[2024-01-24 11:59:51,998] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:52,000] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:52,000] [INFO] DQC Reference Directory: /var/lib/cwl/stge82bb59b-67f8-4df3-9589-8ae5ee780f25/dqc_reference
[2024-01-24 11:59:55,388] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:55,390] [INFO] Task started: Prodigal
[2024-01-24 11:59:55,390] [INFO] Running command: gunzip -c /var/lib/cwl/stgd60bae6e-6eca-494e-a8f9-41df70d850a5/GCF_014642695.1_ASM1464269v1_genomic.fna.gz | prodigal -d GCF_014642695.1_ASM1464269v1_genomic.fna/cds.fna -a GCF_014642695.1_ASM1464269v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:06,221] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:06,222] [INFO] Task started: HMMsearch
[2024-01-24 12:00:06,222] [INFO] Running command: hmmsearch --tblout GCF_014642695.1_ASM1464269v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge82bb59b-67f8-4df3-9589-8ae5ee780f25/dqc_reference/reference_markers.hmm GCF_014642695.1_ASM1464269v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:06,533] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:06,534] [INFO] Found 6/6 markers.
[2024-01-24 12:00:06,596] [INFO] Query marker FASTA was written to GCF_014642695.1_ASM1464269v1_genomic.fna/markers.fasta
[2024-01-24 12:00:06,597] [INFO] Task started: Blastn
[2024-01-24 12:00:06,597] [INFO] Running command: blastn -query GCF_014642695.1_ASM1464269v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge82bb59b-67f8-4df3-9589-8ae5ee780f25/dqc_reference/reference_markers.fasta -out GCF_014642695.1_ASM1464269v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:07,347] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:07,351] [INFO] Selected 11 target genomes.
[2024-01-24 12:00:07,351] [INFO] Target genome list was writen to GCF_014642695.1_ASM1464269v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:07,357] [INFO] Task started: fastANI
[2024-01-24 12:00:07,357] [INFO] Running command: fastANI --query /var/lib/cwl/stgd60bae6e-6eca-494e-a8f9-41df70d850a5/GCF_014642695.1_ASM1464269v1_genomic.fna.gz --refList GCF_014642695.1_ASM1464269v1_genomic.fna/target_genomes.txt --output GCF_014642695.1_ASM1464269v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:18,644] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:18,644] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge82bb59b-67f8-4df3-9589-8ae5ee780f25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:18,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge82bb59b-67f8-4df3-9589-8ae5ee780f25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:18,659] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:00:18,659] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:00:18,660] [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
Pseudoalteromonas profundi	strain=CGMCC 1.15394	GCA_014642695.1	1774956	1774956	type	True	100.0	1651	1654	95	inconclusive
Pseudoalteromonas gelatinilytica	strain=NH153	GCA_001641615.1	1703256	1703256	type	True	97.5893	1432	1654	95	inconclusive
Pseudoalteromonas shioyasakiensis	strain=JCM 18891	GCA_001550135.1	1190813	1190813	suspected-type	True	93.5596	1365	1654	95	below_threshold
Pseudoalteromonas arabiensis	strain=JCM 17292	GCA_001550155.1	874454	874454	type	True	86.4185	1037	1654	95	below_threshold
Pseudoalteromonas lipolytica	strain=LMEB 39	GCA_014925285.1	570156	570156	suspected-type	True	84.0027	1045	1654	95	below_threshold
Pseudoalteromonas lipolytica	strain=CGMCC 1.8499	GCA_900116435.1	570156	570156	suspected-type	True	83.9977	1040	1654	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	79.7918	632	1654	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	79.3842	531	1654	95	below_threshold
Pseudoalteromonas galatheae	strain=S4498	GCA_005886105.2	579562	579562	type	True	78.8362	270	1654	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	76.9607	77	1654	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	76.7792	82	1654	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:18,662] [INFO] DFAST Taxonomy check result was written to GCF_014642695.1_ASM1464269v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:18,663] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:18,663] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:18,663] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge82bb59b-67f8-4df3-9589-8ae5ee780f25/dqc_reference/checkm_data
[2024-01-24 12:00:18,664] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:18,715] [INFO] Task started: CheckM
[2024-01-24 12:00:18,715] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014642695.1_ASM1464269v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014642695.1_ASM1464269v1_genomic.fna/checkm_input GCF_014642695.1_ASM1464269v1_genomic.fna/checkm_result
[2024-01-24 12:00:55,142] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:55,143] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 5.59%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:55,170] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:55,170] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:55,171] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014642695.1_ASM1464269v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:55,171] [INFO] Task started: Blastn
[2024-01-24 12:00:55,171] [INFO] Running command: blastn -query GCF_014642695.1_ASM1464269v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge82bb59b-67f8-4df3-9589-8ae5ee780f25/dqc_reference/reference_markers_gtdb.fasta -out GCF_014642695.1_ASM1464269v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:56,279] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:56,284] [INFO] Selected 10 target genomes.
[2024-01-24 12:00:56,285] [INFO] Target genome list was writen to GCF_014642695.1_ASM1464269v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:56,294] [INFO] Task started: fastANI
[2024-01-24 12:00:56,295] [INFO] Running command: fastANI --query /var/lib/cwl/stgd60bae6e-6eca-494e-a8f9-41df70d850a5/GCF_014642695.1_ASM1464269v1_genomic.fna.gz --refList GCF_014642695.1_ASM1464269v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014642695.1_ASM1464269v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:07,090] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:07,106] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:07,107] [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_001641615.1	s__Pseudoalteromonas gelatinilytica	97.5893	1432	1654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.27	97.45	0.92	0.88	6	conclusive
GCF_001550135.1	s__Pseudoalteromonas shioyasakiensis	93.5596	1365	1654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	97.0029	98.58	98.56	0.94	0.92	4	-
GCA_002684115.1	s__Pseudoalteromonas sp002684115	93.3099	264	1654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	97.0029	97.90	97.71	0.79	0.79	5	-
GCF_013349995.1	s__Pseudoalteromonas sp013349995	93.285	1277	1654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.6093	97.46	97.37	0.85	0.84	6	-
GCF_001469895.1	s__Pseudoalteromonas sp001469895	93.0646	1316	1654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.7314	N/A	N/A	N/A	N/A	1	-
GCF_019134595.1	s__Pseudoalteromonas shioyasakiensis_A	93.0	1330	1654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.6918	N/A	N/A	N/A	N/A	1	-
GCF_001306915.1	s__Pseudoalteromonas lipolytica_A	92.502	1283	1654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.22	97.66	0.91	0.90	9	-
GCF_013391845.1	s__Pseudoalteromonas sp002685175	90.7433	1034	1654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.05	98.96	0.91	0.83	5	-
GCF_004792295.1	s__Pseudoalteromonas lipolytica_C	89.7568	1236	1654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.42	98.24	0.87	0.68	9	-
GCF_001550155.1	s__Pseudoalteromonas arabiensis	86.4072	1038	1654	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.77	95.60	0.91	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:07,110] [INFO] GTDB search result was written to GCF_014642695.1_ASM1464269v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:07,110] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:07,114] [INFO] DFAST_QC result json was written to GCF_014642695.1_ASM1464269v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:07,114] [INFO] DFAST_QC completed!
[2024-01-24 12:01:07,114] [INFO] Total running time: 0h1m15s