[2024-01-25 20:19:05,764] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:19:05,765] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:19:05,766] [INFO] DQC Reference Directory: /var/lib/cwl/stg1997e608-8b5c-44ad-8055-610a2df9d0e5/dqc_reference
[2024-01-25 20:19:06,918] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:19:06,919] [INFO] Task started: Prodigal
[2024-01-25 20:19:06,919] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa2ee2a5-1317-4647-affb-35d5a6132a40/GCF_024721115.1_ASM2472111v1_genomic.fna.gz | prodigal -d GCF_024721115.1_ASM2472111v1_genomic.fna/cds.fna -a GCF_024721115.1_ASM2472111v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:19:20,646] [INFO] Task succeeded: Prodigal
[2024-01-25 20:19:20,646] [INFO] Task started: HMMsearch
[2024-01-25 20:19:20,646] [INFO] Running command: hmmsearch --tblout GCF_024721115.1_ASM2472111v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1997e608-8b5c-44ad-8055-610a2df9d0e5/dqc_reference/reference_markers.hmm GCF_024721115.1_ASM2472111v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:19:20,923] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:19:20,924] [INFO] Found 6/6 markers.
[2024-01-25 20:19:20,971] [INFO] Query marker FASTA was written to GCF_024721115.1_ASM2472111v1_genomic.fna/markers.fasta
[2024-01-25 20:19:20,972] [INFO] Task started: Blastn
[2024-01-25 20:19:20,972] [INFO] Running command: blastn -query GCF_024721115.1_ASM2472111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1997e608-8b5c-44ad-8055-610a2df9d0e5/dqc_reference/reference_markers.fasta -out GCF_024721115.1_ASM2472111v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:21,881] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:21,883] [INFO] Selected 15 target genomes.
[2024-01-25 20:19:21,884] [INFO] Target genome list was writen to GCF_024721115.1_ASM2472111v1_genomic.fna/target_genomes.txt
[2024-01-25 20:19:21,898] [INFO] Task started: fastANI
[2024-01-25 20:19:21,898] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa2ee2a5-1317-4647-affb-35d5a6132a40/GCF_024721115.1_ASM2472111v1_genomic.fna.gz --refList GCF_024721115.1_ASM2472111v1_genomic.fna/target_genomes.txt --output GCF_024721115.1_ASM2472111v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:19:36,759] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:36,759] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1997e608-8b5c-44ad-8055-610a2df9d0e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:19:36,760] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1997e608-8b5c-44ad-8055-610a2df9d0e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:19:36,769] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:19:36,769] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:19:36,770] [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
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	83.6814	1024	1741	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	83.6732	982	1741	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	83.6535	1013	1741	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	83.5735	1073	1741	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	81.8772	835	1741	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	81.4088	809	1741	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	81.3521	861	1741	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	81.304	858	1741	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	80.8944	822	1741	95	below_threshold
Salipiger aestuarii	strain=DSM 22011	GCA_003259905.1	568098	568098	type	True	80.7923	828	1741	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	79.5589	706	1741	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	79.5565	712	1741	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	79.031	575	1741	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	78.8572	583	1741	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.7536	336	1741	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:19:36,772] [INFO] DFAST Taxonomy check result was written to GCF_024721115.1_ASM2472111v1_genomic.fna/tc_result.tsv
[2024-01-25 20:19:36,772] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:19:36,773] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:19:36,773] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1997e608-8b5c-44ad-8055-610a2df9d0e5/dqc_reference/checkm_data
[2024-01-25 20:19:36,774] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:19:36,825] [INFO] Task started: CheckM
[2024-01-25 20:19:36,826] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024721115.1_ASM2472111v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024721115.1_ASM2472111v1_genomic.fna/checkm_input GCF_024721115.1_ASM2472111v1_genomic.fna/checkm_result
[2024-01-25 20:20:25,772] [INFO] Task succeeded: CheckM
[2024-01-25 20:20:25,773] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:20:25,793] [INFO] ===== Completeness check finished =====
[2024-01-25 20:20:25,794] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:20:25,795] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024721115.1_ASM2472111v1_genomic.fna/markers.fasta)
[2024-01-25 20:20:25,795] [INFO] Task started: Blastn
[2024-01-25 20:20:25,795] [INFO] Running command: blastn -query GCF_024721115.1_ASM2472111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1997e608-8b5c-44ad-8055-610a2df9d0e5/dqc_reference/reference_markers_gtdb.fasta -out GCF_024721115.1_ASM2472111v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:27,473] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:27,476] [INFO] Selected 10 target genomes.
[2024-01-25 20:20:27,476] [INFO] Target genome list was writen to GCF_024721115.1_ASM2472111v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:20:27,487] [INFO] Task started: fastANI
[2024-01-25 20:20:27,487] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa2ee2a5-1317-4647-affb-35d5a6132a40/GCF_024721115.1_ASM2472111v1_genomic.fna.gz --refList GCF_024721115.1_ASM2472111v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024721115.1_ASM2472111v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:20:40,654] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:40,661] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:20:40,662] [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_017311415.1	s__Salipiger abyssi_A	87.8802	1148	1741	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	87.6118	1108	1741	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969385.1	s__Salipiger profundus	83.6697	1012	1741	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
GCF_000153725.1	s__Salipiger bermudensis	83.6555	1026	1741	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_900102075.1	s__Salipiger thiooxidans	83.5591	1075	1741	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_900100085.1	s__Salipiger marinus	81.8274	841	1741	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_000442255.1	s__Salipiger mucosus	81.6325	854	1741	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687105.1	s__Salipiger sp001687105	81.5668	843	1741	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	96.47	96.47	0.82	0.82	2	-
GCF_003111685.1	s__Salipiger pacificus_A	81.2202	806	1741	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.69	97.64	0.90	0.89	3	-
GCF_900101505.1	s__Mameliella alba	79.5675	704	1741	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
--------------------------------------------------------------------------------
[2024-01-25 20:20:40,663] [INFO] GTDB search result was written to GCF_024721115.1_ASM2472111v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:20:40,663] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:20:40,666] [INFO] DFAST_QC result json was written to GCF_024721115.1_ASM2472111v1_genomic.fna/dqc_result.json
[2024-01-25 20:20:40,666] [INFO] DFAST_QC completed!
[2024-01-25 20:20:40,666] [INFO] Total running time: 0h1m35s