[2024-01-24 12:52:51,110] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:51,112] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:51,112] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb25e9c3-d5c9-43be-aeb8-0ba685e42e4e/dqc_reference
[2024-01-24 12:52:53,751] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:53,752] [INFO] Task started: Prodigal
[2024-01-24 12:52:53,753] [INFO] Running command: gunzip -c /var/lib/cwl/stgc17ef549-7f61-4d94-a8ab-1778a041a7de/GCF_018760365.1_ASM1876036v1_genomic.fna.gz | prodigal -d GCF_018760365.1_ASM1876036v1_genomic.fna/cds.fna -a GCF_018760365.1_ASM1876036v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:08,414] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:08,415] [INFO] Task started: HMMsearch
[2024-01-24 12:53:08,415] [INFO] Running command: hmmsearch --tblout GCF_018760365.1_ASM1876036v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb25e9c3-d5c9-43be-aeb8-0ba685e42e4e/dqc_reference/reference_markers.hmm GCF_018760365.1_ASM1876036v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:08,708] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:08,710] [INFO] Found 6/6 markers.
[2024-01-24 12:53:08,758] [INFO] Query marker FASTA was written to GCF_018760365.1_ASM1876036v1_genomic.fna/markers.fasta
[2024-01-24 12:53:08,759] [INFO] Task started: Blastn
[2024-01-24 12:53:08,759] [INFO] Running command: blastn -query GCF_018760365.1_ASM1876036v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb25e9c3-d5c9-43be-aeb8-0ba685e42e4e/dqc_reference/reference_markers.fasta -out GCF_018760365.1_ASM1876036v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:09,706] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:09,711] [INFO] Selected 19 target genomes.
[2024-01-24 12:53:09,711] [INFO] Target genome list was writen to GCF_018760365.1_ASM1876036v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:09,733] [INFO] Task started: fastANI
[2024-01-24 12:53:09,733] [INFO] Running command: fastANI --query /var/lib/cwl/stgc17ef549-7f61-4d94-a8ab-1778a041a7de/GCF_018760365.1_ASM1876036v1_genomic.fna.gz --refList GCF_018760365.1_ASM1876036v1_genomic.fna/target_genomes.txt --output GCF_018760365.1_ASM1876036v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:25,705] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:25,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb25e9c3-d5c9-43be-aeb8-0ba685e42e4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:25,707] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb25e9c3-d5c9-43be-aeb8-0ba685e42e4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:25,726] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:53:25,726] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:53:25,727] [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
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	100.0	1713	1720	95	conclusive
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	81.7866	767	1720	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	81.7511	785	1720	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	81.3391	817	1720	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	81.2497	824	1720	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	79.847	636	1720	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	79.8439	642	1720	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	79.5358	668	1720	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	79.459	561	1720	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	78.8599	562	1720	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.623	505	1720	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.5641	623	1720	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	78.3017	566	1720	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.295	472	1720	95	below_threshold
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	77.8061	399	1720	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.7763	374	1720	95	below_threshold
Thalassobius gelatinovorus	strain=CECT 4357	GCA_001458355.1	53501	53501	type	True	77.2694	306	1720	95	below_threshold
Thalassobius gelatinovorus	strain=DSM 5887	GCA_900111045.1	53501	53501	type	True	77.2336	310	1720	95	below_threshold
Paracoccus caeni	strain=MJ17	GCA_016629665.1	657651	657651	type	True	77.1084	348	1720	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:25,729] [INFO] DFAST Taxonomy check result was written to GCF_018760365.1_ASM1876036v1_genomic.fna/tc_result.tsv
[2024-01-24 12:53:25,729] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:25,729] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:25,730] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb25e9c3-d5c9-43be-aeb8-0ba685e42e4e/dqc_reference/checkm_data
[2024-01-24 12:53:25,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:25,781] [INFO] Task started: CheckM
[2024-01-24 12:53:25,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018760365.1_ASM1876036v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018760365.1_ASM1876036v1_genomic.fna/checkm_input GCF_018760365.1_ASM1876036v1_genomic.fna/checkm_result
[2024-01-24 12:54:15,522] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:15,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:15,551] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:15,553] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:15,554] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018760365.1_ASM1876036v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:15,555] [INFO] Task started: Blastn
[2024-01-24 12:54:15,555] [INFO] Running command: blastn -query GCF_018760365.1_ASM1876036v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb25e9c3-d5c9-43be-aeb8-0ba685e42e4e/dqc_reference/reference_markers_gtdb.fasta -out GCF_018760365.1_ASM1876036v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:17,226] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:17,229] [INFO] Selected 13 target genomes.
[2024-01-24 12:54:17,230] [INFO] Target genome list was writen to GCF_018760365.1_ASM1876036v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:17,272] [INFO] Task started: fastANI
[2024-01-24 12:54:17,272] [INFO] Running command: fastANI --query /var/lib/cwl/stgc17ef549-7f61-4d94-a8ab-1778a041a7de/GCF_018760365.1_ASM1876036v1_genomic.fna.gz --refList GCF_018760365.1_ASM1876036v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018760365.1_ASM1876036v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:30,127] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:30,146] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:30,147] [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_009827095.1	s__Pseudooceanicola sp009827095	99.9727	1683	1720	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	conclusive
GCF_900215355.1	s__Pseudooceanicola antarcticus	81.7625	770	1720	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	81.6365	729	1720	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	81.6327	831	1720	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCF_002786295.1	s__Pseudooceanicola marinus	81.3588	815	1720	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCF_011806405.1	s__Pseudooceanicola sp011806405	80.7043	765	1720	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590145.2	s__Pseudooceanicola algae	80.2405	689	1720	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	79.8599	634	1720	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015223355.1	s__Salipiger pacificus_B	79.7592	716	1720	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789075.1	s__Pseudooceanicola pacificus	79.5742	462	1720	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153725.1	s__Salipiger bermudensis	79.5288	669	1720	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	79.2103	624	1720	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526275.1	s__Lutimaribacter sp000526275	77.9811	471	1720	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:30,148] [INFO] GTDB search result was written to GCF_018760365.1_ASM1876036v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:30,149] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:30,153] [INFO] DFAST_QC result json was written to GCF_018760365.1_ASM1876036v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:30,154] [INFO] DFAST_QC completed!
[2024-01-24 12:54:30,154] [INFO] Total running time: 0h1m39s