[2024-01-24 13:19:10,499] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:10,500] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:10,500] [INFO] DQC Reference Directory: /var/lib/cwl/stg8badffdc-5010-4459-bef5-682d7427bb44/dqc_reference
[2024-01-24 13:19:11,884] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:11,885] [INFO] Task started: Prodigal
[2024-01-24 13:19:11,885] [INFO] Running command: gunzip -c /var/lib/cwl/stgca88817a-008e-43d3-bac0-64c5a3a4034c/GCF_007923445.1_ASM792344v1_genomic.fna.gz | prodigal -d GCF_007923445.1_ASM792344v1_genomic.fna/cds.fna -a GCF_007923445.1_ASM792344v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:27,969] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:27,969] [INFO] Task started: HMMsearch
[2024-01-24 13:19:27,969] [INFO] Running command: hmmsearch --tblout GCF_007923445.1_ASM792344v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8badffdc-5010-4459-bef5-682d7427bb44/dqc_reference/reference_markers.hmm GCF_007923445.1_ASM792344v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:28,369] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:28,370] [INFO] Found 6/6 markers.
[2024-01-24 13:19:28,416] [INFO] Query marker FASTA was written to GCF_007923445.1_ASM792344v1_genomic.fna/markers.fasta
[2024-01-24 13:19:28,417] [INFO] Task started: Blastn
[2024-01-24 13:19:28,417] [INFO] Running command: blastn -query GCF_007923445.1_ASM792344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8badffdc-5010-4459-bef5-682d7427bb44/dqc_reference/reference_markers.fasta -out GCF_007923445.1_ASM792344v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:29,495] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:29,499] [INFO] Selected 21 target genomes.
[2024-01-24 13:19:29,499] [INFO] Target genome list was writen to GCF_007923445.1_ASM792344v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:29,538] [INFO] Task started: fastANI
[2024-01-24 13:19:29,539] [INFO] Running command: fastANI --query /var/lib/cwl/stgca88817a-008e-43d3-bac0-64c5a3a4034c/GCF_007923445.1_ASM792344v1_genomic.fna.gz --refList GCF_007923445.1_ASM792344v1_genomic.fna/target_genomes.txt --output GCF_007923445.1_ASM792344v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:50,615] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:50,616] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8badffdc-5010-4459-bef5-682d7427bb44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:50,616] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8badffdc-5010-4459-bef5-682d7427bb44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:50,639] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:50,639] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:50,640] [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
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	100.0	1573	1574	95	conclusive
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	81.4915	863	1574	95	below_threshold
Puniceibacterium antarcticum	strain=SM1211	GCA_002760615.1	1206336	1206336	type	True	81.1637	819	1574	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.6329	616	1574	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	78.5549	584	1574	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	78.5015	494	1574	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.501	538	1574	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	78.4486	428	1574	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	78.2799	548	1574	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	78.2756	549	1574	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.2198	474	1574	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	78.2084	418	1574	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.0061	439	1574	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.9828	449	1574	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.9802	453	1574	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.7495	394	1574	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	77.683	352	1574	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.632	316	1574	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	77.4561	318	1574	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.4197	305	1574	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	77.3953	322	1574	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:50,650] [INFO] DFAST Taxonomy check result was written to GCF_007923445.1_ASM792344v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:50,652] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:50,653] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:50,653] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8badffdc-5010-4459-bef5-682d7427bb44/dqc_reference/checkm_data
[2024-01-24 13:19:50,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:50,711] [INFO] Task started: CheckM
[2024-01-24 13:19:50,711] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007923445.1_ASM792344v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007923445.1_ASM792344v1_genomic.fna/checkm_input GCF_007923445.1_ASM792344v1_genomic.fna/checkm_result
[2024-01-24 13:20:45,981] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:45,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:46,008] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:46,008] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:46,009] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007923445.1_ASM792344v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:46,009] [INFO] Task started: Blastn
[2024-01-24 13:20:46,009] [INFO] Running command: blastn -query GCF_007923445.1_ASM792344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8badffdc-5010-4459-bef5-682d7427bb44/dqc_reference/reference_markers_gtdb.fasta -out GCF_007923445.1_ASM792344v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:47,910] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:47,914] [INFO] Selected 17 target genomes.
[2024-01-24 13:20:47,914] [INFO] Target genome list was writen to GCF_007923445.1_ASM792344v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:47,962] [INFO] Task started: fastANI
[2024-01-24 13:20:47,962] [INFO] Running command: fastANI --query /var/lib/cwl/stgca88817a-008e-43d3-bac0-64c5a3a4034c/GCF_007923445.1_ASM792344v1_genomic.fna.gz --refList GCF_007923445.1_ASM792344v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007923445.1_ASM792344v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:04,386] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:04,406] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:21:04,406] [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_007923445.1	s__Puniceibacterium confluentis	100.0	1573	1574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900188035.1	s__Puniceibacterium sediminis	81.4855	863	1574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002760615.1	s__Puniceibacterium antarcticum	81.1623	820	1574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344785.1	s__Puniceibacterium profundi	79.9037	733	1574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001038505.1	s__Puniceibacterium sp001038505	79.4964	698	1574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	78.7872	554	1574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	78.7609	556	1574	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_900100085.1	s__Salipiger marinus	78.6126	619	1574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_014637725.1	s__Marivita lacus	78.4861	496	1574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	78.4669	426	1574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116195.1	s__Salipiger pacificus	78.2617	551	1574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	78.2058	467	1574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	78.2025	477	1574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_900101475.1	s__Ruegeria_B marina	78.171	423	1574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	78.0133	457	1574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	77.9912	553	1574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196795.1	s__Sagittula marina	77.6557	355	1574	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:21:04,408] [INFO] GTDB search result was written to GCF_007923445.1_ASM792344v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:04,408] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:04,413] [INFO] DFAST_QC result json was written to GCF_007923445.1_ASM792344v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:04,413] [INFO] DFAST_QC completed!
[2024-01-24 13:21:04,413] [INFO] Total running time: 0h1m54s