[2024-01-25 18:20:20,862] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:20:20,874] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:20:20,875] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2c2fb9f-6570-43f0-ac83-c3031179d22e/dqc_reference
[2024-01-25 18:20:22,066] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:20:22,066] [INFO] Task started: Prodigal
[2024-01-25 18:20:22,066] [INFO] Running command: gunzip -c /var/lib/cwl/stg5bd500b4-ee59-4607-94c0-2c73462b8bde/GCF_030717845.1_ASM3071784v1_genomic.fna.gz | prodigal -d GCF_030717845.1_ASM3071784v1_genomic.fna/cds.fna -a GCF_030717845.1_ASM3071784v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:20:31,001] [INFO] Task succeeded: Prodigal
[2024-01-25 18:20:31,001] [INFO] Task started: HMMsearch
[2024-01-25 18:20:31,001] [INFO] Running command: hmmsearch --tblout GCF_030717845.1_ASM3071784v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2c2fb9f-6570-43f0-ac83-c3031179d22e/dqc_reference/reference_markers.hmm GCF_030717845.1_ASM3071784v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:20:31,228] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:20:31,229] [INFO] Found 6/6 markers.
[2024-01-25 18:20:31,257] [INFO] Query marker FASTA was written to GCF_030717845.1_ASM3071784v1_genomic.fna/markers.fasta
[2024-01-25 18:20:31,257] [INFO] Task started: Blastn
[2024-01-25 18:20:31,257] [INFO] Running command: blastn -query GCF_030717845.1_ASM3071784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2c2fb9f-6570-43f0-ac83-c3031179d22e/dqc_reference/reference_markers.fasta -out GCF_030717845.1_ASM3071784v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:20:31,947] [INFO] Task succeeded: Blastn
[2024-01-25 18:20:31,949] [INFO] Selected 29 target genomes.
[2024-01-25 18:20:31,949] [INFO] Target genome list was writen to GCF_030717845.1_ASM3071784v1_genomic.fna/target_genomes.txt
[2024-01-25 18:20:31,977] [INFO] Task started: fastANI
[2024-01-25 18:20:31,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bd500b4-ee59-4607-94c0-2c73462b8bde/GCF_030717845.1_ASM3071784v1_genomic.fna.gz --refList GCF_030717845.1_ASM3071784v1_genomic.fna/target_genomes.txt --output GCF_030717845.1_ASM3071784v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:20:50,259] [INFO] Task succeeded: fastANI
[2024-01-25 18:20:50,260] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2c2fb9f-6570-43f0-ac83-c3031179d22e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:20:50,260] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2c2fb9f-6570-43f0-ac83-c3031179d22e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:20:50,272] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:20:50,272] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:20:50,272] [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
Alkalimonas amylolytica	strain=CGMCC 1.3430	GCA_900107845.1	152573	152573	type	True	79.6364	528	1251	95	below_threshold
Alishewanella tabrizica	strain=KCTC 23723	GCA_014652375.1	671278	671278	type	True	77.7734	139	1251	95	below_threshold
Rheinheimera aquimaris	strain=KCTC 12840	GCA_020531985.1	412437	412437	type	True	77.6112	155	1251	95	below_threshold
Alishewanella jeotgali	strain=KCTC 22429	GCA_000245735.2	545533	545533	type	True	77.5489	182	1251	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	77.5375	200	1251	95	below_threshold
Arsukibacterium perlucidum	strain=DSM 18276	GCA_000382165.1	368811	368811	type	True	77.5208	171	1251	95	below_threshold
Rheinheimera nanhaiensis	strain=E407-8	GCA_000296695.1	1163621	1163621	type	True	77.5166	194	1251	95	below_threshold
Rheinheimera pleomorphica	strain=PKS7	GCA_011634895.1	2703963	2703963	type	True	77.4925	197	1251	95	below_threshold
Alishewanella aestuarii	strain=B11	GCA_000280055.1	453835	453835	type	True	77.4681	183	1251	95	below_threshold
Arsukibacterium indicum	strain=SM2107	GCA_019100565.1	2848612	2848612	type	True	77.4359	191	1251	95	below_threshold
Alishewanella agri	strain=BL06	GCA_000272005.1	553384	553384	type	True	77.4222	185	1251	95	below_threshold
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	77.399	187	1251	95	below_threshold
Arsukibacterium tuosuense	strain=CGMCC 1.12461	GCA_900215315.1	1323745	1323745	type	True	77.3874	180	1251	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	77.3478	172	1251	95	below_threshold
Alishewanella longhuensis	strain=CGMCC 1.7003	GCA_014653435.1	1091037	1091037	type	True	77.2747	174	1251	95	below_threshold
Rheinheimera riviphila	strain=KYPC3	GCA_004005945.1	1834037	1834037	type	True	76.9917	137	1251	95	below_threshold
Pararheinheimera texasensis	strain=DSM 17496	GCA_000711985.1	306205	306205	type	True	76.9733	113	1251	95	below_threshold
Pararheinheimera mesophila	strain=IITR13	GCA_003862465.1	1547515	1547515	type	True	76.9225	127	1251	95	below_threshold
Pararheinheimera mesophila	strain=IITR-13	GCA_000986865.1	1547515	1547515	type	True	76.7108	125	1251	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:20:50,276] [INFO] DFAST Taxonomy check result was written to GCF_030717845.1_ASM3071784v1_genomic.fna/tc_result.tsv
[2024-01-25 18:20:50,276] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:20:50,277] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:20:50,277] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2c2fb9f-6570-43f0-ac83-c3031179d22e/dqc_reference/checkm_data
[2024-01-25 18:20:50,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:20:50,325] [INFO] Task started: CheckM
[2024-01-25 18:20:50,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030717845.1_ASM3071784v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030717845.1_ASM3071784v1_genomic.fna/checkm_input GCF_030717845.1_ASM3071784v1_genomic.fna/checkm_result
[2024-01-25 18:21:21,008] [INFO] Task succeeded: CheckM
[2024-01-25 18:21:21,015] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:21:21,036] [INFO] ===== Completeness check finished =====
[2024-01-25 18:21:21,036] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:21:21,037] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030717845.1_ASM3071784v1_genomic.fna/markers.fasta)
[2024-01-25 18:21:21,037] [INFO] Task started: Blastn
[2024-01-25 18:21:21,037] [INFO] Running command: blastn -query GCF_030717845.1_ASM3071784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2c2fb9f-6570-43f0-ac83-c3031179d22e/dqc_reference/reference_markers_gtdb.fasta -out GCF_030717845.1_ASM3071784v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:21:22,260] [INFO] Task succeeded: Blastn
[2024-01-25 18:21:22,263] [INFO] Selected 27 target genomes.
[2024-01-25 18:21:22,264] [INFO] Target genome list was writen to GCF_030717845.1_ASM3071784v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:21:22,304] [INFO] Task started: fastANI
[2024-01-25 18:21:22,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bd500b4-ee59-4607-94c0-2c73462b8bde/GCF_030717845.1_ASM3071784v1_genomic.fna.gz --refList GCF_030717845.1_ASM3071784v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030717845.1_ASM3071784v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:21:40,178] [INFO] Task succeeded: fastANI
[2024-01-25 18:21:40,191] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:21:40,191] [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_900107845.1	s__Alkalimonas amylolytica	79.6478	528	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alkalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007117525.1	s__Alkalimonas sp007117525	78.8812	201	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alkalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004369005.1	s__Rheinheimera aquimaris	77.7864	145	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	98.51	97.48	0.94	0.92	4	-
GCF_900108485.1	s__Rheinheimera pacifica	77.5539	198	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296695.1	s__Rheinheimera nanhaiensis	77.5166	194	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011634895.1	s__Rheinheimera pleomorphica	77.5074	196	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000987775.1	s__Arsukibacterium ikkense	77.4955	197	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000280055.1	s__Alishewanella aestuarii	77.4768	181	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.6353	96.26	96.26	0.87	0.87	2	-
GCF_000272005.1	s__Alishewanella agri	77.421	185	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.0	96.64	95.87	0.84	0.80	3	-
GCF_013283795.1	s__Rheinheimera sp013283795	77.3982	187	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215315.1	s__Arsukibacterium tuosuense	77.3814	182	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840125.1	s__Rheinheimera sp002840125	77.3243	199	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653435.1	s__Alishewanella longhuensis	77.2888	173	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alishewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000987765.1	s__Arsukibacterium sp000987765	77.1862	148	1251	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	77.1567	181	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302255.1	s__Pararheinheimera sp017302255	77.154	79	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018826295.1	s__Rheinheimera sp018826295	77.0311	190	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	99.95	99.91	0.97	0.92	5	-
GCF_004005945.1	s__Pararheinheimera riviphila	76.9917	137	1251	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	76.9046	140	1251	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	76.7274	124	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pararheinheimera	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:21:40,194] [INFO] GTDB search result was written to GCF_030717845.1_ASM3071784v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:21:40,195] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:21:40,198] [INFO] DFAST_QC result json was written to GCF_030717845.1_ASM3071784v1_genomic.fna/dqc_result.json
[2024-01-25 18:21:40,198] [INFO] DFAST_QC completed!
[2024-01-25 18:21:40,198] [INFO] Total running time: 0h1m19s