[2024-01-24 12:31:17,756] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:17,758] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:17,758] [INFO] DQC Reference Directory: /var/lib/cwl/stge0ab6447-83a6-4651-9f45-44a6234ad741/dqc_reference
[2024-01-24 12:31:18,846] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:18,847] [INFO] Task started: Prodigal
[2024-01-24 12:31:18,847] [INFO] Running command: gunzip -c /var/lib/cwl/stg155f0287-bfbb-44ad-a8a3-a9a7f18d6a90/GCF_000711985.1_ASM71198v1_genomic.fna.gz | prodigal -d GCF_000711985.1_ASM71198v1_genomic.fna/cds.fna -a GCF_000711985.1_ASM71198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:30,193] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:30,194] [INFO] Task started: HMMsearch
[2024-01-24 12:31:30,194] [INFO] Running command: hmmsearch --tblout GCF_000711985.1_ASM71198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0ab6447-83a6-4651-9f45-44a6234ad741/dqc_reference/reference_markers.hmm GCF_000711985.1_ASM71198v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:30,421] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:30,422] [INFO] Found 6/6 markers.
[2024-01-24 12:31:30,457] [INFO] Query marker FASTA was written to GCF_000711985.1_ASM71198v1_genomic.fna/markers.fasta
[2024-01-24 12:31:30,458] [INFO] Task started: Blastn
[2024-01-24 12:31:30,458] [INFO] Running command: blastn -query GCF_000711985.1_ASM71198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0ab6447-83a6-4651-9f45-44a6234ad741/dqc_reference/reference_markers.fasta -out GCF_000711985.1_ASM71198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:31,225] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:31,227] [INFO] Selected 17 target genomes.
[2024-01-24 12:31:31,228] [INFO] Target genome list was writen to GCF_000711985.1_ASM71198v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:31,232] [INFO] Task started: fastANI
[2024-01-24 12:31:31,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg155f0287-bfbb-44ad-a8a3-a9a7f18d6a90/GCF_000711985.1_ASM71198v1_genomic.fna.gz --refList GCF_000711985.1_ASM71198v1_genomic.fna/target_genomes.txt --output GCF_000711985.1_ASM71198v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:42,924] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:42,925] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0ab6447-83a6-4651-9f45-44a6234ad741/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:42,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0ab6447-83a6-4651-9f45-44a6234ad741/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:42,935] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:42,935] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:42,935] [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
Pararheinheimera texasensis	strain=DSM 17496	GCA_000711985.1	306205	306205	type	True	100.0	1523	1523	95	conclusive
Rheinheimera riviphila	strain=KYPC3	GCA_004005945.1	1834037	1834037	type	True	78.8662	528	1523	95	below_threshold
Pararheinheimera mesophila	strain=IITR13	GCA_003862465.1	1547515	1547515	type	True	78.213	292	1523	95	below_threshold
Rheinheimera tangshanensis	strain=JA3-B52	GCA_008017875.1	400153	400153	type	True	78.1182	294	1523	95	below_threshold
Rheinheimera tangshanensis	strain=CGMCC 1.6362	GCA_014645135.1	400153	400153	type	True	78.0679	299	1523	95	below_threshold
Pararheinheimera mesophila	strain=IITR-13	GCA_000986865.1	1547515	1547515	type	True	78.0337	281	1523	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	77.5609	221	1523	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	77.5479	240	1523	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	77.3887	178	1523	95	below_threshold
Arsukibacterium indicum	strain=SM2107	GCA_019100565.1	2848612	2848612	type	True	77.322	154	1523	95	below_threshold
Rheinheimera baltica	strain=DSM 14885	GCA_000425345.1	67576	67576	type	True	77.2442	143	1523	95	below_threshold
Arsukibacterium perlucidum	strain=DSM 18276	GCA_000382165.1	368811	368811	type	True	77.0227	167	1523	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.2837	87	1523	95	below_threshold
Aeromonas sobria	strain=CIP 74.33	GCA_018359945.1	646	646	suspected-type	True	75.8287	55	1523	95	below_threshold
Aeromonas sobria	strain=CECT 4245	GCA_000820145.1	646	646	suspected-type	True	75.8233	55	1523	95	below_threshold
Aeromonas hydrophila subsp. ranae	strain=CIP 107985	GCA_000820325.1	208958	644	type	True	75.7697	50	1523	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:42,937] [INFO] DFAST Taxonomy check result was written to GCF_000711985.1_ASM71198v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:42,938] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:42,938] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:42,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0ab6447-83a6-4651-9f45-44a6234ad741/dqc_reference/checkm_data
[2024-01-24 12:31:42,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:42,982] [INFO] Task started: CheckM
[2024-01-24 12:31:42,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000711985.1_ASM71198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000711985.1_ASM71198v1_genomic.fna/checkm_input GCF_000711985.1_ASM71198v1_genomic.fna/checkm_result
[2024-01-24 12:32:17,712] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:17,713] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:17,731] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:17,731] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:17,732] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000711985.1_ASM71198v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:17,732] [INFO] Task started: Blastn
[2024-01-24 12:32:17,732] [INFO] Running command: blastn -query GCF_000711985.1_ASM71198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0ab6447-83a6-4651-9f45-44a6234ad741/dqc_reference/reference_markers_gtdb.fasta -out GCF_000711985.1_ASM71198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:18,962] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:18,964] [INFO] Selected 7 target genomes.
[2024-01-24 12:32:18,965] [INFO] Target genome list was writen to GCF_000711985.1_ASM71198v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:18,970] [INFO] Task started: fastANI
[2024-01-24 12:32:18,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg155f0287-bfbb-44ad-a8a3-a9a7f18d6a90/GCF_000711985.1_ASM71198v1_genomic.fna.gz --refList GCF_000711985.1_ASM71198v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000711985.1_ASM71198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:25,515] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:25,521] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:25,521] [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_000711985.1	s__Pararheinheimera texasensis	100.0	1523	1523	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_008015325.1	s__Pararheinheimera sp008015325	89.1968	1040	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003543135.1	s__Pararheinheimera sp003543135	78.8861	504	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	98.83	98.83	0.95	0.95	2	-
GCF_004005945.1	s__Pararheinheimera riviphila	78.8651	529	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001669775.1	s__Pararheinheimera sp001669775	78.7164	530	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003482455.1	s__Pararheinheimera sp003482455	78.2564	337	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000987775.1	s__Arsukibacterium ikkense	77.1874	184	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:25,522] [INFO] GTDB search result was written to GCF_000711985.1_ASM71198v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:25,523] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:25,525] [INFO] DFAST_QC result json was written to GCF_000711985.1_ASM71198v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:25,525] [INFO] DFAST_QC completed!
[2024-01-24 12:32:25,525] [INFO] Total running time: 0h1m8s