[2024-01-24 11:50:49,629] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:50:49,632] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:50:49,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg06bba82d-3651-4775-983a-08cfba6d61a1/dqc_reference
[2024-01-24 11:50:50,867] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:50:50,868] [INFO] Task started: Prodigal
[2024-01-24 11:50:50,868] [INFO] Running command: gunzip -c /var/lib/cwl/stgb804d299-4d26-41f8-9ed6-02aa2258237e/GCF_017354985.1_ASM1735498v1_genomic.fna.gz | prodigal -d GCF_017354985.1_ASM1735498v1_genomic.fna/cds.fna -a GCF_017354985.1_ASM1735498v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:03,935] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:03,936] [INFO] Task started: HMMsearch
[2024-01-24 11:51:03,936] [INFO] Running command: hmmsearch --tblout GCF_017354985.1_ASM1735498v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06bba82d-3651-4775-983a-08cfba6d61a1/dqc_reference/reference_markers.hmm GCF_017354985.1_ASM1735498v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:04,219] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:04,221] [INFO] Found 6/6 markers.
[2024-01-24 11:51:04,258] [INFO] Query marker FASTA was written to GCF_017354985.1_ASM1735498v1_genomic.fna/markers.fasta
[2024-01-24 11:51:04,258] [INFO] Task started: Blastn
[2024-01-24 11:51:04,258] [INFO] Running command: blastn -query GCF_017354985.1_ASM1735498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06bba82d-3651-4775-983a-08cfba6d61a1/dqc_reference/reference_markers.fasta -out GCF_017354985.1_ASM1735498v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:05,104] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:05,107] [INFO] Selected 14 target genomes.
[2024-01-24 11:51:05,107] [INFO] Target genome list was writen to GCF_017354985.1_ASM1735498v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:05,125] [INFO] Task started: fastANI
[2024-01-24 11:51:05,125] [INFO] Running command: fastANI --query /var/lib/cwl/stgb804d299-4d26-41f8-9ed6-02aa2258237e/GCF_017354985.1_ASM1735498v1_genomic.fna.gz --refList GCF_017354985.1_ASM1735498v1_genomic.fna/target_genomes.txt --output GCF_017354985.1_ASM1735498v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:16,867] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:16,867] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06bba82d-3651-4775-983a-08cfba6d61a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:16,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06bba82d-3651-4775-983a-08cfba6d61a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:16,885] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:51:16,885] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:51:16,885] [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 cyperi	strain=FJAT-53720	GCA_017354985.1	2814292	2814292	type	True	100.0	1377	1378	95	inconclusive
Shewanella sedimentimangrovi	strain=FJAT-52962	GCA_017354965.1	2814293	2814293	type	True	95.7616	1273	1378	95	inconclusive
Shewanella amazonensis	strain=SB2B	GCA_000015245.1	60478	60478	type	True	80.1522	595	1378	95	below_threshold
Shewanella khirikhana	strain=TH2012	GCA_003957745.1	1965282	1965282	type	True	80.1237	641	1378	95	below_threshold
Shewanella litorisediminis	strain=CCUG 62411	GCA_023349165.1	1173586	1173586	type	True	80.0149	590	1378	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	79.5921	565	1378	95	below_threshold
Shewanella algae	strain=CECT 5071	GCA_009183365.2	38313	38313	type	True	79.3385	494	1378	95	below_threshold
Shewanella salipaludis	strain=SHSM-M6	GCA_012911865.1	2723052	2723052	type	True	79.0682	501	1378	95	below_threshold
Shewanella algae	strain=ATCC 51192	GCA_012396675.1	38313	38313	type	True	79.0662	490	1378	95	below_threshold
Shewanella carassii	strain=08MAS2251	GCA_002777975.1	1987584	1987584	type	True	79.0048	457	1378	95	below_threshold
Shewanella chilikensis	strain=CCUG 57101	GCA_023283475.1	558541	558541	type	True	78.9369	456	1378	95	below_threshold
Shewanella algae	strain=NBRC 103173	GCA_001598875.1	38313	38313	type	True	78.9232	468	1378	95	below_threshold
Shewanella carassii	strain=CGMCC 1.16033	GCA_014644375.1	1987584	1987584	type	True	78.8016	469	1378	95	below_threshold
Shewanella aquimarina	strain=JCM 12193	GCA_023349185.1	260365	260365	type	True	78.0198	374	1378	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:16,887] [INFO] DFAST Taxonomy check result was written to GCF_017354985.1_ASM1735498v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:16,888] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:16,888] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:16,888] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06bba82d-3651-4775-983a-08cfba6d61a1/dqc_reference/checkm_data
[2024-01-24 11:51:16,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:16,929] [INFO] Task started: CheckM
[2024-01-24 11:51:16,929] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017354985.1_ASM1735498v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017354985.1_ASM1735498v1_genomic.fna/checkm_input GCF_017354985.1_ASM1735498v1_genomic.fna/checkm_result
[2024-01-24 11:51:58,107] [INFO] Task succeeded: CheckM
[2024-01-24 11:51:58,109] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:51:58,126] [INFO] ===== Completeness check finished =====
[2024-01-24 11:51:58,126] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:51:58,127] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017354985.1_ASM1735498v1_genomic.fna/markers.fasta)
[2024-01-24 11:51:58,127] [INFO] Task started: Blastn
[2024-01-24 11:51:58,127] [INFO] Running command: blastn -query GCF_017354985.1_ASM1735498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06bba82d-3651-4775-983a-08cfba6d61a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_017354985.1_ASM1735498v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:59,448] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:59,452] [INFO] Selected 11 target genomes.
[2024-01-24 11:51:59,452] [INFO] Target genome list was writen to GCF_017354985.1_ASM1735498v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:51:59,456] [INFO] Task started: fastANI
[2024-01-24 11:51:59,457] [INFO] Running command: fastANI --query /var/lib/cwl/stgb804d299-4d26-41f8-9ed6-02aa2258237e/GCF_017354985.1_ASM1735498v1_genomic.fna.gz --refList GCF_017354985.1_ASM1735498v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017354985.1_ASM1735498v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:08,837] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:08,847] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:08,847] [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_017354985.1	s__Shewanella sp017354985	100.0	1377	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.75	95.81	0.93	0.92	3	conclusive
GCF_016834455.1	s__Shewanella litorisediminis	80.3591	601	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003957745.1	s__Shewanella khirikhana	80.1377	642	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000015245.1	s__Shewanella amazonensis	80.1317	596	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018596335.1	s__Shewanella sp018596335	79.5771	568	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009183365.2	s__Shewanella algae	79.3019	491	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.21	97.66	0.95	0.92	87	-
GCF_012911865.1	s__Shewanella sp012911865	79.0607	503	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002777975.1	s__Shewanella carassii	78.9862	458	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002836945.1	s__Shewanella chilikensis	78.8301	462	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	99.40	98.79	0.97	0.93	5	-
GCF_002836975.1	s__Shewanella indica	78.7679	471	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	98.42	98.01	0.95	0.93	6	-
GCF_000832025.1	s__Shewanella sp000832025	77.9206	373	1378	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 11:52:08,851] [INFO] GTDB search result was written to GCF_017354985.1_ASM1735498v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:08,852] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:08,857] [INFO] DFAST_QC result json was written to GCF_017354985.1_ASM1735498v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:08,857] [INFO] DFAST_QC completed!
[2024-01-24 11:52:08,857] [INFO] Total running time: 0h1m19s