[2024-01-24 14:31:00,278] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:00,280] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:00,280] [INFO] DQC Reference Directory: /var/lib/cwl/stg272bf8c6-0539-42dc-9e7d-ad72126a24eb/dqc_reference
[2024-01-24 14:31:02,103] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:02,104] [INFO] Task started: Prodigal
[2024-01-24 14:31:02,104] [INFO] Running command: gunzip -c /var/lib/cwl/stge566f2fe-b276-4d3a-82ff-93e9ecfb7d68/GCF_003990335.1_ASM399033v1_genomic.fna.gz | prodigal -d GCF_003990335.1_ASM399033v1_genomic.fna/cds.fna -a GCF_003990335.1_ASM399033v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:13,536] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:13,537] [INFO] Task started: HMMsearch
[2024-01-24 14:31:13,537] [INFO] Running command: hmmsearch --tblout GCF_003990335.1_ASM399033v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg272bf8c6-0539-42dc-9e7d-ad72126a24eb/dqc_reference/reference_markers.hmm GCF_003990335.1_ASM399033v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:13,852] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:13,853] [INFO] Found 6/6 markers.
[2024-01-24 14:31:13,921] [INFO] Query marker FASTA was written to GCF_003990335.1_ASM399033v1_genomic.fna/markers.fasta
[2024-01-24 14:31:13,921] [INFO] Task started: Blastn
[2024-01-24 14:31:13,921] [INFO] Running command: blastn -query GCF_003990335.1_ASM399033v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg272bf8c6-0539-42dc-9e7d-ad72126a24eb/dqc_reference/reference_markers.fasta -out GCF_003990335.1_ASM399033v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:14,646] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:14,648] [INFO] Selected 12 target genomes.
[2024-01-24 14:31:14,648] [INFO] Target genome list was writen to GCF_003990335.1_ASM399033v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:14,656] [INFO] Task started: fastANI
[2024-01-24 14:31:14,656] [INFO] Running command: fastANI --query /var/lib/cwl/stge566f2fe-b276-4d3a-82ff-93e9ecfb7d68/GCF_003990335.1_ASM399033v1_genomic.fna.gz --refList GCF_003990335.1_ASM399033v1_genomic.fna/target_genomes.txt --output GCF_003990335.1_ASM399033v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:24,137] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:24,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg272bf8c6-0539-42dc-9e7d-ad72126a24eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:24,138] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg272bf8c6-0539-42dc-9e7d-ad72126a24eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:24,146] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:31:24,147] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:31:24,147] [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
Rheinheimera tangshanensis	strain=CGMCC 1.6362	GCA_014645135.1	400153	400153	type	True	86.2094	1062	1542	95	below_threshold
Rheinheimera tangshanensis	strain=JA3-B52	GCA_008017875.1	400153	400153	type	True	86.2015	1077	1542	95	below_threshold
Pararheinheimera mesophila	strain=IITR-13	GCA_000986865.1	1547515	1547515	type	True	84.9532	975	1542	95	below_threshold
Pararheinheimera mesophila	strain=IITR13	GCA_003862465.1	1547515	1547515	type	True	84.9179	1002	1542	95	below_threshold
Rheinheimera riviphila	strain=KYPC3	GCA_004005945.1	1834037	1834037	type	True	78.6917	333	1542	95	below_threshold
Pararheinheimera texasensis	strain=DSM 17496	GCA_000711985.1	306205	306205	type	True	78.4316	278	1542	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	78.222	254	1542	95	below_threshold
Rheinheimera nanhaiensis	strain=E407-8	GCA_000296695.1	1163621	1163621	type	True	77.8985	227	1542	95	below_threshold
Alishewanella longhuensis	strain=CGMCC 1.7003	GCA_014653435.1	1091037	1091037	type	True	77.8166	167	1542	95	below_threshold
Arsukibacterium indicum	strain=SM2107	GCA_019100565.1	2848612	2848612	type	True	77.7034	177	1542	95	below_threshold
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	77.529	239	1542	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:24,148] [INFO] DFAST Taxonomy check result was written to GCF_003990335.1_ASM399033v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:24,148] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:24,149] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:24,149] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg272bf8c6-0539-42dc-9e7d-ad72126a24eb/dqc_reference/checkm_data
[2024-01-24 14:31:24,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:24,192] [INFO] Task started: CheckM
[2024-01-24 14:31:24,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003990335.1_ASM399033v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003990335.1_ASM399033v1_genomic.fna/checkm_input GCF_003990335.1_ASM399033v1_genomic.fna/checkm_result
[2024-01-24 14:32:00,662] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:00,663] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:00,681] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:00,681] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:00,681] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003990335.1_ASM399033v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:00,681] [INFO] Task started: Blastn
[2024-01-24 14:32:00,681] [INFO] Running command: blastn -query GCF_003990335.1_ASM399033v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg272bf8c6-0539-42dc-9e7d-ad72126a24eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003990335.1_ASM399033v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:01,790] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:01,794] [INFO] Selected 7 target genomes.
[2024-01-24 14:32:01,794] [INFO] Target genome list was writen to GCF_003990335.1_ASM399033v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:01,798] [INFO] Task started: fastANI
[2024-01-24 14:32:01,798] [INFO] Running command: fastANI --query /var/lib/cwl/stge566f2fe-b276-4d3a-82ff-93e9ecfb7d68/GCF_003990335.1_ASM399033v1_genomic.fna.gz --refList GCF_003990335.1_ASM399033v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003990335.1_ASM399033v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:09,364] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:09,370] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:09,370] [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_003990335.1	s__Pararheinheimera sp003990335	100.0	1542	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018815765.1	s__Pararheinheimera sp018815765	88.7551	985	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645135.1	s__Pararheinheimera tangshanensis	86.2094	1062	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	98.63	97.26	0.95	0.91	3	-
GCA_018825965.1	s__Pararheinheimera sp018825965	85.5117	1077	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	99.98	99.95	0.98	0.97	7	-
GCF_000217935.1	s__Pararheinheimera sp000217935	85.4536	1060	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005375.1	s__Pararheinheimera sp004005375	85.1122	1034	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000986865.1	s__Pararheinheimera mesophila	84.9563	974	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:09,372] [INFO] GTDB search result was written to GCF_003990335.1_ASM399033v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:09,372] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:09,375] [INFO] DFAST_QC result json was written to GCF_003990335.1_ASM399033v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:09,375] [INFO] DFAST_QC completed!
[2024-01-24 14:32:09,375] [INFO] Total running time: 0h1m9s