[2024-01-24 14:03:06,511] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:06,516] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:06,516] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc3e9abc-432f-42ba-bbaf-69b46865fadf/dqc_reference
[2024-01-24 14:03:07,840] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:07,841] [INFO] Task started: Prodigal
[2024-01-24 14:03:07,842] [INFO] Running command: gunzip -c /var/lib/cwl/stge5baf72b-eaf2-4018-a9c8-8b58c11f07c9/GCF_014899185.1_ASM1489918v1_genomic.fna.gz | prodigal -d GCF_014899185.1_ASM1489918v1_genomic.fna/cds.fna -a GCF_014899185.1_ASM1489918v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:21,165] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:21,166] [INFO] Task started: HMMsearch
[2024-01-24 14:03:21,166] [INFO] Running command: hmmsearch --tblout GCF_014899185.1_ASM1489918v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc3e9abc-432f-42ba-bbaf-69b46865fadf/dqc_reference/reference_markers.hmm GCF_014899185.1_ASM1489918v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:21,504] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:21,505] [INFO] Found 6/6 markers.
[2024-01-24 14:03:21,570] [INFO] Query marker FASTA was written to GCF_014899185.1_ASM1489918v1_genomic.fna/markers.fasta
[2024-01-24 14:03:21,571] [INFO] Task started: Blastn
[2024-01-24 14:03:21,571] [INFO] Running command: blastn -query GCF_014899185.1_ASM1489918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc3e9abc-432f-42ba-bbaf-69b46865fadf/dqc_reference/reference_markers.fasta -out GCF_014899185.1_ASM1489918v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:22,550] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:22,553] [INFO] Selected 15 target genomes.
[2024-01-24 14:03:22,553] [INFO] Target genome list was writen to GCF_014899185.1_ASM1489918v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:22,567] [INFO] Task started: fastANI
[2024-01-24 14:03:22,567] [INFO] Running command: fastANI --query /var/lib/cwl/stge5baf72b-eaf2-4018-a9c8-8b58c11f07c9/GCF_014899185.1_ASM1489918v1_genomic.fna.gz --refList GCF_014899185.1_ASM1489918v1_genomic.fna/target_genomes.txt --output GCF_014899185.1_ASM1489918v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:35,534] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:35,534] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc3e9abc-432f-42ba-bbaf-69b46865fadf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:35,535] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc3e9abc-432f-42ba-bbaf-69b46865fadf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:35,547] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:35,547] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:35,547] [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
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	100.0	1455	1455	95	conclusive
Pseudopuniceibacterium sediminis	strain=CY03	GCA_003575965.1	2211117	2211117	type	True	85.4427	1044	1455	95	below_threshold
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	80.1168	686	1455	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	80.0054	677	1455	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	79.8355	671	1455	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	79.8213	676	1455	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	79.7178	685	1455	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	79.6567	686	1455	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	78.5241	541	1455	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	78.4839	553	1455	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.9155	530	1455	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.7259	385	1455	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.4845	313	1455	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.389	345	1455	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.269	300	1455	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:35,549] [INFO] DFAST Taxonomy check result was written to GCF_014899185.1_ASM1489918v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:35,550] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:35,550] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:35,550] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc3e9abc-432f-42ba-bbaf-69b46865fadf/dqc_reference/checkm_data
[2024-01-24 14:03:35,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:35,592] [INFO] Task started: CheckM
[2024-01-24 14:03:35,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014899185.1_ASM1489918v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014899185.1_ASM1489918v1_genomic.fna/checkm_input GCF_014899185.1_ASM1489918v1_genomic.fna/checkm_result
[2024-01-24 14:04:22,392] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:22,393] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:22,415] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:22,415] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:22,415] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014899185.1_ASM1489918v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:22,416] [INFO] Task started: Blastn
[2024-01-24 14:04:22,416] [INFO] Running command: blastn -query GCF_014899185.1_ASM1489918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc3e9abc-432f-42ba-bbaf-69b46865fadf/dqc_reference/reference_markers_gtdb.fasta -out GCF_014899185.1_ASM1489918v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:23,850] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:23,853] [INFO] Selected 10 target genomes.
[2024-01-24 14:04:23,853] [INFO] Target genome list was writen to GCF_014899185.1_ASM1489918v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:23,875] [INFO] Task started: fastANI
[2024-01-24 14:04:23,875] [INFO] Running command: fastANI --query /var/lib/cwl/stge5baf72b-eaf2-4018-a9c8-8b58c11f07c9/GCF_014899185.1_ASM1489918v1_genomic.fna.gz --refList GCF_014899185.1_ASM1489918v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014899185.1_ASM1489918v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:33,881] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:33,895] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:33,896] [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_014899185.1	s__Pseudooceanicola antarcticus_A	100.0	1455	1455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003575965.1	s__Pseudooceanicola sediminis	85.4427	1044	1455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.95	99.95	0.93	0.93	2	-
GCF_003590145.2	s__Pseudooceanicola algae	80.132	686	1455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	79.969	629	1455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	79.9013	687	1455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
GCF_011806405.1	s__Pseudooceanicola sp011806405	79.8867	663	1455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215355.1	s__Pseudooceanicola antarcticus	79.8352	671	1455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	79.7676	711	1455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCF_002786295.1	s__Pseudooceanicola marinus	79.716	684	1455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	78.5285	542	1455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:33,897] [INFO] GTDB search result was written to GCF_014899185.1_ASM1489918v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:33,898] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:33,901] [INFO] DFAST_QC result json was written to GCF_014899185.1_ASM1489918v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:33,901] [INFO] DFAST_QC completed!
[2024-01-24 14:04:33,902] [INFO] Total running time: 0h1m27s