[2024-01-24 13:32:29,861] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:29,864] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:29,864] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a171ae0-80f7-4ffa-b3a7-2bfbc43e2006/dqc_reference
[2024-01-24 13:32:31,187] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:31,188] [INFO] Task started: Prodigal
[2024-01-24 13:32:31,188] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d0063b0-5f31-47dc-bb93-4dfb833e19c0/GCF_003254705.1_ASM325470v1_genomic.fna.gz | prodigal -d GCF_003254705.1_ASM325470v1_genomic.fna/cds.fna -a GCF_003254705.1_ASM325470v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:42,130] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:42,131] [INFO] Task started: HMMsearch
[2024-01-24 13:32:42,131] [INFO] Running command: hmmsearch --tblout GCF_003254705.1_ASM325470v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a171ae0-80f7-4ffa-b3a7-2bfbc43e2006/dqc_reference/reference_markers.hmm GCF_003254705.1_ASM325470v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:42,473] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:42,475] [INFO] Found 6/6 markers.
[2024-01-24 13:32:42,517] [INFO] Query marker FASTA was written to GCF_003254705.1_ASM325470v1_genomic.fna/markers.fasta
[2024-01-24 13:32:42,517] [INFO] Task started: Blastn
[2024-01-24 13:32:42,517] [INFO] Running command: blastn -query GCF_003254705.1_ASM325470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a171ae0-80f7-4ffa-b3a7-2bfbc43e2006/dqc_reference/reference_markers.fasta -out GCF_003254705.1_ASM325470v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:43,403] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:43,406] [INFO] Selected 19 target genomes.
[2024-01-24 13:32:43,406] [INFO] Target genome list was writen to GCF_003254705.1_ASM325470v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:43,414] [INFO] Task started: fastANI
[2024-01-24 13:32:43,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d0063b0-5f31-47dc-bb93-4dfb833e19c0/GCF_003254705.1_ASM325470v1_genomic.fna.gz --refList GCF_003254705.1_ASM325470v1_genomic.fna/target_genomes.txt --output GCF_003254705.1_ASM325470v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:58,947] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:58,947] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a171ae0-80f7-4ffa-b3a7-2bfbc43e2006/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:58,948] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a171ae0-80f7-4ffa-b3a7-2bfbc43e2006/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:58,963] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:58,963] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:58,963] [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
Phenylobacterium deserti	strain=YIM 73061	GCA_003254705.1	1914756	1914756	type	True	100.0	1287	1288	95	conclusive
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	81.59	708	1288	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	81.2869	688	1288	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	80.9651	637	1288	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	80.1523	593	1288	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	79.6783	574	1288	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	79.5127	535	1288	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	79.0261	537	1288	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	79.0126	565	1288	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	78.1793	304	1288	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	77.9525	369	1288	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	76.3807	92	1288	95	below_threshold
Palleronia marisminoris	strain=CECT 7066	GCA_900172315.1	315423	315423	type	True	76.2363	104	1288	95	below_threshold
Gemmobacter aquaticus	strain=CGMCC 1.7029	GCA_014645295.1	490185	490185	type	True	76.2209	80	1288	95	below_threshold
Palleronia marisminoris	strain=DSM 26347	GCA_900113405.1	315423	315423	type	True	76.1873	107	1288	95	below_threshold
Gemmobacter aquaticus	strain=A1-9	GCA_007859075.1	490185	490185	type	True	76.1783	82	1288	95	below_threshold
Microvirga massiliensis	strain=JC119	GCA_001006805.1	1033741	1033741	type	True	75.8259	107	1288	95	below_threshold
Paracoccus indicus	strain=IO390502	GCA_003056335.1	2079229	2079229	type	True	75.8158	89	1288	95	below_threshold
Sphingomonas psychrolutea	strain=CGMCC 1.10106	GCA_014636175.1	1259676	1259676	type	True	75.6575	66	1288	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:58,966] [INFO] DFAST Taxonomy check result was written to GCF_003254705.1_ASM325470v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:58,966] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:58,966] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:58,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a171ae0-80f7-4ffa-b3a7-2bfbc43e2006/dqc_reference/checkm_data
[2024-01-24 13:32:58,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:59,011] [INFO] Task started: CheckM
[2024-01-24 13:32:59,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003254705.1_ASM325470v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003254705.1_ASM325470v1_genomic.fna/checkm_input GCF_003254705.1_ASM325470v1_genomic.fna/checkm_result
[2024-01-24 13:33:35,246] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:35,247] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:35,267] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:35,268] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:35,268] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003254705.1_ASM325470v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:35,269] [INFO] Task started: Blastn
[2024-01-24 13:33:35,269] [INFO] Running command: blastn -query GCF_003254705.1_ASM325470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a171ae0-80f7-4ffa-b3a7-2bfbc43e2006/dqc_reference/reference_markers_gtdb.fasta -out GCF_003254705.1_ASM325470v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:36,973] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:36,978] [INFO] Selected 20 target genomes.
[2024-01-24 13:33:36,979] [INFO] Target genome list was writen to GCF_003254705.1_ASM325470v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:37,012] [INFO] Task started: fastANI
[2024-01-24 13:33:37,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d0063b0-5f31-47dc-bb93-4dfb833e19c0/GCF_003254705.1_ASM325470v1_genomic.fna.gz --refList GCF_003254705.1_ASM325470v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003254705.1_ASM325470v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:56,089] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:56,112] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:56,112] [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_003254705.1	s__Phenylobacterium deserti	100.0	1287	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003254505.1	s__Phenylobacterium hankyongense	81.5896	708	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017265.1	s__Phenylobacterium zucineum	81.291	688	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.11	99.11	0.98	0.98	2	-
GCF_003254475.1	s__Phenylobacterium soli	80.9855	635	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799545.1	s__Phenylobacterium sp004799545	80.251	606	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799515.1	s__Phenylobacterium sp004799515	80.2494	597	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018821435.1	s__Phenylobacterium sp018821435	80.237	599	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.99	99.99	0.99	0.99	6	-
GCF_003254525.1	s__Phenylobacterium kunshanense	80.1305	596	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297125.1	s__Phenylobacterium sp004297125	80.0885	649	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124325.1	s__Phenylobacterium sp016124325	79.8785	566	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793225.1	s__Phenylobacterium sp016793225	79.8568	546	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004299445.1	s__Phenylobacterium sp004299445	79.8246	559	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247715.1	s__Palsa-881 sp019247715	77.7156	356	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Palsa-881	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	76.3807	92	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172315.1	s__Palleronia marisminoris	76.2542	103	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_007859075.1	s__Gemmobacter aquaticus	76.2209	80	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014763725.1	s__JACXUX01 sp014763725	75.9473	117	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JACXUX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001828855.1	s__Cypionkella sp001828855	75.8731	66	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	99.95	99.91	0.99	0.97	3	-
GCF_003056335.1	s__Paracoccus indicus	75.8321	88	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636175.1	s__Sphingomonas psychrolutea	75.6575	66	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:56,114] [INFO] GTDB search result was written to GCF_003254705.1_ASM325470v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:56,115] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:56,119] [INFO] DFAST_QC result json was written to GCF_003254705.1_ASM325470v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:56,120] [INFO] DFAST_QC completed!
[2024-01-24 13:33:56,120] [INFO] Total running time: 0h1m26s