[2024-01-24 15:26:36,748] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:36,750] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:36,750] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b0227e0-eba6-4873-b43b-029c27289e41/dqc_reference
[2024-01-24 15:26:39,061] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:39,066] [INFO] Task started: Prodigal
[2024-01-24 15:26:39,066] [INFO] Running command: gunzip -c /var/lib/cwl/stga9e16e83-2541-4661-bf62-fb124548e0df/GCF_014652115.1_ASM1465211v1_genomic.fna.gz | prodigal -d GCF_014652115.1_ASM1465211v1_genomic.fna/cds.fna -a GCF_014652115.1_ASM1465211v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:51,791] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:51,791] [INFO] Task started: HMMsearch
[2024-01-24 15:26:51,792] [INFO] Running command: hmmsearch --tblout GCF_014652115.1_ASM1465211v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b0227e0-eba6-4873-b43b-029c27289e41/dqc_reference/reference_markers.hmm GCF_014652115.1_ASM1465211v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:52,098] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:52,100] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga9e16e83-2541-4661-bf62-fb124548e0df/GCF_014652115.1_ASM1465211v1_genomic.fna.gz]
[2024-01-24 15:26:52,139] [INFO] Query marker FASTA was written to GCF_014652115.1_ASM1465211v1_genomic.fna/markers.fasta
[2024-01-24 15:26:52,139] [INFO] Task started: Blastn
[2024-01-24 15:26:52,140] [INFO] Running command: blastn -query GCF_014652115.1_ASM1465211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b0227e0-eba6-4873-b43b-029c27289e41/dqc_reference/reference_markers.fasta -out GCF_014652115.1_ASM1465211v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:52,956] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:52,959] [INFO] Selected 15 target genomes.
[2024-01-24 15:26:52,960] [INFO] Target genome list was writen to GCF_014652115.1_ASM1465211v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:52,966] [INFO] Task started: fastANI
[2024-01-24 15:26:52,966] [INFO] Running command: fastANI --query /var/lib/cwl/stga9e16e83-2541-4661-bf62-fb124548e0df/GCF_014652115.1_ASM1465211v1_genomic.fna.gz --refList GCF_014652115.1_ASM1465211v1_genomic.fna/target_genomes.txt --output GCF_014652115.1_ASM1465211v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:08,468] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:08,469] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b0227e0-eba6-4873-b43b-029c27289e41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:08,469] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b0227e0-eba6-4873-b43b-029c27289e41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:08,481] [INFO] Found 15 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 15:27:08,481] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 15:27:08,482] [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=KCTC 23171	GCA_014652115.1	768528	768528	type	True	100.0	1430	1434	95	inconclusive
Shewanella indica	strain=KJW27	GCA_002836975.1	768528	768528	type	True	99.9878	1417	1434	95	inconclusive
Shewanella chilikensis	strain=JC5	GCA_003217175.1	558541	558541	type	True	95.8009	1322	1434	95	inconclusive
Shewanella chilikensis	strain=JC5	GCA_002836945.1	558541	558541	type	True	95.7993	1308	1434	95	inconclusive
Shewanella chilikensis	strain=KCTC 22540	GCA_014651975.1	558541	558541	type	True	95.7729	1314	1434	95	inconclusive
Shewanella chilikensis	strain=CCUG 57101	GCA_023283475.1	558541	558541	type	True	95.7587	1320	1434	95	inconclusive
Shewanella algae	strain=ATCC 51192	GCA_012396675.1	38313	38313	type	True	94.2853	1287	1434	95	below_threshold
Shewanella algae	strain=NBRC 103173	GCA_001598875.1	38313	38313	type	True	94.2841	1247	1434	95	below_threshold
Shewanella algae	strain=CECT 5071	GCA_009183365.2	38313	38313	type	True	94.271	1295	1434	95	below_threshold
Shewanella carassii	strain=08MAS2251	GCA_002777975.1	1987584	1987584	type	True	93.8061	1238	1434	95	below_threshold
Shewanella carassii	strain=CGMCC 1.16033	GCA_014644375.1	1987584	1987584	type	True	93.7691	1241	1434	95	below_threshold
Shewanella litorisediminis	strain=CCUG 62411	GCA_023349165.1	1173586	1173586	type	True	78.5244	408	1434	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	78.5033	411	1434	95	below_threshold
Shewanella aquimarina	strain=JCM 12193	GCA_023349185.1	260365	260365	type	True	77.9598	381	1434	95	below_threshold
Shewanella insulae	strain=JBTF-M18	GCA_009831655.1	2681496	2681496	type	True	77.8413	398	1434	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:08,483] [INFO] DFAST Taxonomy check result was written to GCF_014652115.1_ASM1465211v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:08,484] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:08,484] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:08,484] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b0227e0-eba6-4873-b43b-029c27289e41/dqc_reference/checkm_data
[2024-01-24 15:27:08,486] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:08,536] [INFO] Task started: CheckM
[2024-01-24 15:27:08,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652115.1_ASM1465211v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652115.1_ASM1465211v1_genomic.fna/checkm_input GCF_014652115.1_ASM1465211v1_genomic.fna/checkm_result
[2024-01-24 15:27:49,029] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:49,031] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:49,052] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:49,052] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:49,053] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652115.1_ASM1465211v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:49,053] [INFO] Task started: Blastn
[2024-01-24 15:27:49,054] [INFO] Running command: blastn -query GCF_014652115.1_ASM1465211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b0227e0-eba6-4873-b43b-029c27289e41/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652115.1_ASM1465211v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:50,189] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:50,192] [INFO] Selected 8 target genomes.
[2024-01-24 15:27:50,192] [INFO] Target genome list was writen to GCF_014652115.1_ASM1465211v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:50,199] [INFO] Task started: fastANI
[2024-01-24 15:27:50,199] [INFO] Running command: fastANI --query /var/lib/cwl/stga9e16e83-2541-4661-bf62-fb124548e0df/GCF_014652115.1_ASM1465211v1_genomic.fna.gz --refList GCF_014652115.1_ASM1465211v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652115.1_ASM1465211v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:58,860] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:58,868] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 15:27:58,868] [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	99.9878	1417	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	98.42	98.01	0.95	0.93	6	inconclusive
GCF_002836945.1	s__Shewanella chilikensis	95.7932	1309	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	99.40	98.79	0.97	0.93	5	inconclusive
GCF_009183365.2	s__Shewanella algae	94.271	1295	1434	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	93.7924	1239	1434	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	78.873	444	1434	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	78.5	398	1434	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	78.4919	311	1434	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	78.1042	414	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.22	95.22	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:58,870] [INFO] GTDB search result was written to GCF_014652115.1_ASM1465211v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:58,870] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:58,874] [INFO] DFAST_QC result json was written to GCF_014652115.1_ASM1465211v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:58,874] [INFO] DFAST_QC completed!
[2024-01-24 15:27:58,874] [INFO] Total running time: 0h1m22s