM283697v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002836975.1_ASM283697v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:05,253] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:05,265] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:05,265] [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_002836975.1	s__Shewanella indica	100.0	1437	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	98.42	98.01	0.95	0.93	6	conclusive
GCF_002836945.1	s__Shewanella chilikensis	95.7666	1308	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	99.40	98.79	0.97	0.93	5	-
GCF_009183365.2	s__Shewanella algae	94.2387	1307	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.21	97.66	0.95	0.92	87	-
GCF_002777975.1	s__Shewanella carassii	93.7108	1253	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017354985.1	s__Shewanella sp017354985	78.8297	453	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.75	95.81	0.93	0.92	3	-
GCF_012911865.1	s__Shewanella sp012911865	78.5483	399	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003353085.1	s__Shewanella corallii	78.4912	317	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016065.1	s__Shewanella loihica	78.1025	426	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.22	95.22	0.91	0.91	2	-
GCF_018394335.1	s__Shewanella dokdonensis	77.9765	251	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:05,266] [INFO] GTDB search result was written to GCF_002836975.1_ASM283697v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:05,267] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:05,270] [INFO] DFAST_QC result json was written to GCF_002836975.1_ASM283697v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:05,270] [INFO] DFAST_QC completed!
[2024-01-24 11:45:05,271] [INFO] Total running time: 0h1m25s