[2024-01-24 14:05:59,966] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:59,968] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:59,968] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8569b88-7171-4c9b-b8d7-8a1cf4350349/dqc_reference
[2024-01-24 14:06:01,312] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:01,313] [INFO] Task started: Prodigal
[2024-01-24 14:06:01,313] [INFO] Running command: gunzip -c /var/lib/cwl/stg7549eae2-a2e7-445a-9a8c-7b63903403c2/GCF_021290985.1_ASM2129098v1_genomic.fna.gz | prodigal -d GCF_021290985.1_ASM2129098v1_genomic.fna/cds.fna -a GCF_021290985.1_ASM2129098v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:12,189] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:12,190] [INFO] Task started: HMMsearch
[2024-01-24 14:06:12,190] [INFO] Running command: hmmsearch --tblout GCF_021290985.1_ASM2129098v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8569b88-7171-4c9b-b8d7-8a1cf4350349/dqc_reference/reference_markers.hmm GCF_021290985.1_ASM2129098v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:12,546] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:12,548] [INFO] Found 6/6 markers.
[2024-01-24 14:06:12,595] [INFO] Query marker FASTA was written to GCF_021290985.1_ASM2129098v1_genomic.fna/markers.fasta
[2024-01-24 14:06:12,595] [INFO] Task started: Blastn
[2024-01-24 14:06:12,596] [INFO] Running command: blastn -query GCF_021290985.1_ASM2129098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8569b88-7171-4c9b-b8d7-8a1cf4350349/dqc_reference/reference_markers.fasta -out GCF_021290985.1_ASM2129098v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:13,424] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:13,428] [INFO] Selected 14 target genomes.
[2024-01-24 14:06:13,429] [INFO] Target genome list was writen to GCF_021290985.1_ASM2129098v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:13,436] [INFO] Task started: fastANI
[2024-01-24 14:06:13,436] [INFO] Running command: fastANI --query /var/lib/cwl/stg7549eae2-a2e7-445a-9a8c-7b63903403c2/GCF_021290985.1_ASM2129098v1_genomic.fna.gz --refList GCF_021290985.1_ASM2129098v1_genomic.fna/target_genomes.txt --output GCF_021290985.1_ASM2129098v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:23,749] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:23,749] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8569b88-7171-4c9b-b8d7-8a1cf4350349/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:23,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8569b88-7171-4c9b-b8d7-8a1cf4350349/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:23,763] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:23,763] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:23,764] [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=JA3-B52	GCA_008017875.1	400153	400153	type	True	85.7116	1055	1498	95	below_threshold
Rheinheimera tangshanensis	strain=CGMCC 1.6362	GCA_014645135.1	400153	400153	type	True	85.5832	1084	1498	95	below_threshold
Pararheinheimera mesophila	strain=IITR13	GCA_003862465.1	1547515	1547515	type	True	84.4804	984	1498	95	below_threshold
Pararheinheimera mesophila	strain=IITR-13	GCA_000986865.1	1547515	1547515	type	True	84.4669	960	1498	95	below_threshold
Rheinheimera riviphila	strain=KYPC3	GCA_004005945.1	1834037	1834037	type	True	78.516	354	1498	95	below_threshold
Rheinheimera salexigens	strain=KH87	GCA_001752395.1	1628148	1628148	type	True	78.3191	117	1498	95	below_threshold
Rheinheimera nanhaiensis	strain=E407-8	GCA_000296695.1	1163621	1163621	type	True	78.2667	254	1498	95	below_threshold
Rheinheimera aquimaris	strain=KCTC 12840	GCA_020531985.1	412437	412437	type	True	78.2557	247	1498	95	below_threshold
Arsukibacterium indicum	strain=SM2107	GCA_019100565.1	2848612	2848612	type	True	78.0866	189	1498	95	below_threshold
Rheinheimera baltica	strain=DSM 14885	GCA_000425345.1	67576	67576	type	True	77.7037	181	1498	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	77.3032	214	1498	95	below_threshold
Pseudoalteromonas ulvae	strain=UL12	GCA_014925405.1	107327	107327	type	True	76.5756	53	1498	95	below_threshold
Photobacterium salinisoli	strain=LAM9072	GCA_003614885.1	1616783	1616783	type	True	76.3129	53	1498	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:23,765] [INFO] DFAST Taxonomy check result was written to GCF_021290985.1_ASM2129098v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:23,766] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:23,766] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:23,767] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8569b88-7171-4c9b-b8d7-8a1cf4350349/dqc_reference/checkm_data
[2024-01-24 14:06:23,768] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:23,816] [INFO] Task started: CheckM
[2024-01-24 14:06:23,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021290985.1_ASM2129098v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021290985.1_ASM2129098v1_genomic.fna/checkm_input GCF_021290985.1_ASM2129098v1_genomic.fna/checkm_result
[2024-01-24 14:07:00,819] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:00,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:00,842] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:00,843] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:00,843] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021290985.1_ASM2129098v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:00,844] [INFO] Task started: Blastn
[2024-01-24 14:07:00,844] [INFO] Running command: blastn -query GCF_021290985.1_ASM2129098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8569b88-7171-4c9b-b8d7-8a1cf4350349/dqc_reference/reference_markers_gtdb.fasta -out GCF_021290985.1_ASM2129098v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:01,984] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:01,988] [INFO] Selected 6 target genomes.
[2024-01-24 14:07:01,989] [INFO] Target genome list was writen to GCF_021290985.1_ASM2129098v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:01,995] [INFO] Task started: fastANI
[2024-01-24 14:07:01,995] [INFO] Running command: fastANI --query /var/lib/cwl/stg7549eae2-a2e7-445a-9a8c-7b63903403c2/GCF_021290985.1_ASM2129098v1_genomic.fna.gz --refList GCF_021290985.1_ASM2129098v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021290985.1_ASM2129098v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:08,441] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:08,453] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:07:08,454] [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_000217935.1	s__Pararheinheimera sp000217935	89.7315	1165	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018825965.1	s__Pararheinheimera sp018825965	89.2364	1140	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	99.98	99.95	0.98	0.97	7	-
GCF_004005375.1	s__Pararheinheimera sp004005375	87.848	1099	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018815765.1	s__Pararheinheimera sp018815765	87.352	957	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990335.1	s__Pararheinheimera sp003990335	86.6568	1142	1498	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	85.565	1086	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	98.63	97.26	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:08,456] [INFO] GTDB search result was written to GCF_021290985.1_ASM2129098v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:08,456] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:08,460] [INFO] DFAST_QC result json was written to GCF_021290985.1_ASM2129098v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:08,461] [INFO] DFAST_QC completed!
[2024-01-24 14:07:08,461] [INFO] Total running time: 0h1m8s