[2024-01-24 13:41:10,367] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:10,368] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:10,368] [INFO] DQC Reference Directory: /var/lib/cwl/stg3dd6dd4a-66f2-46e3-9a60-7c75f93151e5/dqc_reference
[2024-01-24 13:41:11,620] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:11,621] [INFO] Task started: Prodigal
[2024-01-24 13:41:11,621] [INFO] Running command: gunzip -c /var/lib/cwl/stg9aa43ce9-8dd8-4ffb-b238-d9f7a2bc5126/GCF_000299895.1_ASM29989v1_genomic.fna.gz | prodigal -d GCF_000299895.1_ASM29989v1_genomic.fna/cds.fna -a GCF_000299895.1_ASM29989v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:20,358] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:20,358] [INFO] Task started: HMMsearch
[2024-01-24 13:41:20,358] [INFO] Running command: hmmsearch --tblout GCF_000299895.1_ASM29989v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3dd6dd4a-66f2-46e3-9a60-7c75f93151e5/dqc_reference/reference_markers.hmm GCF_000299895.1_ASM29989v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:20,586] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:20,587] [INFO] Found 6/6 markers.
[2024-01-24 13:41:20,616] [INFO] Query marker FASTA was written to GCF_000299895.1_ASM29989v1_genomic.fna/markers.fasta
[2024-01-24 13:41:20,616] [INFO] Task started: Blastn
[2024-01-24 13:41:20,616] [INFO] Running command: blastn -query GCF_000299895.1_ASM29989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3dd6dd4a-66f2-46e3-9a60-7c75f93151e5/dqc_reference/reference_markers.fasta -out GCF_000299895.1_ASM29989v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:21,334] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:21,338] [INFO] Selected 30 target genomes.
[2024-01-24 13:41:21,338] [INFO] Target genome list was writen to GCF_000299895.1_ASM29989v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:21,348] [INFO] Task started: fastANI
[2024-01-24 13:41:21,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aa43ce9-8dd8-4ffb-b238-d9f7a2bc5126/GCF_000299895.1_ASM29989v1_genomic.fna.gz --refList GCF_000299895.1_ASM29989v1_genomic.fna/target_genomes.txt --output GCF_000299895.1_ASM29989v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:37,911] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:37,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3dd6dd4a-66f2-46e3-9a60-7c75f93151e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:37,912] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3dd6dd4a-66f2-46e3-9a60-7c75f93151e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:37,925] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:37,925] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:37,926] [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
Idiomarina xiamenensis	strain=10-D-4	GCA_000299895.1	1207041	1207041	type	True	100.0	934	937	95	conclusive
Idiomarina baltica	strain=OS145	GCA_000152885.1	190892	190892	type	True	79.0876	83	937	95	below_threshold
Pseudidiomarina tainanensis	strain=PIN1	GCA_004214835.1	502365	502365	type	True	78.4143	91	937	95	below_threshold
Pseudidiomarina maritima	strain=CGMCC 1.7285	GCA_900115255.1	519453	519453	type	True	78.3543	91	937	95	below_threshold
Idiomarina piscisalsi	strain=TPS4-2	GCA_003987095.1	1096243	1096243	type	True	78.2693	62	937	95	below_threshold
Pseudidiomarina donghaiensis	strain=908033	GCA_003987405.1	519452	519452	type	True	78.1553	89	937	95	below_threshold
Idiomarina fontislapidosi	strain=F23	GCA_003987025.1	263723	263723	type	True	78.1261	85	937	95	below_threshold
Idiomarina fontislapidosi	strain=CECT 5859	GCA_003226255.1	263723	263723	type	True	78.019	82	937	95	below_threshold
Idiomarina aquatica	strain=SN-14	GCA_003987185.1	1327752	1327752	type	True	77.9936	108	937	95	below_threshold
Pseudidiomarina donghaiensis	strain=CGMCC 1.7284	GCA_900116895.1	519452	519452	type	True	77.9354	88	937	95	below_threshold
Pseudidiomarina aestuarii	strain=KYW314	GCA_003987355.1	624146	624146	suspected-type	True	77.8581	67	937	95	below_threshold
Pseudidiomarina planktonica	strain=CGMCC 1.12458	GCA_900177775.1	1323738	1323738	type	True	77.4975	101	937	95	below_threshold
Pseudidiomarina planktonica	strain=TS-T11	GCA_003987425.1	1323738	1323738	type	True	77.4786	99	937	95	below_threshold
Aliidiomarina maris	strain=CF12-14	GCA_003987335.1	531312	531312	type	True	77.3804	71	937	95	below_threshold
Aliidiomarina halalkaliphila	strain=IM 1326	GCA_007096385.1	2593535	2593535	type	True	76.7824	52	937	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:37,927] [INFO] DFAST Taxonomy check result was written to GCF_000299895.1_ASM29989v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:37,928] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:37,928] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:37,928] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3dd6dd4a-66f2-46e3-9a60-7c75f93151e5/dqc_reference/checkm_data
[2024-01-24 13:41:37,930] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:37,964] [INFO] Task started: CheckM
[2024-01-24 13:41:37,965] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000299895.1_ASM29989v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000299895.1_ASM29989v1_genomic.fna/checkm_input GCF_000299895.1_ASM29989v1_genomic.fna/checkm_result
[2024-01-24 13:42:09,105] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:09,106] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:09,123] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:09,124] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:09,124] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000299895.1_ASM29989v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:09,124] [INFO] Task started: Blastn
[2024-01-24 13:42:09,124] [INFO] Running command: blastn -query GCF_000299895.1_ASM29989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3dd6dd4a-66f2-46e3-9a60-7c75f93151e5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000299895.1_ASM29989v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:10,203] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:10,206] [INFO] Selected 27 target genomes.
[2024-01-24 13:42:10,207] [INFO] Target genome list was writen to GCF_000299895.1_ASM29989v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:10,255] [INFO] Task started: fastANI
[2024-01-24 13:42:10,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aa43ce9-8dd8-4ffb-b238-d9f7a2bc5126/GCF_000299895.1_ASM29989v1_genomic.fna.gz --refList GCF_000299895.1_ASM29989v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000299895.1_ASM29989v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:23,514] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:23,528] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:23,528] [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_000299895.1	s__Idiomarina xiamenensis	100.0	934	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000152885.1	s__Idiomarina baltica	79.0876	83	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	98.48	98.19	0.90	0.79	8	-
GCF_001870515.1	s__Idiomarina sp001870515	78.443	89	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214835.1	s__Pseudidiomarina tainanensis	78.4318	90	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.72	97.72	0.94	0.94	2	-
GCF_900104245.1	s__Pseudidiomarina indica	78.3906	54	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003226255.1	s__Idiomarina fontislapidosi	78.019	82	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900116895.1	s__Pseudidiomarina donghaiensis	78.0005	87	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004362895.1	s__Idiomarina sp002729675	77.9656	99	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.61	97.37	0.88	0.80	5	-
GCF_003987355.1	s__Pseudidiomarina aestuarii	77.8581	67	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418345.1	s__Pseudidiomarina woesei	77.8333	93	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002685255.1	s__Idiomarina sp002685255	77.6902	75	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	99.23	98.54	0.93	0.91	3	-
GCA_002279005.1	s__Pseudidiomarina sp002279005	77.6016	70	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177775.1	s__Pseudidiomarina planktonica	77.4975	101	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003987335.1	s__Aliidiomarina maris	77.3804	71	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	99.15	98.30	0.97	0.95	3	-
GCF_009734345.1	s__Pseudidiomarina andamanensis	77.3542	93	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007096385.1	s__Aliidiomarina sp007096385	76.7895	53	937	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	76.757	62	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:23,529] [INFO] GTDB search result was written to GCF_000299895.1_ASM29989v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:23,530] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:23,533] [INFO] DFAST_QC result json was written to GCF_000299895.1_ASM29989v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:23,534] [INFO] DFAST_QC completed!
[2024-01-24 13:42:23,534] [INFO] Total running time: 0h1m13s