[2024-01-24 15:02:45,699] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:45,701] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:45,701] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c3c08a8-2123-4e2e-803e-fa683d27ebe7/dqc_reference
[2024-01-24 15:02:46,932] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:46,939] [INFO] Task started: Prodigal
[2024-01-24 15:02:46,940] [INFO] Running command: gunzip -c /var/lib/cwl/stgd969055c-831d-4a0d-a929-083024140f23/GCF_003201205.1_ASM320120v1_genomic.fna.gz | prodigal -d GCF_003201205.1_ASM320120v1_genomic.fna/cds.fna -a GCF_003201205.1_ASM320120v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:59,924] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:59,924] [INFO] Task started: HMMsearch
[2024-01-24 15:02:59,924] [INFO] Running command: hmmsearch --tblout GCF_003201205.1_ASM320120v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c3c08a8-2123-4e2e-803e-fa683d27ebe7/dqc_reference/reference_markers.hmm GCF_003201205.1_ASM320120v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:00,256] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:00,258] [INFO] Found 6/6 markers.
[2024-01-24 15:03:00,295] [INFO] Query marker FASTA was written to GCF_003201205.1_ASM320120v1_genomic.fna/markers.fasta
[2024-01-24 15:03:00,295] [INFO] Task started: Blastn
[2024-01-24 15:03:00,295] [INFO] Running command: blastn -query GCF_003201205.1_ASM320120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c3c08a8-2123-4e2e-803e-fa683d27ebe7/dqc_reference/reference_markers.fasta -out GCF_003201205.1_ASM320120v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:01,304] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:01,308] [INFO] Selected 12 target genomes.
[2024-01-24 15:03:01,308] [INFO] Target genome list was writen to GCF_003201205.1_ASM320120v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:01,313] [INFO] Task started: fastANI
[2024-01-24 15:03:01,314] [INFO] Running command: fastANI --query /var/lib/cwl/stgd969055c-831d-4a0d-a929-083024140f23/GCF_003201205.1_ASM320120v1_genomic.fna.gz --refList GCF_003201205.1_ASM320120v1_genomic.fna/target_genomes.txt --output GCF_003201205.1_ASM320120v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:12,102] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:12,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c3c08a8-2123-4e2e-803e-fa683d27ebe7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:12,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c3c08a8-2123-4e2e-803e-fa683d27ebe7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:12,116] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:03:12,116] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:03:12,116] [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
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	80.554	650	1449	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	80.3949	661	1449	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	80.3207	630	1449	95	below_threshold
Solimonas fluminis	strain=HR-BB	GCA_002930645.1	2086571	2086571	type	True	80.1892	670	1449	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	79.5644	560	1449	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	79.4926	529	1449	95	below_threshold
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	79.3962	558	1449	95	below_threshold
Flagellatimonas centrodinii	strain=R2A-3	GCA_016918765.2	2806210	2806210	type	True	78.444	334	1449	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	77.014	213	1449	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	76.5301	277	1449	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.4657	261	1449	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	76.4411	257	1449	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:12,118] [INFO] DFAST Taxonomy check result was written to GCF_003201205.1_ASM320120v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:12,118] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:12,119] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:12,119] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c3c08a8-2123-4e2e-803e-fa683d27ebe7/dqc_reference/checkm_data
[2024-01-24 15:03:12,120] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:12,165] [INFO] Task started: CheckM
[2024-01-24 15:03:12,165] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003201205.1_ASM320120v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003201205.1_ASM320120v1_genomic.fna/checkm_input GCF_003201205.1_ASM320120v1_genomic.fna/checkm_result
[2024-01-24 15:04:00,424] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:00,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:00,450] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:00,451] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:00,452] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003201205.1_ASM320120v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:00,452] [INFO] Task started: Blastn
[2024-01-24 15:04:00,452] [INFO] Running command: blastn -query GCF_003201205.1_ASM320120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c3c08a8-2123-4e2e-803e-fa683d27ebe7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003201205.1_ASM320120v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:02,475] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:02,480] [INFO] Selected 9 target genomes.
[2024-01-24 15:04:02,481] [INFO] Target genome list was writen to GCF_003201205.1_ASM320120v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:02,510] [INFO] Task started: fastANI
[2024-01-24 15:04:02,510] [INFO] Running command: fastANI --query /var/lib/cwl/stgd969055c-831d-4a0d-a929-083024140f23/GCF_003201205.1_ASM320120v1_genomic.fna.gz --refList GCF_003201205.1_ASM320120v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003201205.1_ASM320120v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:11,333] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:11,341] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:11,341] [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_003201205.1	s__Sinimarinibacterium flocculans	100.0	1449	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Sinimarinibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000382285.1	s__Solimonas variicoloris	80.5313	652	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_000426685.1	s__Solimonas flava	80.3593	665	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_000474945.1	s__Solimonas soli	80.2805	634	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002930645.1	s__Solimonas_A fluminis	80.1978	669	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003428335.1	s__Solimonas_A sp003428335	79.9324	669	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113085.1	s__Fontimonas thermophila	79.6634	532	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Fontimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111015.1	s__Solimonas aquatica	79.4315	537	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012241385.1	s__Solimonas marina	79.4092	557	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:11,343] [INFO] GTDB search result was written to GCF_003201205.1_ASM320120v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:11,344] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:11,346] [INFO] DFAST_QC result json was written to GCF_003201205.1_ASM320120v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:11,347] [INFO] DFAST_QC completed!
[2024-01-24 15:04:11,347] [INFO] Total running time: 0h1m26s