[2024-01-24 11:51:11,272] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:11,274] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:11,274] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b392ab1-3453-4874-899a-879631889823/dqc_reference
[2024-01-24 11:51:12,688] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:12,689] [INFO] Task started: Prodigal
[2024-01-24 11:51:12,690] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2823c70-1641-47ae-9fc1-9400db1de742/GCF_019218285.1_ASM1921828v1_genomic.fna.gz | prodigal -d GCF_019218285.1_ASM1921828v1_genomic.fna/cds.fna -a GCF_019218285.1_ASM1921828v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:29,777] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:29,777] [INFO] Task started: HMMsearch
[2024-01-24 11:51:29,777] [INFO] Running command: hmmsearch --tblout GCF_019218285.1_ASM1921828v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b392ab1-3453-4874-899a-879631889823/dqc_reference/reference_markers.hmm GCF_019218285.1_ASM1921828v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:30,072] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:30,074] [INFO] Found 6/6 markers.
[2024-01-24 11:51:30,124] [INFO] Query marker FASTA was written to GCF_019218285.1_ASM1921828v1_genomic.fna/markers.fasta
[2024-01-24 11:51:30,124] [INFO] Task started: Blastn
[2024-01-24 11:51:30,124] [INFO] Running command: blastn -query GCF_019218285.1_ASM1921828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b392ab1-3453-4874-899a-879631889823/dqc_reference/reference_markers.fasta -out GCF_019218285.1_ASM1921828v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:30,964] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:30,968] [INFO] Selected 19 target genomes.
[2024-01-24 11:51:30,968] [INFO] Target genome list was writen to GCF_019218285.1_ASM1921828v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:30,975] [INFO] Task started: fastANI
[2024-01-24 11:51:30,975] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2823c70-1641-47ae-9fc1-9400db1de742/GCF_019218285.1_ASM1921828v1_genomic.fna.gz --refList GCF_019218285.1_ASM1921828v1_genomic.fna/target_genomes.txt --output GCF_019218285.1_ASM1921828v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:47,919] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:47,919] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b392ab1-3453-4874-899a-879631889823/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:47,919] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b392ab1-3453-4874-899a-879631889823/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:47,935] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:47,935] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:47,935] [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
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	100.0	1697	1697	95	conclusive
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	82.797	1117	1697	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	82.7749	1115	1697	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.4669	578	1697	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	78.3866	506	1697	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	78.3864	500	1697	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.3742	559	1697	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	78.2551	525	1697	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	78.1311	431	1697	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	78.1025	495	1697	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.0612	434	1697	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	78.0255	451	1697	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.6172	362	1697	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	77.5677	273	1697	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	77.3845	343	1697	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	77.2572	335	1697	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.08	298	1697	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_003149265.1	475081	475081	type	True	77.0044	327	1697	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_900116765.1	475081	475081	type	True	76.997	328	1697	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:47,937] [INFO] DFAST Taxonomy check result was written to GCF_019218285.1_ASM1921828v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:47,937] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:47,938] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:47,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b392ab1-3453-4874-899a-879631889823/dqc_reference/checkm_data
[2024-01-24 11:51:47,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:47,989] [INFO] Task started: CheckM
[2024-01-24 11:51:47,989] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019218285.1_ASM1921828v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019218285.1_ASM1921828v1_genomic.fna/checkm_input GCF_019218285.1_ASM1921828v1_genomic.fna/checkm_result
[2024-01-24 11:52:42,236] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:42,237] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:42,257] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:42,257] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:42,258] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019218285.1_ASM1921828v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:42,258] [INFO] Task started: Blastn
[2024-01-24 11:52:42,258] [INFO] Running command: blastn -query GCF_019218285.1_ASM1921828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b392ab1-3453-4874-899a-879631889823/dqc_reference/reference_markers_gtdb.fasta -out GCF_019218285.1_ASM1921828v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:43,463] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:43,467] [INFO] Selected 12 target genomes.
[2024-01-24 11:52:43,467] [INFO] Target genome list was writen to GCF_019218285.1_ASM1921828v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:43,474] [INFO] Task started: fastANI
[2024-01-24 11:52:43,474] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2823c70-1641-47ae-9fc1-9400db1de742/GCF_019218285.1_ASM1921828v1_genomic.fna.gz --refList GCF_019218285.1_ASM1921828v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019218285.1_ASM1921828v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:54,541] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:54,551] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:54,552] [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
GCA_019218285.1	s__DP3N28-2 sp019218285	100.0	1697	1697	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__DP3N28-2	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900101505.1	s__Mameliella alba	82.7579	1117	1697	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCF_900188425.1	s__Antarctobacter heliothermus	81.2883	983	1697	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarctobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184945.1	s__Maliponia aquimaris	81.0499	964	1697	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maliponia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237555.1	s__Antarctobacter heliothermus_B	80.8521	958	1697	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarctobacter	95.0	97.31	97.29	0.90	0.89	3	-
GCF_001482405.1	s__Ponticoccus marisrubri	79.7858	796	1697	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667315.2	s__Tropicibacter sp003667315	79.6821	750	1697	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	79.2498	724	1697	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	78.7851	634	1697	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016888515.1	s__Shimia_A biformata	78.2024	455	1697	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302505.1	s__Pseudoprimorskyibacter insulae	78.0336	450	1697	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoprimorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403795.1	s__Jannaschia donghaensis	76.9369	247	1697	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:54,553] [INFO] GTDB search result was written to GCF_019218285.1_ASM1921828v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:54,554] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:54,557] [INFO] DFAST_QC result json was written to GCF_019218285.1_ASM1921828v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:54,557] [INFO] DFAST_QC completed!
[2024-01-24 11:52:54,557] [INFO] Total running time: 0h1m43s