[2024-01-24 12:36:58,145] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:58,147] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:58,147] [INFO] DQC Reference Directory: /var/lib/cwl/stg4727d81e-4ce7-497a-924e-59350dfe1173/dqc_reference
[2024-01-24 12:36:59,479] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:59,480] [INFO] Task started: Prodigal
[2024-01-24 12:36:59,480] [INFO] Running command: gunzip -c /var/lib/cwl/stg63442857-9ad3-4644-a5b1-8c81ac511dd9/GCF_008017875.1_ASM801787v1_genomic.fna.gz | prodigal -d GCF_008017875.1_ASM801787v1_genomic.fna/cds.fna -a GCF_008017875.1_ASM801787v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:09,568] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:09,569] [INFO] Task started: HMMsearch
[2024-01-24 12:37:09,569] [INFO] Running command: hmmsearch --tblout GCF_008017875.1_ASM801787v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4727d81e-4ce7-497a-924e-59350dfe1173/dqc_reference/reference_markers.hmm GCF_008017875.1_ASM801787v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:09,930] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:09,931] [INFO] Found 6/6 markers.
[2024-01-24 12:37:09,969] [INFO] Query marker FASTA was written to GCF_008017875.1_ASM801787v1_genomic.fna/markers.fasta
[2024-01-24 12:37:09,970] [INFO] Task started: Blastn
[2024-01-24 12:37:09,970] [INFO] Running command: blastn -query GCF_008017875.1_ASM801787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4727d81e-4ce7-497a-924e-59350dfe1173/dqc_reference/reference_markers.fasta -out GCF_008017875.1_ASM801787v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:10,815] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:10,818] [INFO] Selected 12 target genomes.
[2024-01-24 12:37:10,818] [INFO] Target genome list was writen to GCF_008017875.1_ASM801787v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:10,825] [INFO] Task started: fastANI
[2024-01-24 12:37:10,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg63442857-9ad3-4644-a5b1-8c81ac511dd9/GCF_008017875.1_ASM801787v1_genomic.fna.gz --refList GCF_008017875.1_ASM801787v1_genomic.fna/target_genomes.txt --output GCF_008017875.1_ASM801787v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:21,268] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:21,268] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4727d81e-4ce7-497a-924e-59350dfe1173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:21,268] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4727d81e-4ce7-497a-924e-59350dfe1173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:21,285] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:37:21,285] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:21,286] [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	100.0	1342	1344	95	conclusive
Rheinheimera tangshanensis	strain=CGMCC 1.6362	GCA_014645135.1	400153	400153	type	True	99.9951	1339	1344	95	conclusive
Pararheinheimera mesophila	strain=IITR13	GCA_003862465.1	1547515	1547515	type	True	86.76	1063	1344	95	below_threshold
Pararheinheimera mesophila	strain=IITR-13	GCA_000986865.1	1547515	1547515	type	True	86.6618	1013	1344	95	below_threshold
Rheinheimera riviphila	strain=KYPC3	GCA_004005945.1	1834037	1834037	type	True	78.4789	327	1344	95	below_threshold
Pararheinheimera texasensis	strain=DSM 17496	GCA_000711985.1	306205	306205	type	True	78.0716	299	1344	95	below_threshold
Rheinheimera nanhaiensis	strain=E407-8	GCA_000296695.1	1163621	1163621	type	True	77.9589	211	1344	95	below_threshold
Arsukibacterium indicum	strain=SM2107	GCA_019100565.1	2848612	2848612	type	True	77.8251	163	1344	95	below_threshold
Arsukibacterium perlucidum	strain=DSM 18276	GCA_000382165.1	368811	368811	type	True	77.823	178	1344	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	77.4451	265	1344	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	77.3421	194	1344	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:21,289] [INFO] DFAST Taxonomy check result was written to GCF_008017875.1_ASM801787v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:21,290] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:21,290] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:21,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4727d81e-4ce7-497a-924e-59350dfe1173/dqc_reference/checkm_data
[2024-01-24 12:37:21,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:21,337] [INFO] Task started: CheckM
[2024-01-24 12:37:21,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008017875.1_ASM801787v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008017875.1_ASM801787v1_genomic.fna/checkm_input GCF_008017875.1_ASM801787v1_genomic.fna/checkm_result
[2024-01-24 12:37:57,010] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:57,011] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:57,031] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:57,031] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:57,032] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008017875.1_ASM801787v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:57,032] [INFO] Task started: Blastn
[2024-01-24 12:37:57,032] [INFO] Running command: blastn -query GCF_008017875.1_ASM801787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4727d81e-4ce7-497a-924e-59350dfe1173/dqc_reference/reference_markers_gtdb.fasta -out GCF_008017875.1_ASM801787v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:58,196] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:58,201] [INFO] Selected 7 target genomes.
[2024-01-24 12:37:58,202] [INFO] Target genome list was writen to GCF_008017875.1_ASM801787v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:58,209] [INFO] Task started: fastANI
[2024-01-24 12:37:58,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg63442857-9ad3-4644-a5b1-8c81ac511dd9/GCF_008017875.1_ASM801787v1_genomic.fna.gz --refList GCF_008017875.1_ASM801787v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008017875.1_ASM801787v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:05,237] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:05,250] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:05,250] [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_014645135.1	s__Pararheinheimera tangshanensis	99.9951	1339	1344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	98.63	97.26	0.95	0.91	3	conclusive
GCF_000986865.1	s__Pararheinheimera mesophila	86.6619	1013	1344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	100.00	100.00	0.99	0.99	2	-
GCA_018815765.1	s__Pararheinheimera sp018815765	86.3816	937	1344	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	86.1713	1075	1344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000217935.1	s__Pararheinheimera sp000217935	84.8478	978	1344	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	84.6711	1000	1344	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	84.4988	970	1344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:05,254] [INFO] GTDB search result was written to GCF_008017875.1_ASM801787v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:05,255] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:05,258] [INFO] DFAST_QC result json was written to GCF_008017875.1_ASM801787v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:05,258] [INFO] DFAST_QC completed!
[2024-01-24 12:38:05,258] [INFO] Total running time: 0h1m7s