[2024-01-24 13:40:43,224] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:43,230] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:43,230] [INFO] DQC Reference Directory: /var/lib/cwl/stg15809f83-e1da-48f5-8057-094ea1eef66a/dqc_reference
[2024-01-24 13:40:44,620] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:44,621] [INFO] Task started: Prodigal
[2024-01-24 13:40:44,621] [INFO] Running command: gunzip -c /var/lib/cwl/stg62d36fd0-af83-402f-923f-62a7a2b947eb/GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna/cds.fna -a GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:54,980] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:54,980] [INFO] Task started: HMMsearch
[2024-01-24 13:40:54,981] [INFO] Running command: hmmsearch --tblout GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15809f83-e1da-48f5-8057-094ea1eef66a/dqc_reference/reference_markers.hmm GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:55,293] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:55,295] [INFO] Found 6/6 markers.
[2024-01-24 13:40:55,325] [INFO] Query marker FASTA was written to GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:40:55,325] [INFO] Task started: Blastn
[2024-01-24 13:40:55,325] [INFO] Running command: blastn -query GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg15809f83-e1da-48f5-8057-094ea1eef66a/dqc_reference/reference_markers.fasta -out GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:56,557] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:56,560] [INFO] Selected 23 target genomes.
[2024-01-24 13:40:56,561] [INFO] Target genome list was writen to GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:40:56,573] [INFO] Task started: fastANI
[2024-01-24 13:40:56,574] [INFO] Running command: fastANI --query /var/lib/cwl/stg62d36fd0-af83-402f-923f-62a7a2b947eb/GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna.gz --refList GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:13,597] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:13,597] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15809f83-e1da-48f5-8057-094ea1eef66a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:13,598] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15809f83-e1da-48f5-8057-094ea1eef66a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:13,616] [INFO] Found 23 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:13,616] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:13,616] [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
Meinhardsimonia xiamenensis	strain=CGMCC 1.10789	GCA_900102905.1	990712	990712	type	True	100.0	1029	1031	95	conclusive
Meinhardsimonia xiamenensis	strain=DSM 24422	GCA_003001835.1	990712	990712	type	True	99.9972	1026	1031	95	conclusive
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.0805	487	1031	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.5915	414	1031	95	below_threshold
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	78.4749	427	1031	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.4448	391	1031	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	78.4271	375	1031	95	below_threshold
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	78.3427	389	1031	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.3322	406	1031	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	78.323	423	1031	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	78.3101	417	1031	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	78.2529	418	1031	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	78.2315	396	1031	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	78.054	376	1031	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	78.0494	332	1031	95	below_threshold
Celeribacter indicus	strain=P73	GCA_000819565.1	1208324	1208324	type	True	78.0456	376	1031	95	below_threshold
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	78.0345	374	1031	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.9992	344	1031	95	below_threshold
Celeribacter indicus	strain=P73	GCA_900106965.1	1208324	1208324	type	True	77.9435	380	1031	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.8832	328	1031	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	77.8333	367	1031	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.7968	321	1031	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.5412	309	1031	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:13,618] [INFO] DFAST Taxonomy check result was written to GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:41:13,618] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:13,619] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:13,619] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15809f83-e1da-48f5-8057-094ea1eef66a/dqc_reference/checkm_data
[2024-01-24 13:41:13,620] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:13,656] [INFO] Task started: CheckM
[2024-01-24 13:41:13,657] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna/checkm_input GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:42:06,825] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:06,830] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:06,849] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:06,849] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:06,850] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:42:06,850] [INFO] Task started: Blastn
[2024-01-24 13:42:06,850] [INFO] Running command: blastn -query GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg15809f83-e1da-48f5-8057-094ea1eef66a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:08,884] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:08,889] [INFO] Selected 21 target genomes.
[2024-01-24 13:42:08,889] [INFO] Target genome list was writen to GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:08,928] [INFO] Task started: fastANI
[2024-01-24 13:42:08,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg62d36fd0-af83-402f-923f-62a7a2b947eb/GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna.gz --refList GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:22,056] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:22,086] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:22,086] [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_900102905.1	s__Meinhardsimonia xiamenensis	100.0	1029	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Meinhardsimonia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_015487335.1	s__S012-89 sp015487335	79.6381	383	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__S012-89	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	79.2513	513	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102015.1	s__Limimaricola pyoseonensis	79.0947	484	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385555.1	s__Rhodosalinus sediminis	79.0719	460	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003694465.1	s__Muriiphilus sp003694465	78.8786	257	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003298775.1	s__Rhodosalinus sp003298775	78.8347	483	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172235.1	s__Pseudoruegeria aquimaris	78.7145	461	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131945.1	s__Pararhodobacter sp007131945	78.7079	346	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	99.16	99.15	0.86	0.82	3	-
GCF_003340565.1	s__HLUCCA09 sp003340565	78.6548	476	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342445.1	s__Rhodovulum euryhalinum	78.581	415	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172345.1	s__Limimaricola soesokkakensis	78.5652	419	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001314685.1	s__HLUCCA09 sp001314685	78.4648	408	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002834145.1	s__Roseovarius salinarum	78.4527	397	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842835.1	s__PHEG01 sp002842835	78.4525	270	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__PHEG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002967695.1	s__Rhodobaculum sp002967695	78.4478	404	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003558415.1	s__Rhodobaculum sp003558415	78.3879	218	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002166865.1	s__Roseovarius sp002166865	78.3504	394	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649175.1	s__Rhodovulum strictum	78.326	406	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551745.1	s__Rhodobaculum sp003551745	78.2095	292	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009904055.1	s__Rubellimicrobium sp009904055	78.0923	359	1031	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:22,088] [INFO] GTDB search result was written to GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:22,089] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:22,097] [INFO] DFAST_QC result json was written to GCF_900102905.1_IMG-taxon_2663762716_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:42:22,098] [INFO] DFAST_QC completed!
[2024-01-24 13:42:22,098] [INFO] Total running time: 0h1m39s