[2024-01-24 12:40:20,717] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:20,719] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:20,719] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b2b99a7-735d-4626-949d-f85224a47319/dqc_reference
[2024-01-24 12:40:21,962] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:21,963] [INFO] Task started: Prodigal
[2024-01-24 12:40:21,963] [INFO] Running command: gunzip -c /var/lib/cwl/stg2dfe15ad-de5e-4da9-ace3-9478bbb74415/GCF_001482405.1_ASM148240v1_genomic.fna.gz | prodigal -d GCF_001482405.1_ASM148240v1_genomic.fna/cds.fna -a GCF_001482405.1_ASM148240v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:35,384] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:35,384] [INFO] Task started: HMMsearch
[2024-01-24 12:40:35,385] [INFO] Running command: hmmsearch --tblout GCF_001482405.1_ASM148240v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b2b99a7-735d-4626-949d-f85224a47319/dqc_reference/reference_markers.hmm GCF_001482405.1_ASM148240v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:35,657] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:35,659] [INFO] Found 6/6 markers.
[2024-01-24 12:40:35,700] [INFO] Query marker FASTA was written to GCF_001482405.1_ASM148240v1_genomic.fna/markers.fasta
[2024-01-24 12:40:35,701] [INFO] Task started: Blastn
[2024-01-24 12:40:35,701] [INFO] Running command: blastn -query GCF_001482405.1_ASM148240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b2b99a7-735d-4626-949d-f85224a47319/dqc_reference/reference_markers.fasta -out GCF_001482405.1_ASM148240v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:36,665] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:36,669] [INFO] Selected 14 target genomes.
[2024-01-24 12:40:36,669] [INFO] Target genome list was writen to GCF_001482405.1_ASM148240v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:36,675] [INFO] Task started: fastANI
[2024-01-24 12:40:36,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dfe15ad-de5e-4da9-ace3-9478bbb74415/GCF_001482405.1_ASM148240v1_genomic.fna.gz --refList GCF_001482405.1_ASM148240v1_genomic.fna/target_genomes.txt --output GCF_001482405.1_ASM148240v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:49,723] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:49,723] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b2b99a7-735d-4626-949d-f85224a47319/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:49,723] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b2b99a7-735d-4626-949d-f85224a47319/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:49,735] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:40:49,735] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:40:49,735] [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	81.1062	903	1490	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	81.0869	900	1490	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	80.7315	785	1490	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	80.4599	726	1490	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	80.3977	703	1490	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	80.3173	782	1490	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	80.1544	718	1490	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	80.1216	690	1490	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	79.9758	756	1490	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	79.8388	742	1490	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	79.3207	582	1490	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	79.2256	591	1490	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	79.0575	550	1490	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	78.5613	456	1490	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:49,737] [INFO] DFAST Taxonomy check result was written to GCF_001482405.1_ASM148240v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:49,737] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:49,737] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:49,737] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b2b99a7-735d-4626-949d-f85224a47319/dqc_reference/checkm_data
[2024-01-24 12:40:49,738] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:49,781] [INFO] Task started: CheckM
[2024-01-24 12:40:49,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001482405.1_ASM148240v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001482405.1_ASM148240v1_genomic.fna/checkm_input GCF_001482405.1_ASM148240v1_genomic.fna/checkm_result
[2024-01-24 12:41:41,299] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:41,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:41,321] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:41,322] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:41,322] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001482405.1_ASM148240v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:41,322] [INFO] Task started: Blastn
[2024-01-24 12:41:41,322] [INFO] Running command: blastn -query GCF_001482405.1_ASM148240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b2b99a7-735d-4626-949d-f85224a47319/dqc_reference/reference_markers_gtdb.fasta -out GCF_001482405.1_ASM148240v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:43,039] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:43,043] [INFO] Selected 16 target genomes.
[2024-01-24 12:41:43,043] [INFO] Target genome list was writen to GCF_001482405.1_ASM148240v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:43,055] [INFO] Task started: fastANI
[2024-01-24 12:41:43,055] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dfe15ad-de5e-4da9-ace3-9478bbb74415/GCF_001482405.1_ASM148240v1_genomic.fna.gz --refList GCF_001482405.1_ASM148240v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001482405.1_ASM148240v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:42:02,623] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:02,639] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:42:02,639] [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_001482405.1	s__Ponticoccus marisrubri	100.0	1488	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900184945.1	s__Maliponia aquimaris	81.783	943	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maliponia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255395.1	s__AWRV01 sp017255395	81.5887	876	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	81.2893	866	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	81.1267	809	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101505.1	s__Mameliella alba	81.0809	902	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCA_016806125.1	s__AWRV01 sp000504185	81.0724	873	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	99.97	99.97	1.00	1.00	2	-
GCF_900107235.1	s__Citreimonas salinaria	80.9369	719	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	80.8971	754	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	80.7565	844	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153725.1	s__Salipiger bermudensis	80.7222	784	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_017311415.1	s__Salipiger abyssi_A	80.5592	772	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969385.1	s__Salipiger profundus	80.4447	725	1490	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	80.3634	776	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_900100085.1	s__Salipiger marinus	79.877	736	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_001687105.1	s__Salipiger sp001687105	79.7287	727	1490	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	96.47	96.47	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:42:02,641] [INFO] GTDB search result was written to GCF_001482405.1_ASM148240v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:42:02,641] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:42:02,644] [INFO] DFAST_QC result json was written to GCF_001482405.1_ASM148240v1_genomic.fna/dqc_result.json
[2024-01-24 12:42:02,645] [INFO] DFAST_QC completed!
[2024-01-24 12:42:02,645] [INFO] Total running time: 0h1m42s