[2024-01-24 15:26:33,100] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:33,101] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:33,102] [INFO] DQC Reference Directory: /var/lib/cwl/stged545a0c-a8db-4e05-b643-54a856c55aba/dqc_reference
[2024-01-24 15:26:35,760] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:35,761] [INFO] Task started: Prodigal
[2024-01-24 15:26:35,762] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0fc328d-86d0-4e27-b542-88a9b67af306/GCF_003999375.1_ASM399937v1_genomic.fna.gz | prodigal -d GCF_003999375.1_ASM399937v1_genomic.fna/cds.fna -a GCF_003999375.1_ASM399937v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:42,640] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:42,641] [INFO] Task started: HMMsearch
[2024-01-24 15:26:42,641] [INFO] Running command: hmmsearch --tblout GCF_003999375.1_ASM399937v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged545a0c-a8db-4e05-b643-54a856c55aba/dqc_reference/reference_markers.hmm GCF_003999375.1_ASM399937v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:42,936] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:42,938] [INFO] Found 6/6 markers.
[2024-01-24 15:26:42,961] [INFO] Query marker FASTA was written to GCF_003999375.1_ASM399937v1_genomic.fna/markers.fasta
[2024-01-24 15:26:42,961] [INFO] Task started: Blastn
[2024-01-24 15:26:42,961] [INFO] Running command: blastn -query GCF_003999375.1_ASM399937v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged545a0c-a8db-4e05-b643-54a856c55aba/dqc_reference/reference_markers.fasta -out GCF_003999375.1_ASM399937v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:44,293] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:44,298] [INFO] Selected 25 target genomes.
[2024-01-24 15:26:44,298] [INFO] Target genome list was writen to GCF_003999375.1_ASM399937v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:44,458] [INFO] Task started: fastANI
[2024-01-24 15:26:44,459] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0fc328d-86d0-4e27-b542-88a9b67af306/GCF_003999375.1_ASM399937v1_genomic.fna.gz --refList GCF_003999375.1_ASM399937v1_genomic.fna/target_genomes.txt --output GCF_003999375.1_ASM399937v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:26:56,806] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:56,806] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged545a0c-a8db-4e05-b643-54a856c55aba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:26:56,807] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged545a0c-a8db-4e05-b643-54a856c55aba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:26:56,824] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:26:56,824] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:26:56,825] [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 mangrovi	strain=ZQ330	GCA_003999375.1	2487133	2487133	type	True	100.0	814	814	95	conclusive
Pseudidiomarina donghaiensis	strain=908033	GCA_003987405.1	519452	519452	type	True	78.8044	212	814	95	below_threshold
Pseudidiomarina marina	strain=PIM1	GCA_003987045.1	502366	502366	type	True	78.777	166	814	95	below_threshold
Pseudidiomarina donghaiensis	strain=CGMCC 1.7284	GCA_900116895.1	519452	519452	type	True	78.6641	215	814	95	below_threshold
Pseudidiomarina taiwanensis	strain=PIT1	GCA_003987435.1	337250	337250	type	True	78.5847	145	814	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001418345.1	1381080	1381080	type	True	78.3568	183	814	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001517265.1	1381080	1381080	type	True	78.3446	182	814	95	below_threshold
Pseudidiomarina tainanensis	strain=PIN1	GCA_004214835.1	502365	502365	type	True	78.3068	186	814	95	below_threshold
Pseudidiomarina aquimaris	strain=SW15	GCA_003987395.1	641841	641841	type	True	78.2036	166	814	95	below_threshold
Pseudidiomarina sediminum	strain=c121	GCA_003987265.1	431675	431675	type	True	78.1212	156	814	95	below_threshold
Idiomarina seosinensis	strain=CL-SP19	GCA_003987275.1	281739	281739	type	True	78.0597	61	814	95	below_threshold
Pseudidiomarina sediminum	strain=DSM 21906	GCA_000423165.1	431675	431675	type	True	78.045	156	814	95	below_threshold
Pseudidiomarina salinarum	strain=ISL-52	GCA_003987105.1	435908	435908	type	True	77.8991	162	814	95	below_threshold
Pseudidiomarina salinarum	strain=ISL-52	GCA_000753715.1	435908	435908	type	True	77.7091	158	814	95	below_threshold
Arsukibacterium indicum	strain=SM2107	GCA_019100565.1	2848612	2848612	type	True	77.1237	56	814	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:26:56,826] [INFO] DFAST Taxonomy check result was written to GCF_003999375.1_ASM399937v1_genomic.fna/tc_result.tsv
[2024-01-24 15:26:56,827] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:26:56,827] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:26:56,827] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged545a0c-a8db-4e05-b643-54a856c55aba/dqc_reference/checkm_data
[2024-01-24 15:26:56,829] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:26:56,857] [INFO] Task started: CheckM
[2024-01-24 15:26:56,857] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003999375.1_ASM399937v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003999375.1_ASM399937v1_genomic.fna/checkm_input GCF_003999375.1_ASM399937v1_genomic.fna/checkm_result
[2024-01-24 15:27:23,437] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:23,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:23,463] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:23,463] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:23,464] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003999375.1_ASM399937v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:23,464] [INFO] Task started: Blastn
[2024-01-24 15:27:23,464] [INFO] Running command: blastn -query GCF_003999375.1_ASM399937v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged545a0c-a8db-4e05-b643-54a856c55aba/dqc_reference/reference_markers_gtdb.fasta -out GCF_003999375.1_ASM399937v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:24,675] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:24,684] [INFO] Selected 19 target genomes.
[2024-01-24 15:27:24,685] [INFO] Target genome list was writen to GCF_003999375.1_ASM399937v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:24,721] [INFO] Task started: fastANI
[2024-01-24 15:27:24,721] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0fc328d-86d0-4e27-b542-88a9b67af306/GCF_003999375.1_ASM399937v1_genomic.fna.gz --refList GCF_003999375.1_ASM399937v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003999375.1_ASM399937v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:35,636] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:35,649] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:35,649] [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_003999375.1	s__Pseudidiomarina mangrovi	100.0	814	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002423905.1	s__Pseudidiomarina sp002423905	81.4866	390	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182315.1	s__Pseudidiomarina maritima_A	79.19	179	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	98.70	97.84	0.93	0.89	6	-
GCF_003987045.1	s__Pseudidiomarina marina	78.777	166	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.46	97.46	0.94	0.94	2	-
GCF_900116895.1	s__Pseudidiomarina donghaiensis	78.6534	217	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003987435.1	s__Pseudidiomarina taiwanensis	78.5746	144	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004025325.1	s__Pseudidiomarina gelatinasegens	78.4287	180	814	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	78.3652	182	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018222985.1	s__Pseudidiomarina sp018222985	78.2086	187	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987395.1	s__Pseudidiomarina aquimaris	78.176	169	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.26	97.14	0.86	0.77	3	-
GCF_003987225.1	s__Pseudidiomarina homiensis	78.1683	148	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987275.1	s__Idiomarina seosinensis	78.0625	64	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423165.1	s__Pseudidiomarina sediminum	78.045	156	814	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000753715.1	s__Pseudidiomarina salinarum	77.7035	159	814	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 15:27:35,651] [INFO] GTDB search result was written to GCF_003999375.1_ASM399937v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:35,651] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:35,655] [INFO] DFAST_QC result json was written to GCF_003999375.1_ASM399937v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:35,656] [INFO] DFAST_QC completed!
[2024-01-24 15:27:35,656] [INFO] Total running time: 0h1m3s