[2024-01-24 12:31:58,446] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:58,449] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:58,449] [INFO] DQC Reference Directory: /var/lib/cwl/stg3580195f-62e6-45d2-8cf0-4018d92b293e/dqc_reference
[2024-01-24 12:31:59,846] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:59,847] [INFO] Task started: Prodigal
[2024-01-24 12:31:59,847] [INFO] Running command: gunzip -c /var/lib/cwl/stg842335f8-8080-4138-b03a-ee135469be7c/GCF_003051025.1_ASM305102v1_genomic.fna.gz | prodigal -d GCF_003051025.1_ASM305102v1_genomic.fna/cds.fna -a GCF_003051025.1_ASM305102v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:16,399] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:16,399] [INFO] Task started: HMMsearch
[2024-01-24 12:32:16,399] [INFO] Running command: hmmsearch --tblout GCF_003051025.1_ASM305102v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3580195f-62e6-45d2-8cf0-4018d92b293e/dqc_reference/reference_markers.hmm GCF_003051025.1_ASM305102v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:16,714] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:16,715] [INFO] Found 6/6 markers.
[2024-01-24 12:32:16,761] [INFO] Query marker FASTA was written to GCF_003051025.1_ASM305102v1_genomic.fna/markers.fasta
[2024-01-24 12:32:16,762] [INFO] Task started: Blastn
[2024-01-24 12:32:16,762] [INFO] Running command: blastn -query GCF_003051025.1_ASM305102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3580195f-62e6-45d2-8cf0-4018d92b293e/dqc_reference/reference_markers.fasta -out GCF_003051025.1_ASM305102v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:17,677] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:17,680] [INFO] Selected 18 target genomes.
[2024-01-24 12:32:17,681] [INFO] Target genome list was writen to GCF_003051025.1_ASM305102v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:17,690] [INFO] Task started: fastANI
[2024-01-24 12:32:17,690] [INFO] Running command: fastANI --query /var/lib/cwl/stg842335f8-8080-4138-b03a-ee135469be7c/GCF_003051025.1_ASM305102v1_genomic.fna.gz --refList GCF_003051025.1_ASM305102v1_genomic.fna/target_genomes.txt --output GCF_003051025.1_ASM305102v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:35,610] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:35,611] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3580195f-62e6-45d2-8cf0-4018d92b293e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:35,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3580195f-62e6-45d2-8cf0-4018d92b293e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:35,627] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:32:35,628] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:35,628] [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
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	100.0	1736	1737	95	conclusive
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	99.9978	1732	1737	95	conclusive
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	82.6278	1149	1737	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	79.515	728	1737	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	79.4538	662	1737	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	79.4272	727	1737	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	79.4117	698	1737	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.8618	586	1737	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.8332	670	1737	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	78.7804	540	1737	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.6773	574	1737	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	78.6717	554	1737	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	78.318	549	1737	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	78.2036	472	1737	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.9728	389	1737	95	below_threshold
Marivita cryptomonadis	strain=CL-SK44	GCA_002115725.1	505252	505252	type	True	77.9634	405	1737	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.8464	408	1737	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.4861	391	1737	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:35,630] [INFO] DFAST Taxonomy check result was written to GCF_003051025.1_ASM305102v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:35,630] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:35,630] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:35,631] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3580195f-62e6-45d2-8cf0-4018d92b293e/dqc_reference/checkm_data
[2024-01-24 12:32:35,632] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:35,684] [INFO] Task started: CheckM
[2024-01-24 12:32:35,684] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003051025.1_ASM305102v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003051025.1_ASM305102v1_genomic.fna/checkm_input GCF_003051025.1_ASM305102v1_genomic.fna/checkm_result
[2024-01-24 12:33:32,449] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:32,450] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:32,478] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:32,479] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:32,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003051025.1_ASM305102v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:32,480] [INFO] Task started: Blastn
[2024-01-24 12:33:32,480] [INFO] Running command: blastn -query GCF_003051025.1_ASM305102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3580195f-62e6-45d2-8cf0-4018d92b293e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003051025.1_ASM305102v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:33,915] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:33,919] [INFO] Selected 14 target genomes.
[2024-01-24 12:33:33,919] [INFO] Target genome list was writen to GCF_003051025.1_ASM305102v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:33,930] [INFO] Task started: fastANI
[2024-01-24 12:33:33,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg842335f8-8080-4138-b03a-ee135469be7c/GCF_003051025.1_ASM305102v1_genomic.fna.gz --refList GCF_003051025.1_ASM305102v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003051025.1_ASM305102v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:49,562] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:49,577] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:49,577] [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_900101505.1	s__Mameliella alba	99.9978	1732	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	conclusive
GCF_900184945.1	s__Maliponia aquimaris	82.6295	1099	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maliponia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019218285.1	s__DP3N28-2 sp019218285	82.6277	1149	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__DP3N28-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188425.1	s__Antarctobacter heliothermus	81.6602	1054	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarctobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	81.0038	902	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255395.1	s__AWRV01 sp017255395	80.8054	900	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237555.1	s__Antarctobacter heliothermus_B	80.777	1000	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarctobacter	95.0	97.31	97.29	0.90	0.89	3	-
GCA_016806125.1	s__AWRV01 sp000504185	80.5446	887	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	99.97	99.97	1.00	1.00	2	-
GCF_002814095.1	s__Sagittula sp002814095	80.2708	901	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	80.25	819	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	79.7764	707	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969385.1	s__Salipiger profundus	79.4308	694	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
GCF_900102075.1	s__Salipiger thiooxidans	79.4277	727	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_017311415.1	s__Salipiger abyssi_A	79.2654	687	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:49,579] [INFO] GTDB search result was written to GCF_003051025.1_ASM305102v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:49,580] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:49,583] [INFO] DFAST_QC result json was written to GCF_003051025.1_ASM305102v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:49,584] [INFO] DFAST_QC completed!
[2024-01-24 12:33:49,584] [INFO] Total running time: 0h1m51s