[2024-01-24 13:31:57,792] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:57,794] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:57,794] [INFO] DQC Reference Directory: /var/lib/cwl/stg544e1dcf-ec9c-4a07-9cf9-6dc9c2ea9b3f/dqc_reference
[2024-01-24 13:31:59,119] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:59,125] [INFO] Task started: Prodigal
[2024-01-24 13:31:59,126] [INFO] Running command: gunzip -c /var/lib/cwl/stg33706268-3fd7-4f7d-b29c-232fc75239a3/GCF_003987345.1_ASM398734v1_genomic.fna.gz | prodigal -d GCF_003987345.1_ASM398734v1_genomic.fna/cds.fna -a GCF_003987345.1_ASM398734v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:06,255] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:06,255] [INFO] Task started: HMMsearch
[2024-01-24 13:32:06,256] [INFO] Running command: hmmsearch --tblout GCF_003987345.1_ASM398734v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg544e1dcf-ec9c-4a07-9cf9-6dc9c2ea9b3f/dqc_reference/reference_markers.hmm GCF_003987345.1_ASM398734v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:06,476] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:06,480] [INFO] Found 6/6 markers.
[2024-01-24 13:32:06,505] [INFO] Query marker FASTA was written to GCF_003987345.1_ASM398734v1_genomic.fna/markers.fasta
[2024-01-24 13:32:06,506] [INFO] Task started: Blastn
[2024-01-24 13:32:06,506] [INFO] Running command: blastn -query GCF_003987345.1_ASM398734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg544e1dcf-ec9c-4a07-9cf9-6dc9c2ea9b3f/dqc_reference/reference_markers.fasta -out GCF_003987345.1_ASM398734v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:07,259] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:07,262] [INFO] Selected 22 target genomes.
[2024-01-24 13:32:07,262] [INFO] Target genome list was writen to GCF_003987345.1_ASM398734v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:07,268] [INFO] Task started: fastANI
[2024-01-24 13:32:07,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg33706268-3fd7-4f7d-b29c-232fc75239a3/GCF_003987345.1_ASM398734v1_genomic.fna.gz --refList GCF_003987345.1_ASM398734v1_genomic.fna/target_genomes.txt --output GCF_003987345.1_ASM398734v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:20,876] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:20,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg544e1dcf-ec9c-4a07-9cf9-6dc9c2ea9b3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:20,877] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg544e1dcf-ec9c-4a07-9cf9-6dc9c2ea9b3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:20,887] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:20,888] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:20,888] [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 shirensis	strain=AIS	GCA_003987345.1	1048642	1048642	type	True	100.0	897	898	95	conclusive
Aliidiomarina iranensis	strain=GBPy7	GCA_003987135.1	1434071	1434071	type	True	81.6466	516	898	95	below_threshold
Aliidiomarina indica	strain=SW123	GCA_015354615.1	2749147	2749147	type	True	79.0522	131	898	95	below_threshold
Aliidiomarina sanyensis	strain=GYP-17	GCA_003987175.1	1249555	1249555	type	True	78.5899	121	898	95	below_threshold
Pseudidiomarina aquimaris	strain=SW15	GCA_003987395.1	641841	641841	type	True	78.3946	59	898	95	below_threshold
Aliidiomarina halalkaliphila	strain=IM 1326	GCA_007096385.1	2593535	2593535	type	True	78.3395	147	898	95	below_threshold
Aliidiomarina haloalkalitolerans	strain=AK5	GCA_003987315.1	859059	859059	type	True	78.1357	152	898	95	below_threshold
Aliidiomarina celeris	strain=F3105	GCA_003316875.1	2249428	2249428	type	True	78.064	91	898	95	below_threshold
Aliidiomarina maris	strain=CF12-14	GCA_003987335.1	531312	531312	type	True	78.0588	74	898	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:20,889] [INFO] DFAST Taxonomy check result was written to GCF_003987345.1_ASM398734v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:20,890] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:20,890] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:20,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg544e1dcf-ec9c-4a07-9cf9-6dc9c2ea9b3f/dqc_reference/checkm_data
[2024-01-24 13:32:20,892] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:20,918] [INFO] Task started: CheckM
[2024-01-24 13:32:20,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003987345.1_ASM398734v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003987345.1_ASM398734v1_genomic.fna/checkm_input GCF_003987345.1_ASM398734v1_genomic.fna/checkm_result
[2024-01-24 13:32:45,928] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:45,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:45,948] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:45,949] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:45,949] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003987345.1_ASM398734v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:45,949] [INFO] Task started: Blastn
[2024-01-24 13:32:45,950] [INFO] Running command: blastn -query GCF_003987345.1_ASM398734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg544e1dcf-ec9c-4a07-9cf9-6dc9c2ea9b3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003987345.1_ASM398734v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:47,075] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:47,079] [INFO] Selected 15 target genomes.
[2024-01-24 13:32:47,079] [INFO] Target genome list was writen to GCF_003987345.1_ASM398734v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:47,088] [INFO] Task started: fastANI
[2024-01-24 13:32:47,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg33706268-3fd7-4f7d-b29c-232fc75239a3/GCF_003987345.1_ASM398734v1_genomic.fna.gz --refList GCF_003987345.1_ASM398734v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003987345.1_ASM398734v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:54,866] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:54,876] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:54,876] [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_003987345.1	s__Aliidiomarina shirensis	100.0	897	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	99.30	99.30	0.95	0.95	2	conclusive
GCF_000218785.1	s__Aliidiomarina sp000218785	84.0562	646	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987135.1	s__Aliidiomarina iranensis	81.6605	516	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015354615.1	s__Aliidiomarina sp015354615	79.0522	131	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987175.1	s__Aliidiomarina sanyensis	78.6523	120	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987315.1	s__Aliidiomarina haloalkalitolerans	78.1357	152	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001458075.1	s__Aliidiomarina sp001458075	78.0805	94	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003182315.1	s__Pseudidiomarina maritima_A	77.9716	67	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	98.70	97.84	0.93	0.89	6	-
GCF_900116895.1	s__Pseudidiomarina donghaiensis	77.7918	72	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001418345.1	s__Pseudidiomarina woesei	77.7897	58	898	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:54,878] [INFO] GTDB search result was written to GCF_003987345.1_ASM398734v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:54,879] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:54,881] [INFO] DFAST_QC result json was written to GCF_003987345.1_ASM398734v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:54,882] [INFO] DFAST_QC completed!
[2024-01-24 13:32:54,882] [INFO] Total running time: 0h0m57s