[2024-01-24 13:49:19,501] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:19,504] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:19,504] [INFO] DQC Reference Directory: /var/lib/cwl/stgf39eebda-eef6-4b0d-80ec-daec2836f5e7/dqc_reference
[2024-01-24 13:49:20,888] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:20,889] [INFO] Task started: Prodigal
[2024-01-24 13:49:20,889] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4bb9be7-b06c-41ac-bc40-8a5f7e9cbc5b/GCF_003987435.1_ASM398743v1_genomic.fna.gz | prodigal -d GCF_003987435.1_ASM398743v1_genomic.fna/cds.fna -a GCF_003987435.1_ASM398743v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:27,294] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:27,294] [INFO] Task started: HMMsearch
[2024-01-24 13:49:27,295] [INFO] Running command: hmmsearch --tblout GCF_003987435.1_ASM398743v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf39eebda-eef6-4b0d-80ec-daec2836f5e7/dqc_reference/reference_markers.hmm GCF_003987435.1_ASM398743v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:27,575] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:27,577] [INFO] Found 6/6 markers.
[2024-01-24 13:49:27,600] [INFO] Query marker FASTA was written to GCF_003987435.1_ASM398743v1_genomic.fna/markers.fasta
[2024-01-24 13:49:27,600] [INFO] Task started: Blastn
[2024-01-24 13:49:27,600] [INFO] Running command: blastn -query GCF_003987435.1_ASM398743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf39eebda-eef6-4b0d-80ec-daec2836f5e7/dqc_reference/reference_markers.fasta -out GCF_003987435.1_ASM398743v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:28,407] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:28,411] [INFO] Selected 27 target genomes.
[2024-01-24 13:49:28,411] [INFO] Target genome list was writen to GCF_003987435.1_ASM398743v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:28,425] [INFO] Task started: fastANI
[2024-01-24 13:49:28,425] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4bb9be7-b06c-41ac-bc40-8a5f7e9cbc5b/GCF_003987435.1_ASM398743v1_genomic.fna.gz --refList GCF_003987435.1_ASM398743v1_genomic.fna/target_genomes.txt --output GCF_003987435.1_ASM398743v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:41,713] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:41,713] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf39eebda-eef6-4b0d-80ec-daec2836f5e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:41,714] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf39eebda-eef6-4b0d-80ec-daec2836f5e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:41,728] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:41,729] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:41,729] [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
Pseudidiomarina taiwanensis	strain=PIT1	GCA_003987435.1	337250	337250	type	True	100.0	730	730	95	conclusive
Pseudidiomarina gelatinasegens	strain=R04H25	GCA_004025325.1	2487740	2487740	type	True	79.4284	136	730	95	below_threshold
Pseudidiomarina indica	strain=CGMCC 1.10824	GCA_900104245.1	1159017	1159017	type	True	79.1969	112	730	95	below_threshold
Pseudidiomarina atlantica	strain=MCCC 1A10513	GCA_000753735.1	1517416	1517416	type	True	79.1597	139	730	95	below_threshold
Pseudidiomarina tainanensis	strain=PIN1	GCA_004214835.1	502365	502365	type	True	79.15	138	730	95	below_threshold
Pseudidiomarina piscicola	strain=CECT 9734	GCA_902806985.1	2614830	2614830	type	True	79.0773	131	730	95	below_threshold
Pseudidiomarina marina	strain=PIM1	GCA_003987045.1	502366	502366	type	True	78.8643	142	730	95	below_threshold
Pseudidiomarina sediminum	strain=c121	GCA_003987265.1	431675	431675	type	True	78.7718	139	730	95	below_threshold
Pseudidiomarina sediminum	strain=DSM 21906	GCA_000423165.1	431675	431675	type	True	78.7575	140	730	95	below_threshold
Pseudidiomarina maritima	strain=CGMCC 1.7285	GCA_900115255.1	519453	519453	type	True	78.708	148	730	95	below_threshold
Pseudidiomarina aquimaris	strain=SW15	GCA_003987395.1	641841	641841	type	True	78.6043	155	730	95	below_threshold
Idiomarina mangrovi	strain=ZQ330	GCA_003999375.1	2487133	2487133	type	True	78.5862	143	730	95	below_threshold
Pseudidiomarina donghaiensis	strain=908033	GCA_003987405.1	519452	519452	type	True	78.5822	156	730	95	below_threshold
Pseudidiomarina donghaiensis	strain=CGMCC 1.7284	GCA_900116895.1	519452	519452	type	True	78.4575	155	730	95	below_threshold
Idiomarina fontislapidosi	strain=CECT 5859	GCA_003226255.1	263723	263723	type	True	78.1065	70	730	95	below_threshold
Pseudidiomarina salinarum	strain=ISL-52	GCA_000753715.1	435908	435908	type	True	78.0976	113	730	95	below_threshold
Idiomarina fontislapidosi	strain=F23	GCA_003987025.1	263723	263723	type	True	78.0676	71	730	95	below_threshold
Pseudidiomarina salinarum	strain=ISL-52	GCA_003987105.1	435908	435908	type	True	78.0505	118	730	95	below_threshold
Aliidiomarina soli	strain=Y4G10-17	GCA_003986975.1	1928574	1928574	type	True	77.0211	64	730	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:41,731] [INFO] DFAST Taxonomy check result was written to GCF_003987435.1_ASM398743v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:41,731] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:41,731] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:41,732] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf39eebda-eef6-4b0d-80ec-daec2836f5e7/dqc_reference/checkm_data
[2024-01-24 13:49:41,733] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:41,768] [INFO] Task started: CheckM
[2024-01-24 13:49:41,769] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003987435.1_ASM398743v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003987435.1_ASM398743v1_genomic.fna/checkm_input GCF_003987435.1_ASM398743v1_genomic.fna/checkm_result
[2024-01-24 13:50:06,863] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:06,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:06,880] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:06,880] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:06,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003987435.1_ASM398743v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:06,881] [INFO] Task started: Blastn
[2024-01-24 13:50:06,881] [INFO] Running command: blastn -query GCF_003987435.1_ASM398743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf39eebda-eef6-4b0d-80ec-daec2836f5e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003987435.1_ASM398743v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:08,049] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:08,052] [INFO] Selected 24 target genomes.
[2024-01-24 13:50:08,052] [INFO] Target genome list was writen to GCF_003987435.1_ASM398743v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:08,068] [INFO] Task started: fastANI
[2024-01-24 13:50:08,069] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4bb9be7-b06c-41ac-bc40-8a5f7e9cbc5b/GCF_003987435.1_ASM398743v1_genomic.fna.gz --refList GCF_003987435.1_ASM398743v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003987435.1_ASM398743v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:20,463] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:20,481] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:20,482] [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_003987435.1	s__Pseudidiomarina taiwanensis	100.0	730	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004025325.1	s__Pseudidiomarina gelatinasegens	79.4334	137	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104245.1	s__Pseudidiomarina indica	79.2259	112	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000753735.1	s__Pseudidiomarina atlantica	79.1922	138	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214835.1	s__Pseudidiomarina tainanensis	79.1515	138	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.72	97.72	0.94	0.94	2	-
GCF_902806985.1	s__Pseudidiomarina piscicola	79.0525	131	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009734345.1	s__Pseudidiomarina andamanensis	79.0324	143	730	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	78.9855	131	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003987045.1	s__Pseudidiomarina marina	78.8377	141	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.46	97.46	0.94	0.94	2	-
GCA_002279005.1	s__Pseudidiomarina sp002279005	78.836	117	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987065.1	s__Pseudidiomarina insulisalsae	78.777	130	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423165.1	s__Pseudidiomarina sediminum	78.7672	141	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003987395.1	s__Pseudidiomarina aquimaris	78.6072	154	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.26	97.14	0.86	0.77	3	-
GCF_003999375.1	s__Pseudidiomarina mangrovi	78.6036	141	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987345.1	s__Aliidiomarina shirensis	78.2817	52	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	99.30	99.30	0.95	0.95	2	-
GCF_000753715.1	s__Pseudidiomarina salinarum	78.1299	112	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003226255.1	s__Idiomarina fontislapidosi	78.1065	70	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002685255.1	s__Idiomarina sp002685255	77.6752	60	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	99.23	98.54	0.93	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:20,489] [INFO] GTDB search result was written to GCF_003987435.1_ASM398743v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:20,490] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:20,497] [INFO] DFAST_QC result json was written to GCF_003987435.1_ASM398743v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:20,498] [INFO] DFAST_QC completed!
[2024-01-24 13:50:20,498] [INFO] Total running time: 0h1m1s