[2024-01-24 12:36:34,424] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:34,425] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:34,426] [INFO] DQC Reference Directory: /var/lib/cwl/stga2319a4d-abdb-4928-9288-bb1da43a2c4f/dqc_reference
[2024-01-24 12:36:35,676] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:35,677] [INFO] Task started: Prodigal
[2024-01-24 12:36:35,677] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a5432ea-ab80-4434-9cfa-05fe31faff70/GCF_014645355.1_ASM1464535v1_genomic.fna.gz | prodigal -d GCF_014645355.1_ASM1464535v1_genomic.fna/cds.fna -a GCF_014645355.1_ASM1464535v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:48,070] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:48,070] [INFO] Task started: HMMsearch
[2024-01-24 12:36:48,070] [INFO] Running command: hmmsearch --tblout GCF_014645355.1_ASM1464535v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2319a4d-abdb-4928-9288-bb1da43a2c4f/dqc_reference/reference_markers.hmm GCF_014645355.1_ASM1464535v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:48,453] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:48,454] [INFO] Found 6/6 markers.
[2024-01-24 12:36:48,495] [INFO] Query marker FASTA was written to GCF_014645355.1_ASM1464535v1_genomic.fna/markers.fasta
[2024-01-24 12:36:48,496] [INFO] Task started: Blastn
[2024-01-24 12:36:48,496] [INFO] Running command: blastn -query GCF_014645355.1_ASM1464535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2319a4d-abdb-4928-9288-bb1da43a2c4f/dqc_reference/reference_markers.fasta -out GCF_014645355.1_ASM1464535v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:49,287] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:49,293] [INFO] Selected 22 target genomes.
[2024-01-24 12:36:49,293] [INFO] Target genome list was writen to GCF_014645355.1_ASM1464535v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:49,321] [INFO] Task started: fastANI
[2024-01-24 12:36:49,321] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a5432ea-ab80-4434-9cfa-05fe31faff70/GCF_014645355.1_ASM1464535v1_genomic.fna.gz --refList GCF_014645355.1_ASM1464535v1_genomic.fna/target_genomes.txt --output GCF_014645355.1_ASM1464535v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:04,127] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:04,128] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2319a4d-abdb-4928-9288-bb1da43a2c4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:04,129] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2319a4d-abdb-4928-9288-bb1da43a2c4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:04,146] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:04,146] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:04,146] [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
Bowmanella pacifica	strain=CGMCC 1.7086	GCA_014645355.1	502051	502051	type	True	100.0	1506	1506	95	conclusive
Bowmanella dokdonensis	strain=JCM 30855	GCA_017254865.1	751969	751969	type	True	77.9787	305	1506	95	below_threshold
Aestuariibacter halophilus	strain=JC2043	GCA_020687825.1	226011	226011	type	True	77.3527	122	1506	95	below_threshold
Lacimicrobium alkaliphilum	strain=X13M-12	GCA_002591895.1	1526571	1526571	type	True	77.2655	210	1506	95	below_threshold
Lacimicrobium alkaliphilum	strain=CGMCC 1.12923	GCA_014640135.1	1526571	1526571	type	True	77.2443	213	1506	95	below_threshold
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	77.0933	83	1506	95	below_threshold
Alteromonas halophila	strain=KCTC 22164	GCA_014651815.1	516698	516698	type	True	76.8377	91	1506	95	below_threshold
Alteromonas confluentis	strain=KCTC 42603	GCA_001757105.1	1656094	1656094	type	True	76.7953	88	1506	95	below_threshold
Shewanella algae	strain=CECT 5071	GCA_009183365.2	38313	38313	type	True	76.2098	54	1506	95	below_threshold
Shewanella algae	strain=ATCC 51192	GCA_012396675.1	38313	38313	type	True	76.1891	54	1506	95	below_threshold
Shewanella algae	strain=NBRC 103173	GCA_001598875.1	38313	38313	type	True	76.0342	54	1506	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	75.9237	59	1506	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:04,148] [INFO] DFAST Taxonomy check result was written to GCF_014645355.1_ASM1464535v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:04,149] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:04,149] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:04,149] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2319a4d-abdb-4928-9288-bb1da43a2c4f/dqc_reference/checkm_data
[2024-01-24 12:37:04,151] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:04,197] [INFO] Task started: CheckM
[2024-01-24 12:37:04,197] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645355.1_ASM1464535v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645355.1_ASM1464535v1_genomic.fna/checkm_input GCF_014645355.1_ASM1464535v1_genomic.fna/checkm_result
[2024-01-24 12:37:44,947] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:44,948] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:44,972] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:44,972] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:44,972] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645355.1_ASM1464535v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:44,973] [INFO] Task started: Blastn
[2024-01-24 12:37:44,973] [INFO] Running command: blastn -query GCF_014645355.1_ASM1464535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2319a4d-abdb-4928-9288-bb1da43a2c4f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645355.1_ASM1464535v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:46,138] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:46,143] [INFO] Selected 17 target genomes.
[2024-01-24 12:37:46,144] [INFO] Target genome list was writen to GCF_014645355.1_ASM1464535v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:46,176] [INFO] Task started: fastANI
[2024-01-24 12:37:46,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a5432ea-ab80-4434-9cfa-05fe31faff70/GCF_014645355.1_ASM1464535v1_genomic.fna.gz --refList GCF_014645355.1_ASM1464535v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645355.1_ASM1464535v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:58,971] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:58,992] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:58,992] [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_014645355.1	s__Bowmanella pacifica	100.0	1506	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018531185.1	s__Bowmanella sp018531185	84.7811	1136	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	96.11	96.11	0.88	0.88	2	-
GCF_002887595.1	s__Bowmanella denitrificans	79.9228	718	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254865.1	s__Bowmanella dokdonensis	77.9672	306	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004329715.1	s__JS7-9 sp004329715	77.365	129	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__JS7-9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001466725.1	s__Lacimicrobium alkaliphilum_B	77.2882	266	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Lacimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002591895.1	s__Lacimicrobium alkaliphilum	77.2535	211	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Lacimicrobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_012911815.1	s__Alteromonas ponticola	76.9963	65	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003731635.1	s__Alteromonas oceani	76.85	105	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001757105.1	s__Alteromonas confluentis	76.7953	88	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691625.1	s__Alteromonas sp002691625	76.4965	77	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.62	99.31	0.91	0.90	3	-
GCF_009183365.2	s__Shewanella algae	76.2098	54	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.21	97.66	0.95	0.92	87	-
GCF_018596335.1	s__Shewanella sp018596335	75.9237	59	1506	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 12:37:58,994] [INFO] GTDB search result was written to GCF_014645355.1_ASM1464535v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:58,995] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:58,998] [INFO] DFAST_QC result json was written to GCF_014645355.1_ASM1464535v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:58,998] [INFO] DFAST_QC completed!
[2024-01-24 12:37:58,998] [INFO] Total running time: 0h1m25s