[2023-06-28 16:36:00,880] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:36:00,882] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:36:00,882] [INFO] DQC Reference Directory: /var/lib/cwl/stg5571692c-cad7-4e27-9ec2-bcd3c3ecf2d9/dqc_reference
[2023-06-28 16:36:01,987] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:36:01,988] [INFO] Task started: Prodigal
[2023-06-28 16:36:01,988] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ddc4b4b-0a4c-419c-bab5-e689bc3833e9/GCA_020832105.1_ASM2083210v1_genomic.fna.gz | prodigal -d GCA_020832105.1_ASM2083210v1_genomic.fna/cds.fna -a GCA_020832105.1_ASM2083210v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:36:08,906] [INFO] Task succeeded: Prodigal
[2023-06-28 16:36:08,906] [INFO] Task started: HMMsearch
[2023-06-28 16:36:08,906] [INFO] Running command: hmmsearch --tblout GCA_020832105.1_ASM2083210v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5571692c-cad7-4e27-9ec2-bcd3c3ecf2d9/dqc_reference/reference_markers.hmm GCA_020832105.1_ASM2083210v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:36:09,120] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:36:09,121] [INFO] Found 6/6 markers.
[2023-06-28 16:36:09,147] [INFO] Query marker FASTA was written to GCA_020832105.1_ASM2083210v1_genomic.fna/markers.fasta
[2023-06-28 16:36:09,148] [INFO] Task started: Blastn
[2023-06-28 16:36:09,148] [INFO] Running command: blastn -query GCA_020832105.1_ASM2083210v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5571692c-cad7-4e27-9ec2-bcd3c3ecf2d9/dqc_reference/reference_markers.fasta -out GCA_020832105.1_ASM2083210v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:36:09,791] [INFO] Task succeeded: Blastn
[2023-06-28 16:36:09,795] [INFO] Selected 25 target genomes.
[2023-06-28 16:36:09,796] [INFO] Target genome list was writen to GCA_020832105.1_ASM2083210v1_genomic.fna/target_genomes.txt
[2023-06-28 16:36:09,798] [INFO] Task started: fastANI
[2023-06-28 16:36:09,798] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ddc4b4b-0a4c-419c-bab5-e689bc3833e9/GCA_020832105.1_ASM2083210v1_genomic.fna.gz --refList GCA_020832105.1_ASM2083210v1_genomic.fna/target_genomes.txt --output GCA_020832105.1_ASM2083210v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:36:23,198] [INFO] Task succeeded: fastANI
[2023-06-28 16:36:23,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5571692c-cad7-4e27-9ec2-bcd3c3ecf2d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:36:23,199] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5571692c-cad7-4e27-9ec2-bcd3c3ecf2d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:36:23,206] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:36:23,207] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:36:23,207] [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
Aliidiomarina soli	strain=Y4G10-17	GCA_003986975.1	1928574	1928574	type	True	78.6256	256	964	95	below_threshold
Aliidiomarina maris	strain=CF12-14	GCA_003987335.1	531312	531312	type	True	78.4592	272	964	95	below_threshold
Aliidiomarina sedimenti	strain=GBSy1	GCA_003986955.1	1933879	1933879	type	True	78.3229	281	964	95	below_threshold
Aliidiomarina minuta	strain=MLST1	GCA_003987145.1	880057	880057	type	True	77.9592	177	964	95	below_threshold
Pseudidiomarina gelatinasegens	strain=R04H25	GCA_004025325.1	2487740	2487740	type	True	77.4014	53	964	95	below_threshold
Aliidiomarina haloalkalitolerans	strain=AK5	GCA_003987315.1	859059	859059	type	True	76.8708	68	964	95	below_threshold
Pseudidiomarina taiwanensis	strain=PIT1	GCA_003987435.1	337250	337250	type	True	76.7596	51	964	95	below_threshold
Aliidiomarina indica	strain=SW123	GCA_015354615.1	2749147	2749147	type	True	76.5857	64	964	95	below_threshold
Pseudidiomarina sediminum	strain=c121	GCA_003987265.1	431675	431675	type	True	76.2093	50	964	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:36:23,208] [INFO] DFAST Taxonomy check result was written to GCA_020832105.1_ASM2083210v1_genomic.fna/tc_result.tsv
[2023-06-28 16:36:23,209] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:36:23,209] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:36:23,209] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5571692c-cad7-4e27-9ec2-bcd3c3ecf2d9/dqc_reference/checkm_data
[2023-06-28 16:36:23,210] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:36:23,241] [INFO] Task started: CheckM
[2023-06-28 16:36:23,241] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020832105.1_ASM2083210v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020832105.1_ASM2083210v1_genomic.fna/checkm_input GCA_020832105.1_ASM2083210v1_genomic.fna/checkm_result
[2023-06-28 16:36:47,961] [INFO] Task succeeded: CheckM
[2023-06-28 16:36:47,962] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:36:47,984] [INFO] ===== Completeness check finished =====
[2023-06-28 16:36:47,984] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:36:47,985] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020832105.1_ASM2083210v1_genomic.fna/markers.fasta)
[2023-06-28 16:36:47,985] [INFO] Task started: Blastn
[2023-06-28 16:36:47,985] [INFO] Running command: blastn -query GCA_020832105.1_ASM2083210v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5571692c-cad7-4e27-9ec2-bcd3c3ecf2d9/dqc_reference/reference_markers_gtdb.fasta -out GCA_020832105.1_ASM2083210v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:36:48,911] [INFO] Task succeeded: Blastn
[2023-06-28 16:36:48,914] [INFO] Selected 25 target genomes.
[2023-06-28 16:36:48,914] [INFO] Target genome list was writen to GCA_020832105.1_ASM2083210v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:36:48,978] [INFO] Task started: fastANI
[2023-06-28 16:36:48,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ddc4b4b-0a4c-419c-bab5-e689bc3833e9/GCA_020832105.1_ASM2083210v1_genomic.fna.gz --refList GCA_020832105.1_ASM2083210v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020832105.1_ASM2083210v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:37:04,395] [INFO] Task succeeded: fastANI
[2023-06-28 16:37:04,402] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 16:37:04,402] [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_003986975.1	s__Aliidiomarina soli	78.626	255	964	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0513	N/A	N/A	N/A	N/A	1	-
GCF_003987335.1	s__Aliidiomarina maris	78.449	272	964	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	99.15	98.30	0.97	0.95	3	-
GCF_003986955.1	s__Aliidiomarina sedimenti	78.3237	282	964	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0513	N/A	N/A	N/A	N/A	1	-
GCF_003987145.1	s__Aliidiomarina minuta	77.9592	177	964	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004025325.1	s__Pseudidiomarina gelatinasegens	77.3774	52	964	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987315.1	s__Aliidiomarina haloalkalitolerans	76.879	66	964	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987435.1	s__Pseudidiomarina taiwanensis	76.7643	51	964	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015354615.1	s__Aliidiomarina sp015354615	76.5567	63	964	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:37:04,404] [INFO] GTDB search result was written to GCA_020832105.1_ASM2083210v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:37:04,404] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:37:04,407] [INFO] DFAST_QC result json was written to GCA_020832105.1_ASM2083210v1_genomic.fna/dqc_result.json
[2023-06-28 16:37:04,408] [INFO] DFAST_QC completed!
[2023-06-28 16:37:04,408] [INFO] Total running time: 0h1m4s