[2024-01-24 12:15:04,042] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:04,044] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:04,045] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf8e1554-9d9e-4b69-a39c-26848abc7821/dqc_reference
[2024-01-24 12:15:05,443] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:05,444] [INFO] Task started: Prodigal
[2024-01-24 12:15:05,444] [INFO] Running command: gunzip -c /var/lib/cwl/stg32ef3c5e-b584-4fd2-b29e-1d2001cce3f9/GCF_005434965.1_ASM543496v1_genomic.fna.gz | prodigal -d GCF_005434965.1_ASM543496v1_genomic.fna/cds.fna -a GCF_005434965.1_ASM543496v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:18,800] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:18,801] [INFO] Task started: HMMsearch
[2024-01-24 12:15:18,801] [INFO] Running command: hmmsearch --tblout GCF_005434965.1_ASM543496v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf8e1554-9d9e-4b69-a39c-26848abc7821/dqc_reference/reference_markers.hmm GCF_005434965.1_ASM543496v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:19,122] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:19,124] [INFO] Found 6/6 markers.
[2024-01-24 12:15:19,166] [INFO] Query marker FASTA was written to GCF_005434965.1_ASM543496v1_genomic.fna/markers.fasta
[2024-01-24 12:15:19,167] [INFO] Task started: Blastn
[2024-01-24 12:15:19,167] [INFO] Running command: blastn -query GCF_005434965.1_ASM543496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf8e1554-9d9e-4b69-a39c-26848abc7821/dqc_reference/reference_markers.fasta -out GCF_005434965.1_ASM543496v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:20,124] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:20,129] [INFO] Selected 28 target genomes.
[2024-01-24 12:15:20,129] [INFO] Target genome list was writen to GCF_005434965.1_ASM543496v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:20,139] [INFO] Task started: fastANI
[2024-01-24 12:15:20,139] [INFO] Running command: fastANI --query /var/lib/cwl/stg32ef3c5e-b584-4fd2-b29e-1d2001cce3f9/GCF_005434965.1_ASM543496v1_genomic.fna.gz --refList GCF_005434965.1_ASM543496v1_genomic.fna/target_genomes.txt --output GCF_005434965.1_ASM543496v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:42,650] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:42,651] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf8e1554-9d9e-4b69-a39c-26848abc7821/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:42,651] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf8e1554-9d9e-4b69-a39c-26848abc7821/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:42,671] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:42,672] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:42,672] [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
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	79.6693	587	1433	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	79.4239	604	1433	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	79.417	575	1433	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	79.393	573	1433	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	79.3677	577	1433	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	79.1906	575	1433	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	79.1694	495	1433	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	79.1609	593	1433	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	79.1519	520	1433	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	79.0671	496	1433	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	78.8326	520	1433	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	78.7655	472	1433	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	78.7239	514	1433	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	78.6173	513	1433	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	78.5985	475	1433	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	78.421	449	1433	95	below_threshold
Roseovarius aestuariivivens	strain=GHTF-24	GCA_004761875.1	1888910	1888910	type	True	78.4005	420	1433	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	78.3704	428	1433	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	78.3579	448	1433	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.343	387	1433	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.3278	414	1433	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.2871	437	1433	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.2291	493	1433	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	78.1076	429	1433	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	78.0866	408	1433	95	below_threshold
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	78.0833	403	1433	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.155	258	1433	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.1138	276	1433	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:42,673] [INFO] DFAST Taxonomy check result was written to GCF_005434965.1_ASM543496v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:42,676] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:42,676] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:42,676] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf8e1554-9d9e-4b69-a39c-26848abc7821/dqc_reference/checkm_data
[2024-01-24 12:15:42,677] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:42,722] [INFO] Task started: CheckM
[2024-01-24 12:15:42,722] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005434965.1_ASM543496v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005434965.1_ASM543496v1_genomic.fna/checkm_input GCF_005434965.1_ASM543496v1_genomic.fna/checkm_result
[2024-01-24 12:16:24,473] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:24,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:24,501] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:24,501] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:24,502] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005434965.1_ASM543496v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:24,502] [INFO] Task started: Blastn
[2024-01-24 12:16:24,502] [INFO] Running command: blastn -query GCF_005434965.1_ASM543496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf8e1554-9d9e-4b69-a39c-26848abc7821/dqc_reference/reference_markers_gtdb.fasta -out GCF_005434965.1_ASM543496v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:26,076] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:26,082] [INFO] Selected 15 target genomes.
[2024-01-24 12:16:26,082] [INFO] Target genome list was writen to GCF_005434965.1_ASM543496v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:26,092] [INFO] Task started: fastANI
[2024-01-24 12:16:26,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg32ef3c5e-b584-4fd2-b29e-1d2001cce3f9/GCF_005434965.1_ASM543496v1_genomic.fna.gz --refList GCF_005434965.1_ASM543496v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005434965.1_ASM543496v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:39,043] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:39,058] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:39,058] [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_005434965.1	s__Marimonas lutisalis	100.0	1433	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011389685.1	s__Aquicoccus sp011389685	81.9695	713	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aquicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369105.1	s__Aquicoccus porphyridii	81.7805	790	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aquicoccus	95.0	99.99	99.99	1.00	1.00	2	-
GCA_001314705.1	s__Aquicoccus sp001314705	81.3902	725	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aquicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	79.997	665	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	79.6797	586	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	79.4074	607	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728195.1	s__Roseovarius indicus	79.4047	574	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_004358185.1	s__Antarcticimicrobium luteum	79.1529	595	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008555.2	s__Pukyongiella litopenaei	79.0047	539	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pukyongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789075.1	s__Pseudooceanicola pacificus	78.9827	347	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002917925.1	s__Roseovarius confluentis	78.7393	512	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCF_000153725.1	s__Salipiger bermudensis	78.6469	510	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_000442255.1	s__Salipiger mucosus	78.544	495	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004761875.1	s__Roseovarius aestuariivivens	78.4096	419	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:39,060] [INFO] GTDB search result was written to GCF_005434965.1_ASM543496v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:39,060] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:39,065] [INFO] DFAST_QC result json was written to GCF_005434965.1_ASM543496v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:39,066] [INFO] DFAST_QC completed!
[2024-01-24 12:16:39,066] [INFO] Total running time: 0h1m35s