[2024-01-24 13:41:40,496] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:40,504] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:40,505] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7d44cd5-85b0-4ca6-b2d3-8cf0a693c4ff/dqc_reference
[2024-01-24 13:41:41,885] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:41,886] [INFO] Task started: Prodigal
[2024-01-24 13:41:41,886] [INFO] Running command: gunzip -c /var/lib/cwl/stg3bbd235c-c490-4ef8-9794-d84126f71c5d/GCF_005871115.1_ASM587111v1_genomic.fna.gz | prodigal -d GCF_005871115.1_ASM587111v1_genomic.fna/cds.fna -a GCF_005871115.1_ASM587111v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:55,160] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:55,161] [INFO] Task started: HMMsearch
[2024-01-24 13:41:55,161] [INFO] Running command: hmmsearch --tblout GCF_005871115.1_ASM587111v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7d44cd5-85b0-4ca6-b2d3-8cf0a693c4ff/dqc_reference/reference_markers.hmm GCF_005871115.1_ASM587111v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:55,451] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:55,453] [INFO] Found 6/6 markers.
[2024-01-24 13:41:55,495] [INFO] Query marker FASTA was written to GCF_005871115.1_ASM587111v1_genomic.fna/markers.fasta
[2024-01-24 13:41:55,496] [INFO] Task started: Blastn
[2024-01-24 13:41:55,496] [INFO] Running command: blastn -query GCF_005871115.1_ASM587111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7d44cd5-85b0-4ca6-b2d3-8cf0a693c4ff/dqc_reference/reference_markers.fasta -out GCF_005871115.1_ASM587111v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:56,388] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:56,391] [INFO] Selected 16 target genomes.
[2024-01-24 13:41:56,392] [INFO] Target genome list was writen to GCF_005871115.1_ASM587111v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:56,401] [INFO] Task started: fastANI
[2024-01-24 13:41:56,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bbd235c-c490-4ef8-9794-d84126f71c5d/GCF_005871115.1_ASM587111v1_genomic.fna.gz --refList GCF_005871115.1_ASM587111v1_genomic.fna/target_genomes.txt --output GCF_005871115.1_ASM587111v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:10,597] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:10,598] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7d44cd5-85b0-4ca6-b2d3-8cf0a693c4ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:10,599] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7d44cd5-85b0-4ca6-b2d3-8cf0a693c4ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:10,616] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:42:10,616] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:42:10,616] [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
Maritimibacter alexandrii	strain=LZ-17	GCA_005871115.1	2570355	2570355	type	True	100.0	1427	1428	95	inconclusive
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_008124775.1	404236	404236	type	True	96.9703	1279	1428	95	inconclusive
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_000152805.1	404236	404236	type	True	96.9324	1288	1428	95	inconclusive
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	82.3212	897	1428	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.521	501	1428	95	below_threshold
Celeribacter indicus	strain=P73	GCA_000819565.1	1208324	1208324	type	True	78.0891	408	1428	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	78.0526	442	1428	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	77.9352	448	1428	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.9156	356	1428	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.8377	414	1428	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.8258	375	1428	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	77.7047	358	1428	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	77.5614	357	1428	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.4395	336	1428	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	77.3433	348	1428	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	77.3012	335	1428	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:10,618] [INFO] DFAST Taxonomy check result was written to GCF_005871115.1_ASM587111v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:10,619] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:10,619] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:10,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7d44cd5-85b0-4ca6-b2d3-8cf0a693c4ff/dqc_reference/checkm_data
[2024-01-24 13:42:10,622] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:10,670] [INFO] Task started: CheckM
[2024-01-24 13:42:10,670] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005871115.1_ASM587111v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005871115.1_ASM587111v1_genomic.fna/checkm_input GCF_005871115.1_ASM587111v1_genomic.fna/checkm_result
[2024-01-24 13:42:54,840] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:54,842] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:54,864] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:54,864] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:54,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005871115.1_ASM587111v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:54,865] [INFO] Task started: Blastn
[2024-01-24 13:42:54,865] [INFO] Running command: blastn -query GCF_005871115.1_ASM587111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7d44cd5-85b0-4ca6-b2d3-8cf0a693c4ff/dqc_reference/reference_markers_gtdb.fasta -out GCF_005871115.1_ASM587111v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:56,352] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:56,356] [INFO] Selected 12 target genomes.
[2024-01-24 13:42:56,357] [INFO] Target genome list was writen to GCF_005871115.1_ASM587111v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:56,392] [INFO] Task started: fastANI
[2024-01-24 13:42:56,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bbd235c-c490-4ef8-9794-d84126f71c5d/GCF_005871115.1_ASM587111v1_genomic.fna.gz --refList GCF_005871115.1_ASM587111v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005871115.1_ASM587111v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:07,806] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:07,826] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:07,827] [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_000152805.1	s__Maritimibacter alkaliphilus	96.9304	1288	1428	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	97.94	96.90	0.93	0.88	4	conclusive
GCA_002695005.1	s__Maritimibacter sp002695005	83.3093	964	1428	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_009882975.1	s__Maritimibacter harenae	82.3111	899	1428	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019218265.1	s__Maritimibacter sp019218265	81.5315	767	1428	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001626765.1	s__Maritimibacter sp001626765	81.3815	751	1428	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	99.88	99.88	0.89	0.89	2	-
GCF_019218295.1	s__Maritimibacter sp019218295	80.4589	727	1428	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	80.365	541	1428	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003520545.1	s__Maritimibacter sp003520545	79.9903	534	1428	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640115.1	s__Muriiphilus lacisalsi	78.8284	508	1428	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034995.1	s__Phaeovulum veldkampii	77.6309	268	1428	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	99.98	99.97	0.97	0.94	3	-
GCF_002847445.1	s__Paracoccus zhejiangensis	77.3981	322	1428	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003709565.1	s__Paracoccus siganidrum	77.3221	349	1428	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:07,829] [INFO] GTDB search result was written to GCF_005871115.1_ASM587111v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:07,830] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:07,833] [INFO] DFAST_QC result json was written to GCF_005871115.1_ASM587111v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:07,833] [INFO] DFAST_QC completed!
[2024-01-24 13:43:07,833] [INFO] Total running time: 0h1m27s