[2024-01-25 19:51:50,524] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:51:50,526] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:51:50,526] [INFO] DQC Reference Directory: /var/lib/cwl/stg69f3eeed-f029-46b9-8f35-a8620105829c/dqc_reference
[2024-01-25 19:51:51,699] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:51:51,700] [INFO] Task started: Prodigal
[2024-01-25 19:51:51,700] [INFO] Running command: gunzip -c /var/lib/cwl/stg8da181e0-531d-4d5e-8137-0b2f0bb15aa2/GCF_002075795.1_ASM207579v1_genomic.fna.gz | prodigal -d GCF_002075795.1_ASM207579v1_genomic.fna/cds.fna -a GCF_002075795.1_ASM207579v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:52:01,053] [INFO] Task succeeded: Prodigal
[2024-01-25 19:52:01,054] [INFO] Task started: HMMsearch
[2024-01-25 19:52:01,054] [INFO] Running command: hmmsearch --tblout GCF_002075795.1_ASM207579v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69f3eeed-f029-46b9-8f35-a8620105829c/dqc_reference/reference_markers.hmm GCF_002075795.1_ASM207579v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:52:01,311] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:52:01,314] [INFO] Found 6/6 markers.
[2024-01-25 19:52:01,353] [INFO] Query marker FASTA was written to GCF_002075795.1_ASM207579v1_genomic.fna/markers.fasta
[2024-01-25 19:52:01,354] [INFO] Task started: Blastn
[2024-01-25 19:52:01,354] [INFO] Running command: blastn -query GCF_002075795.1_ASM207579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69f3eeed-f029-46b9-8f35-a8620105829c/dqc_reference/reference_markers.fasta -out GCF_002075795.1_ASM207579v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:02,079] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:02,081] [INFO] Selected 12 target genomes.
[2024-01-25 19:52:02,081] [INFO] Target genome list was writen to GCF_002075795.1_ASM207579v1_genomic.fna/target_genomes.txt
[2024-01-25 19:52:02,092] [INFO] Task started: fastANI
[2024-01-25 19:52:02,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg8da181e0-531d-4d5e-8137-0b2f0bb15aa2/GCF_002075795.1_ASM207579v1_genomic.fna.gz --refList GCF_002075795.1_ASM207579v1_genomic.fna/target_genomes.txt --output GCF_002075795.1_ASM207579v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:52:13,132] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:13,133] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69f3eeed-f029-46b9-8f35-a8620105829c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:52:13,133] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69f3eeed-f029-46b9-8f35-a8620105829c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:52:13,141] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:52:13,141] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:52:13,141] [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 japonica	strain=KCTC 22435	GCA_002075795.1	93973	93973	type	True	100.0	1658	1658	95	conclusive
Shewanella olleyana	strain=LMG 21437	GCA_023283825.1	135626	135626	type	True	82.5005	932	1658	95	below_threshold
Shewanella electrodiphila	strain=DSM 24955	GCA_023283985.1	934143	934143	type	True	81.9948	1003	1658	95	below_threshold
Shewanella donghaensis	strain=LT17	GCA_007567505.1	238836	238836	type	True	80.7043	819	1658	95	below_threshold
Shewanella intestini	strain=MCCC 1A01895	GCA_018221465.1	2017544	2017544	type	True	79.2137	372	1658	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	78.6628	371	1658	95	below_threshold
Shewanella saliphila	strain=JCM 32304	GCA_014648295.1	2282698	2282698	type	True	78.5447	381	1658	95	below_threshold
Shewanella aestuarii	strain=JCM 17801	GCA_023283685.1	1028752	1028752	type	True	78.4904	374	1658	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	78.4485	382	1658	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	78.4008	389	1658	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	78.1265	361	1658	95	below_threshold
Shewanella fidelis	strain=ATCC BAA-318	GCA_000518605.1	173509	173509	type	True	77.9978	311	1658	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:52:13,142] [INFO] DFAST Taxonomy check result was written to GCF_002075795.1_ASM207579v1_genomic.fna/tc_result.tsv
[2024-01-25 19:52:13,143] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:52:13,143] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:52:13,143] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69f3eeed-f029-46b9-8f35-a8620105829c/dqc_reference/checkm_data
[2024-01-25 19:52:13,144] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:52:13,192] [INFO] Task started: CheckM
[2024-01-25 19:52:13,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002075795.1_ASM207579v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002075795.1_ASM207579v1_genomic.fna/checkm_input GCF_002075795.1_ASM207579v1_genomic.fna/checkm_result
[2024-01-25 19:52:44,419] [INFO] Task succeeded: CheckM
[2024-01-25 19:52:44,420] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:52:44,437] [INFO] ===== Completeness check finished =====
[2024-01-25 19:52:44,437] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:52:44,438] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002075795.1_ASM207579v1_genomic.fna/markers.fasta)
[2024-01-25 19:52:44,438] [INFO] Task started: Blastn
[2024-01-25 19:52:44,438] [INFO] Running command: blastn -query GCF_002075795.1_ASM207579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69f3eeed-f029-46b9-8f35-a8620105829c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002075795.1_ASM207579v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:45,552] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:45,555] [INFO] Selected 6 target genomes.
[2024-01-25 19:52:45,555] [INFO] Target genome list was writen to GCF_002075795.1_ASM207579v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:52:45,565] [INFO] Task started: fastANI
[2024-01-25 19:52:45,565] [INFO] Running command: fastANI --query /var/lib/cwl/stg8da181e0-531d-4d5e-8137-0b2f0bb15aa2/GCF_002075795.1_ASM207579v1_genomic.fna.gz --refList GCF_002075795.1_ASM207579v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002075795.1_ASM207579v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:52:52,330] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:52,335] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:52:52,335] [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_002075795.1	s__Shewanella japonica	100.0	1658	1658	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.37	97.91	0.95	0.93	6	conclusive
GCF_009663145.1	s__Shewanella sp009663145	82.3176	1009	1658	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002873615.1	s__Shewanella sp002873615	82.0777	961	1658	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001957135.1	s__Shewanella sp001957135	80.8543	752	1658	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007567505.1	s__Shewanella donghaensis	80.743	819	1658	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002873135.1	s__Shewanella sp002873135	80.695	744	1658	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.89	98.82	0.90	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:52:52,336] [INFO] GTDB search result was written to GCF_002075795.1_ASM207579v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:52:52,336] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:52:52,339] [INFO] DFAST_QC result json was written to GCF_002075795.1_ASM207579v1_genomic.fna/dqc_result.json
[2024-01-25 19:52:52,339] [INFO] DFAST_QC completed!
[2024-01-25 19:52:52,339] [INFO] Total running time: 0h1m2s