[2023-06-30 12:41:58,224] [INFO] DFAST_QC pipeline started.
[2023-06-30 12:41:58,228] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 12:41:58,228] [INFO] DQC Reference Directory: /var/lib/cwl/stgde6d5402-9205-4370-8542-4a1cfa8adb93/dqc_reference
[2023-06-30 12:41:59,524] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 12:41:59,525] [INFO] Task started: Prodigal
[2023-06-30 12:41:59,525] [INFO] Running command: gunzip -c /var/lib/cwl/stg06f07d28-e37b-4ac2-b3ad-3556be2ba8bc/GCA_007129065.1_ASM712906v1_genomic.fna.gz | prodigal -d GCA_007129065.1_ASM712906v1_genomic.fna/cds.fna -a GCA_007129065.1_ASM712906v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 12:42:07,312] [INFO] Task succeeded: Prodigal
[2023-06-30 12:42:07,313] [INFO] Task started: HMMsearch
[2023-06-30 12:42:07,313] [INFO] Running command: hmmsearch --tblout GCA_007129065.1_ASM712906v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde6d5402-9205-4370-8542-4a1cfa8adb93/dqc_reference/reference_markers.hmm GCA_007129065.1_ASM712906v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 12:42:07,590] [INFO] Task succeeded: HMMsearch
[2023-06-30 12:42:07,591] [INFO] Found 6/6 markers.
[2023-06-30 12:42:07,619] [INFO] Query marker FASTA was written to GCA_007129065.1_ASM712906v1_genomic.fna/markers.fasta
[2023-06-30 12:42:07,619] [INFO] Task started: Blastn
[2023-06-30 12:42:07,619] [INFO] Running command: blastn -query GCA_007129065.1_ASM712906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde6d5402-9205-4370-8542-4a1cfa8adb93/dqc_reference/reference_markers.fasta -out GCA_007129065.1_ASM712906v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:42:08,436] [INFO] Task succeeded: Blastn
[2023-06-30 12:42:08,440] [INFO] Selected 23 target genomes.
[2023-06-30 12:42:08,441] [INFO] Target genome list was writen to GCA_007129065.1_ASM712906v1_genomic.fna/target_genomes.txt
[2023-06-30 12:42:08,447] [INFO] Task started: fastANI
[2023-06-30 12:42:08,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg06f07d28-e37b-4ac2-b3ad-3556be2ba8bc/GCA_007129065.1_ASM712906v1_genomic.fna.gz --refList GCA_007129065.1_ASM712906v1_genomic.fna/target_genomes.txt --output GCA_007129065.1_ASM712906v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 12:42:24,171] [INFO] Task succeeded: fastANI
[2023-06-30 12:42:24,172] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde6d5402-9205-4370-8542-4a1cfa8adb93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 12:42:24,172] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde6d5402-9205-4370-8542-4a1cfa8adb93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 12:42:24,200] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 12:42:24,201] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 12:42:24,201] [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
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	81.5533	448	751	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	77.9497	202	751	95	below_threshold
Alkalilacustris brevis	strain=34079	GCA_003350345.1	2026338	2026338	type	True	77.9159	214	751	95	below_threshold
Roseicitreum antarcticum	strain=ZS2-28	GCA_014681765.1	564137	564137	type	True	77.6774	205	751	95	below_threshold
Roseicitreum antarcticum	strain=CGMCC 1.8894	GCA_900107025.1	564137	564137	type	True	77.5966	203	751	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	77.5838	208	751	95	below_threshold
Roseinatronobacter thiooxidans	strain=ALG1	GCA_001870675.1	121821	121821	type	True	77.5032	189	751	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.4425	204	751	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	77.4252	193	751	95	below_threshold
Pararhodobacter marinus	strain=CIC4N-9	GCA_003122215.1	2184063	2184063	type	True	77.3938	213	751	95	below_threshold
Rhodobaca barguzinensis	strain=alga05	GCA_001870665.2	441209	441209	suspected-type	True	77.389	166	751	95	below_threshold
Rhodobaca barguzinensis	strain=DSM 19920	GCA_004365885.1	441209	441209	suspected-type	True	77.388	166	751	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	77.3702	202	751	95	below_threshold
Rhodobaca bogoriensis	strain=DSM 18756	GCA_004366635.1	119542	119542	suspected-type	True	77.3003	168	751	95	below_threshold
Roseibaca ekhonensis	strain=CECT 7235	GCA_900499075.1	254356	254356	type	True	77.2981	169	751	95	below_threshold
Rhodobaca bogoriensis	strain=LBB1	GCA_014197665.1	119542	119542	suspected-type	True	77.2947	166	751	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_003387045.1	34007	34007	type	True	77.2158	216	751	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.1815	186	751	95	below_threshold
Paracoccus alkenifer	strain=DSM 11593	GCA_900108405.1	65735	65735	type	True	77.1532	153	751	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	77.1486	213	751	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	77.1345	168	751	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.075	164	751	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.7224	165	751	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 12:42:24,203] [INFO] DFAST Taxonomy check result was written to GCA_007129065.1_ASM712906v1_genomic.fna/tc_result.tsv
[2023-06-30 12:42:24,204] [INFO] ===== Taxonomy check completed =====
[2023-06-30 12:42:24,204] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 12:42:24,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde6d5402-9205-4370-8542-4a1cfa8adb93/dqc_reference/checkm_data
[2023-06-30 12:42:24,206] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 12:42:24,237] [INFO] Task started: CheckM
[2023-06-30 12:42:24,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_007129065.1_ASM712906v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_007129065.1_ASM712906v1_genomic.fna/checkm_input GCA_007129065.1_ASM712906v1_genomic.fna/checkm_result
[2023-06-30 12:42:53,658] [INFO] Task succeeded: CheckM
[2023-06-30 12:42:53,660] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.39%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 12:42:53,685] [INFO] ===== Completeness check finished =====
[2023-06-30 12:42:53,685] [INFO] ===== Start GTDB Search =====
[2023-06-30 12:42:53,685] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_007129065.1_ASM712906v1_genomic.fna/markers.fasta)
[2023-06-30 12:42:53,686] [INFO] Task started: Blastn
[2023-06-30 12:42:53,686] [INFO] Running command: blastn -query GCA_007129065.1_ASM712906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde6d5402-9205-4370-8542-4a1cfa8adb93/dqc_reference/reference_markers_gtdb.fasta -out GCA_007129065.1_ASM712906v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:42:55,074] [INFO] Task succeeded: Blastn
[2023-06-30 12:42:55,077] [INFO] Selected 16 target genomes.
[2023-06-30 12:42:55,078] [INFO] Target genome list was writen to GCA_007129065.1_ASM712906v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 12:42:55,086] [INFO] Task started: fastANI
[2023-06-30 12:42:55,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg06f07d28-e37b-4ac2-b3ad-3556be2ba8bc/GCA_007129065.1_ASM712906v1_genomic.fna.gz --refList GCA_007129065.1_ASM712906v1_genomic.fna/target_genomes_gtdb.txt --output GCA_007129065.1_ASM712906v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 12:43:04,160] [INFO] Task succeeded: fastANI
[2023-06-30 12:43:04,177] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 12:43:04,178] [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_007123625.1	s__PUOA01 sp007123625	98.7141	523	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__PUOA01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013415485.1	s__PUOA01 sp003567395	81.596	445	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__PUOA01	95.0	98.54	98.26	0.95	0.89	5	-
GCA_007121115.1	s__PUOA01 sp007121115	81.5825	388	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__PUOA01	95.0	99.30	99.15	0.84	0.78	4	-
GCA_003551925.1	s__PUOA01 sp003551925	79.8092	306	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__PUOA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003564655.1	s__Roseinatronobacter sp003564655	78.3449	225	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007120685.1	s__Pararhodobacter sp007120685	78.0983	207	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	99.30	99.30	0.84	0.84	2	-
GCA_007134865.1	s__Roseinatronobacter sp007134865	77.969	201	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.54	99.18	0.88	0.81	5	-
GCA_001314715.1	s__Pararhodobacter sp001314715	77.8999	234	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007117005.1	s__Pararhodobacter sp007117005	77.8539	211	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	98.98	98.98	0.82	0.82	2	-
GCA_007694945.1	s__Roseinatronobacter sp007694945	77.7788	194	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908405.1	s__Roseinatronobacter sp009908405	77.7772	165	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017811755.1	s__Pararhodobacter sp017811755	77.7741	243	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001517585.1	s__Roseinatronobacter calidilacus	77.5834	177	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007134405.1	s__Pararhodobacter sp007134405	77.4841	149	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	98.66	98.61	0.77	0.76	3	-
GCF_003990445.1	s__Pararhodobacter zhoushanensis	77.2085	187	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017303295.1	s__Pararhodobacter sp017303295	77.1682	190	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 12:43:04,180] [INFO] GTDB search result was written to GCA_007129065.1_ASM712906v1_genomic.fna/result_gtdb.tsv
[2023-06-30 12:43:04,181] [INFO] ===== GTDB Search completed =====
[2023-06-30 12:43:04,185] [INFO] DFAST_QC result json was written to GCA_007129065.1_ASM712906v1_genomic.fna/dqc_result.json
[2023-06-30 12:43:04,185] [INFO] DFAST_QC completed!
[2023-06-30 12:43:04,186] [INFO] Total running time: 0h1m6s