[2024-01-24 13:27:31,883] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:31,885] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:31,885] [INFO] DQC Reference Directory: /var/lib/cwl/stgceccf840-e9cf-470f-a868-8bc7a6281f97/dqc_reference
[2024-01-24 13:27:33,266] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:33,267] [INFO] Task started: Prodigal
[2024-01-24 13:27:33,267] [INFO] Running command: gunzip -c /var/lib/cwl/stgff17726c-c9c7-4e99-861f-d0a0372a0b2c/GCF_000382285.1_ASM38228v1_genomic.fna.gz | prodigal -d GCF_000382285.1_ASM38228v1_genomic.fna/cds.fna -a GCF_000382285.1_ASM38228v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:43,953] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:43,954] [INFO] Task started: HMMsearch
[2024-01-24 13:27:43,954] [INFO] Running command: hmmsearch --tblout GCF_000382285.1_ASM38228v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgceccf840-e9cf-470f-a868-8bc7a6281f97/dqc_reference/reference_markers.hmm GCF_000382285.1_ASM38228v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:44,238] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:44,239] [INFO] Found 6/6 markers.
[2024-01-24 13:27:44,277] [INFO] Query marker FASTA was written to GCF_000382285.1_ASM38228v1_genomic.fna/markers.fasta
[2024-01-24 13:27:44,278] [INFO] Task started: Blastn
[2024-01-24 13:27:44,278] [INFO] Running command: blastn -query GCF_000382285.1_ASM38228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgceccf840-e9cf-470f-a868-8bc7a6281f97/dqc_reference/reference_markers.fasta -out GCF_000382285.1_ASM38228v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:45,288] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:45,294] [INFO] Selected 12 target genomes.
[2024-01-24 13:27:45,295] [INFO] Target genome list was writen to GCF_000382285.1_ASM38228v1_genomic.fna/target_genomes.txt
[2024-01-24 13:27:45,301] [INFO] Task started: fastANI
[2024-01-24 13:27:45,302] [INFO] Running command: fastANI --query /var/lib/cwl/stgff17726c-c9c7-4e99-861f-d0a0372a0b2c/GCF_000382285.1_ASM38228v1_genomic.fna.gz --refList GCF_000382285.1_ASM38228v1_genomic.fna/target_genomes.txt --output GCF_000382285.1_ASM38228v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:27:57,416] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:57,417] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgceccf840-e9cf-470f-a868-8bc7a6281f97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:27:57,417] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgceccf840-e9cf-470f-a868-8bc7a6281f97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:27:57,429] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:27:57,429] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:27:57,429] [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	100.0	1349	1350	95	conclusive
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	94.9732	1234	1350	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	85.9802	943	1350	95	below_threshold
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	82.5096	857	1350	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	82.3958	832	1350	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	80.4733	681	1350	95	below_threshold
Solimonas fluminis	strain=HR-BB	GCA_002930645.1	2086571	2086571	type	True	80.2041	667	1350	95	below_threshold
Flagellatimonas centrodinii	strain=R2A-3	GCA_016918765.2	2806210	2806210	type	True	77.8519	311	1350	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	76.6026	265	1350	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.3612	299	1350	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.2648	299	1350	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	76.1462	335	1350	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:27:57,431] [INFO] DFAST Taxonomy check result was written to GCF_000382285.1_ASM38228v1_genomic.fna/tc_result.tsv
[2024-01-24 13:27:57,432] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:27:57,432] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:27:57,432] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgceccf840-e9cf-470f-a868-8bc7a6281f97/dqc_reference/checkm_data
[2024-01-24 13:27:57,433] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:27:57,474] [INFO] Task started: CheckM
[2024-01-24 13:27:57,474] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000382285.1_ASM38228v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000382285.1_ASM38228v1_genomic.fna/checkm_input GCF_000382285.1_ASM38228v1_genomic.fna/checkm_result
[2024-01-24 13:28:47,040] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:47,041] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:47,066] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:47,066] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:47,066] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000382285.1_ASM38228v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:47,067] [INFO] Task started: Blastn
[2024-01-24 13:28:47,067] [INFO] Running command: blastn -query GCF_000382285.1_ASM38228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgceccf840-e9cf-470f-a868-8bc7a6281f97/dqc_reference/reference_markers_gtdb.fasta -out GCF_000382285.1_ASM38228v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:49,074] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:49,078] [INFO] Selected 7 target genomes.
[2024-01-24 13:28:49,079] [INFO] Target genome list was writen to GCF_000382285.1_ASM38228v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:49,101] [INFO] Task started: fastANI
[2024-01-24 13:28:49,102] [INFO] Running command: fastANI --query /var/lib/cwl/stgff17726c-c9c7-4e99-861f-d0a0372a0b2c/GCF_000382285.1_ASM38228v1_genomic.fna.gz --refList GCF_000382285.1_ASM38228v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000382285.1_ASM38228v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:57,197] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:57,211] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:57,211] [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_000382285.1	s__Solimonas variicoloris	100.0	1349	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	conclusive
GCF_000426685.1	s__Solimonas flava	94.9897	1233	1350	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	86.0209	939	1350	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	82.5053	858	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011067135.1	s__Solimonas terrae	82.4044	831	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111015.1	s__Solimonas aquatica	80.448	684	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201205.1	s__Sinimarinibacterium flocculans	80.4111	669	1350	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Sinimarinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:57,213] [INFO] GTDB search result was written to GCF_000382285.1_ASM38228v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:57,214] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:57,216] [INFO] DFAST_QC result json was written to GCF_000382285.1_ASM38228v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:57,216] [INFO] DFAST_QC completed!
[2024-01-24 13:28:57,217] [INFO] Total running time: 0h1m25s