[2024-01-25 17:49:05,623] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:49:05,624] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:49:05,624] [INFO] DQC Reference Directory: /var/lib/cwl/stg6103b2d1-461e-4832-9a64-513c5bdab3f5/dqc_reference
[2024-01-25 17:49:06,756] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:49:06,757] [INFO] Task started: Prodigal
[2024-01-25 17:49:06,757] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd0d45e5-aa0e-4316-84d1-bc2631d91bb1/GCF_020511155.1_ASM2051115v1_genomic.fna.gz | prodigal -d GCF_020511155.1_ASM2051115v1_genomic.fna/cds.fna -a GCF_020511155.1_ASM2051115v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:49:15,116] [INFO] Task succeeded: Prodigal
[2024-01-25 17:49:15,117] [INFO] Task started: HMMsearch
[2024-01-25 17:49:15,117] [INFO] Running command: hmmsearch --tblout GCF_020511155.1_ASM2051115v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6103b2d1-461e-4832-9a64-513c5bdab3f5/dqc_reference/reference_markers.hmm GCF_020511155.1_ASM2051115v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:49:15,357] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:49:15,358] [INFO] Found 6/6 markers.
[2024-01-25 17:49:15,393] [INFO] Query marker FASTA was written to GCF_020511155.1_ASM2051115v1_genomic.fna/markers.fasta
[2024-01-25 17:49:15,393] [INFO] Task started: Blastn
[2024-01-25 17:49:15,393] [INFO] Running command: blastn -query GCF_020511155.1_ASM2051115v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6103b2d1-461e-4832-9a64-513c5bdab3f5/dqc_reference/reference_markers.fasta -out GCF_020511155.1_ASM2051115v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:16,088] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:16,090] [INFO] Selected 17 target genomes.
[2024-01-25 17:49:16,091] [INFO] Target genome list was writen to GCF_020511155.1_ASM2051115v1_genomic.fna/target_genomes.txt
[2024-01-25 17:49:16,106] [INFO] Task started: fastANI
[2024-01-25 17:49:16,106] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd0d45e5-aa0e-4316-84d1-bc2631d91bb1/GCF_020511155.1_ASM2051115v1_genomic.fna.gz --refList GCF_020511155.1_ASM2051115v1_genomic.fna/target_genomes.txt --output GCF_020511155.1_ASM2051115v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:49:30,824] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:30,824] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6103b2d1-461e-4832-9a64-513c5bdab3f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:49:30,824] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6103b2d1-461e-4832-9a64-513c5bdab3f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:49:30,835] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:49:30,835] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:49:30,835] [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 glacialimarina	strain=TZS-4	GCA_020511155.1	2590884	2590884	type	True	100.0	1482	1485	95	conclusive
Shewanella aestuarii	strain=JCM 17801	GCA_023283685.1	1028752	1028752	type	True	81.6824	829	1485	95	below_threshold
Shewanella aestuarii	strain=JCM 17801	GCA_014647215.1	1028752	1028752	type	True	81.6562	841	1485	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	80.5387	570	1485	95	below_threshold
Shewanella vesiculosa	strain=LMG 24424	GCA_003797885.1	518738	518738	type	True	80.5154	562	1485	95	below_threshold
Shewanella livingstonensis	strain=LMG 19866	GCA_003855395.1	150120	150120	type	True	80.1503	559	1485	95	below_threshold
Shewanella polaris	strain=SM1901	GCA_006385555.1	2588449	2588449	type	True	79.938	517	1485	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	79.6572	528	1485	95	below_threshold
Shewanella ulleungensis	strain=JCM 32305	GCA_014648315.1	2282699	2282699	type	True	79.6007	522	1485	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_009828585.1	2282700	2282700	type	True	79.5428	534	1485	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	79.4209	501	1485	95	below_threshold
Shewanella saliphila	strain=JCM 32304	GCA_014648295.1	2282698	2282698	type	True	79.3679	512	1485	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	79.339	504	1485	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	79.2932	512	1485	95	below_threshold
Shewanella olleyana	strain=LMG 21437	GCA_023283825.1	135626	135626	type	True	78.5391	374	1485	95	below_threshold
Shewanella intestini	strain=MCCC 1A01895	GCA_018221465.1	2017544	2017544	type	True	78.3241	334	1485	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:49:30,837] [INFO] DFAST Taxonomy check result was written to GCF_020511155.1_ASM2051115v1_genomic.fna/tc_result.tsv
[2024-01-25 17:49:30,837] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:49:30,837] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:49:30,837] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6103b2d1-461e-4832-9a64-513c5bdab3f5/dqc_reference/checkm_data
[2024-01-25 17:49:30,838] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:49:30,881] [INFO] Task started: CheckM
[2024-01-25 17:49:30,881] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020511155.1_ASM2051115v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020511155.1_ASM2051115v1_genomic.fna/checkm_input GCF_020511155.1_ASM2051115v1_genomic.fna/checkm_result
[2024-01-25 17:49:59,107] [INFO] Task succeeded: CheckM
[2024-01-25 17:49:59,108] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:49:59,123] [INFO] ===== Completeness check finished =====
[2024-01-25 17:49:59,123] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:49:59,124] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020511155.1_ASM2051115v1_genomic.fna/markers.fasta)
[2024-01-25 17:49:59,124] [INFO] Task started: Blastn
[2024-01-25 17:49:59,124] [INFO] Running command: blastn -query GCF_020511155.1_ASM2051115v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6103b2d1-461e-4832-9a64-513c5bdab3f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_020511155.1_ASM2051115v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:00,256] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:00,258] [INFO] Selected 19 target genomes.
[2024-01-25 17:50:00,258] [INFO] Target genome list was writen to GCF_020511155.1_ASM2051115v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:00,288] [INFO] Task started: fastANI
[2024-01-25 17:50:00,288] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd0d45e5-aa0e-4316-84d1-bc2631d91bb1/GCF_020511155.1_ASM2051115v1_genomic.fna.gz --refList GCF_020511155.1_ASM2051115v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020511155.1_ASM2051115v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:50:15,696] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:15,705] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:50:15,705] [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_014647215.1	s__Shewanella aestuarii	81.6544	841	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797885.1	s__Shewanella vesiculosa	80.5305	563	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.53	98.48	0.92	0.86	17	-
GCF_003797125.1	s__Shewanella frigidimarina	80.2739	557	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.50	96.12	0.90	0.86	5	-
GCF_003855395.1	s__Shewanella livingstonensis	80.0849	560	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010092445.1	s__Shewanella sp002836315	79.9951	581	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.47	98.34	0.91	0.90	4	-
GCF_011765625.1	s__Shewanella aestuarii_A	79.9913	614	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385555.1	s__Shewanella polaris	79.9237	515	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.84	97.84	0.89	0.89	2	-
GCF_014648035.1	s__Shewanella algicola	79.7173	503	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_003855155.1	s__Shewanella sp002836275	79.7148	510	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.14	98.29	0.96	0.92	3	-
GCF_014648315.1	s__Shewanella ulleungensis	79.5808	523	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828585.1	s__Shewanella litoralis	79.5277	536	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014648295.1	s__Shewanella saliphila	79.3767	512	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_009663145.1	s__Shewanella sp009663145	78.3596	350	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018221465.1	s__Shewanella intestini	78.3238	334	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_011378715.1	s__Psychromonas sp011378715	77.1387	63	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:50:15,707] [INFO] GTDB search result was written to GCF_020511155.1_ASM2051115v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:50:15,711] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:50:15,719] [INFO] DFAST_QC result json was written to GCF_020511155.1_ASM2051115v1_genomic.fna/dqc_result.json
[2024-01-25 17:50:15,719] [INFO] DFAST_QC completed!
[2024-01-25 17:50:15,719] [INFO] Total running time: 0h1m10s