[2024-01-25 18:06:20,651] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:20,653] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:20,653] [INFO] DQC Reference Directory: /var/lib/cwl/stgc94b2652-5dae-4798-b1ab-15e656eeea9a/dqc_reference
[2024-01-25 18:06:21,796] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:21,797] [INFO] Task started: Prodigal
[2024-01-25 18:06:21,797] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c7daaac-8eaf-450e-83c7-c13c4f6ea692/GCF_000600335.2_Rumeso_genomic.fna.gz | prodigal -d GCF_000600335.2_Rumeso_genomic.fna/cds.fna -a GCF_000600335.2_Rumeso_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:33,185] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:33,186] [INFO] Task started: HMMsearch
[2024-01-25 18:06:33,186] [INFO] Running command: hmmsearch --tblout GCF_000600335.2_Rumeso_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc94b2652-5dae-4798-b1ab-15e656eeea9a/dqc_reference/reference_markers.hmm GCF_000600335.2_Rumeso_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:33,462] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:33,463] [INFO] Found 6/6 markers.
[2024-01-25 18:06:33,506] [INFO] Query marker FASTA was written to GCF_000600335.2_Rumeso_genomic.fna/markers.fasta
[2024-01-25 18:06:33,506] [INFO] Task started: Blastn
[2024-01-25 18:06:33,506] [INFO] Running command: blastn -query GCF_000600335.2_Rumeso_genomic.fna/markers.fasta -db /var/lib/cwl/stgc94b2652-5dae-4798-b1ab-15e656eeea9a/dqc_reference/reference_markers.fasta -out GCF_000600335.2_Rumeso_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:34,470] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:34,473] [INFO] Selected 23 target genomes.
[2024-01-25 18:06:34,473] [INFO] Target genome list was writen to GCF_000600335.2_Rumeso_genomic.fna/target_genomes.txt
[2024-01-25 18:06:34,485] [INFO] Task started: fastANI
[2024-01-25 18:06:34,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c7daaac-8eaf-450e-83c7-c13c4f6ea692/GCF_000600335.2_Rumeso_genomic.fna.gz --refList GCF_000600335.2_Rumeso_genomic.fna/target_genomes.txt --output GCF_000600335.2_Rumeso_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:52,536] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:52,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc94b2652-5dae-4798-b1ab-15e656eeea9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:52,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc94b2652-5dae-4798-b1ab-15e656eeea9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:52,550] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:06:52,550] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:06:52,550] [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
Rubellimicrobium mesophilum	strain=DSM 19309	GCA_000600335.2	1123067	1123067	type	True	100.0	1573	1580	95	conclusive
Rubellimicrobium aerolatum	strain=DSM 19297	GCA_017872975.1	490979	490979	type	True	83.9663	814	1580	95	below_threshold
Rubellimicrobium roseum	strain=YIM 48858	GCA_006152145.1	687525	687525	type	True	83.5343	907	1580	95	below_threshold
Rubellimicrobium rubrum	strain=YIM 131921	GCA_006152115.1	2585369	2585369	type	True	81.4703	754	1580	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	79.0666	485	1580	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	79.0272	574	1580	95	below_threshold
Rubellimicrobium thermophilum	strain=DSM 16684	GCA_000442315.1	295419	295419	type	True	78.8741	501	1580	95	below_threshold
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	78.6724	437	1580	95	below_threshold
Limimaricola soesokkakensis	strain=CECT 8367	GCA_900172345.1	1343159	1343159	type	True	78.6236	451	1580	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.5019	461	1580	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.3658	430	1580	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.2694	427	1580	95	below_threshold
Hasllibacter halocynthiae	strain=DSM 29318	GCA_003003095.1	595589	595589	type	True	78.0161	372	1580	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	77.9604	309	1580	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	77.861	397	1580	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.7935	387	1580	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.6769	313	1580	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	77.5758	359	1580	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.4586	319	1580	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.2851	251	1580	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	77.2028	314	1580	95	below_threshold
Rhodovibrio salinarum	strain=DSM 9154	GCA_000515255.1	1087	1087	type	True	76.2475	128	1580	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	75.916	144	1580	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:52,552] [INFO] DFAST Taxonomy check result was written to GCF_000600335.2_Rumeso_genomic.fna/tc_result.tsv
[2024-01-25 18:06:52,553] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:52,553] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:52,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc94b2652-5dae-4798-b1ab-15e656eeea9a/dqc_reference/checkm_data
[2024-01-25 18:06:52,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:52,601] [INFO] Task started: CheckM
[2024-01-25 18:06:52,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000600335.2_Rumeso_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000600335.2_Rumeso_genomic.fna/checkm_input GCF_000600335.2_Rumeso_genomic.fna/checkm_result
[2024-01-25 18:07:29,778] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:29,780] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:29,803] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:29,803] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:29,804] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000600335.2_Rumeso_genomic.fna/markers.fasta)
[2024-01-25 18:07:29,804] [INFO] Task started: Blastn
[2024-01-25 18:07:29,804] [INFO] Running command: blastn -query GCF_000600335.2_Rumeso_genomic.fna/markers.fasta -db /var/lib/cwl/stgc94b2652-5dae-4798-b1ab-15e656eeea9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000600335.2_Rumeso_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:31,653] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:31,656] [INFO] Selected 9 target genomes.
[2024-01-25 18:07:31,656] [INFO] Target genome list was writen to GCF_000600335.2_Rumeso_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:31,669] [INFO] Task started: fastANI
[2024-01-25 18:07:31,669] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c7daaac-8eaf-450e-83c7-c13c4f6ea692/GCF_000600335.2_Rumeso_genomic.fna.gz --refList GCF_000600335.2_Rumeso_genomic.fna/target_genomes_gtdb.txt --output GCF_000600335.2_Rumeso_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:40,582] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:40,589] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:40,589] [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_000600335.2	s__Rubellimicrobium mesophilum	100.0	1573	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017872975.1	s__Rubellimicrobium aerolatum	83.978	813	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006152145.1	s__Rubellimicrobium roseum	83.5296	908	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916275.1	s__Rubellimicrobium sp017916275	82.6321	841	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902805995.1	s__Rubellimicrobium sp902805995	82.3184	523	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006152115.1	s__Rubellimicrobium rubrum	81.443	757	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009904055.1	s__Rubellimicrobium sp009904055	79.9711	579	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442315.1	s__Rubellimicrobium thermophilum	78.8568	503	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172345.1	s__Limimaricola soesokkakensis	78.6137	452	1580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:40,591] [INFO] GTDB search result was written to GCF_000600335.2_Rumeso_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:40,591] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:40,594] [INFO] DFAST_QC result json was written to GCF_000600335.2_Rumeso_genomic.fna/dqc_result.json
[2024-01-25 18:07:40,595] [INFO] DFAST_QC completed!
[2024-01-25 18:07:40,595] [INFO] Total running time: 0h1m20s