[2024-01-24 11:35:22,689] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:22,692] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:22,692] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ecc7243-f175-402d-86e1-8f1d45ac53d1/dqc_reference
[2024-01-24 11:35:26,239] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,241] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,241] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6e2c84b-879b-45cd-8076-ba826d8df10b/GCF_019100565.1_ASM1910056v1_genomic.fna.gz | prodigal -d GCF_019100565.1_ASM1910056v1_genomic.fna/cds.fna -a GCF_019100565.1_ASM1910056v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:36,146] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:36,146] [INFO] Task started: HMMsearch
[2024-01-24 11:35:36,147] [INFO] Running command: hmmsearch --tblout GCF_019100565.1_ASM1910056v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ecc7243-f175-402d-86e1-8f1d45ac53d1/dqc_reference/reference_markers.hmm GCF_019100565.1_ASM1910056v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:36,487] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:36,489] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd6e2c84b-879b-45cd-8076-ba826d8df10b/GCF_019100565.1_ASM1910056v1_genomic.fna.gz]
[2024-01-24 11:35:36,528] [INFO] Query marker FASTA was written to GCF_019100565.1_ASM1910056v1_genomic.fna/markers.fasta
[2024-01-24 11:35:36,528] [INFO] Task started: Blastn
[2024-01-24 11:35:36,528] [INFO] Running command: blastn -query GCF_019100565.1_ASM1910056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ecc7243-f175-402d-86e1-8f1d45ac53d1/dqc_reference/reference_markers.fasta -out GCF_019100565.1_ASM1910056v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:37,254] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:37,257] [INFO] Selected 16 target genomes.
[2024-01-24 11:35:37,257] [INFO] Target genome list was writen to GCF_019100565.1_ASM1910056v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:37,264] [INFO] Task started: fastANI
[2024-01-24 11:35:37,264] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6e2c84b-879b-45cd-8076-ba826d8df10b/GCF_019100565.1_ASM1910056v1_genomic.fna.gz --refList GCF_019100565.1_ASM1910056v1_genomic.fna/target_genomes.txt --output GCF_019100565.1_ASM1910056v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:49,282] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:49,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ecc7243-f175-402d-86e1-8f1d45ac53d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:49,283] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ecc7243-f175-402d-86e1-8f1d45ac53d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:49,297] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:49,297] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:49,298] [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
Arsukibacterium indicum	strain=SM2107	GCA_019100565.1	2848612	2848612	type	True	100.0	1337	1338	95	conclusive
Arsukibacterium tuosuense	strain=CGMCC 1.12461	GCA_900215315.1	1323745	1323745	type	True	82.828	939	1338	95	below_threshold
Arsukibacterium perlucidum	strain=DSM 18276	GCA_000382165.1	368811	368811	type	True	82.6117	911	1338	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	79.2119	439	1338	95	below_threshold
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	79.0614	424	1338	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	78.9843	389	1338	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_017824735.1	2793282	2793282	type	True	78.9298	385	1338	95	below_threshold
Rheinheimera pleomorphica	strain=PKS7	GCA_011634895.1	2703963	2703963	type	True	78.8731	414	1338	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	78.7989	414	1338	95	below_threshold
Alishewanella jeotgali	strain=KCTC 22429	GCA_000245735.2	545533	545533	type	True	78.6587	338	1338	95	below_threshold
Alishewanella aestuarii	strain=B11	GCA_000280055.1	453835	453835	type	True	78.6554	333	1338	95	below_threshold
Rheinheimera baltica	strain=DSM 14885	GCA_000425345.1	67576	67576	type	True	78.5606	319	1338	95	below_threshold
Pararheinheimera mesophila	strain=IITR13	GCA_003862465.1	1547515	1547515	type	True	77.529	158	1338	95	below_threshold
Rheinheimera riviphila	strain=KYPC3	GCA_004005945.1	1834037	1834037	type	True	77.4128	182	1338	95	below_threshold
Pararheinheimera mesophila	strain=IITR-13	GCA_000986865.1	1547515	1547515	type	True	77.2444	148	1338	95	below_threshold
Pararheinheimera texasensis	strain=DSM 17496	GCA_000711985.1	306205	306205	type	True	77.1683	149	1338	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:49,299] [INFO] DFAST Taxonomy check result was written to GCF_019100565.1_ASM1910056v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:49,300] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:49,300] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:49,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ecc7243-f175-402d-86e1-8f1d45ac53d1/dqc_reference/checkm_data
[2024-01-24 11:35:49,301] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:49,341] [INFO] Task started: CheckM
[2024-01-24 11:35:49,342] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019100565.1_ASM1910056v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019100565.1_ASM1910056v1_genomic.fna/checkm_input GCF_019100565.1_ASM1910056v1_genomic.fna/checkm_result
[2024-01-24 11:36:22,884] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:22,885] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:22,903] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:22,904] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:22,904] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019100565.1_ASM1910056v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:22,905] [INFO] Task started: Blastn
[2024-01-24 11:36:22,905] [INFO] Running command: blastn -query GCF_019100565.1_ASM1910056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ecc7243-f175-402d-86e1-8f1d45ac53d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_019100565.1_ASM1910056v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:23,982] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:23,985] [INFO] Selected 8 target genomes.
[2024-01-24 11:36:23,985] [INFO] Target genome list was writen to GCF_019100565.1_ASM1910056v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:23,992] [INFO] Task started: fastANI
[2024-01-24 11:36:23,992] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6e2c84b-879b-45cd-8076-ba826d8df10b/GCF_019100565.1_ASM1910056v1_genomic.fna.gz --refList GCF_019100565.1_ASM1910056v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019100565.1_ASM1910056v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:32,362] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:32,374] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:32,374] [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_019100565.1	s__Arsukibacterium sp019100565	100.0	1337	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900215315.1	s__Arsukibacterium tuosuense	82.828	939	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402695.1	s__Arsukibacterium sp018402695	82.6544	961	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382165.1	s__Arsukibacterium perlucidum	82.6209	910	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002415085.1	s__Arsukibacterium sp002415085	82.1067	895	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	99.96	99.86	0.96	0.90	7	-
GCA_002364615.1	s__Arsukibacterium sp002364615	81.4963	857	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	99.93	99.93	0.99	0.99	2	-
GCF_000987775.1	s__Arsukibacterium ikkense	81.0666	801	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513785.1	s__Rheinheimera sp001513785	78.7069	447	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:32,376] [INFO] GTDB search result was written to GCF_019100565.1_ASM1910056v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:32,376] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:32,380] [INFO] DFAST_QC result json was written to GCF_019100565.1_ASM1910056v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:32,380] [INFO] DFAST_QC completed!
[2024-01-24 11:36:32,380] [INFO] Total running time: 0h1m10s