[2024-01-24 12:28:34,537] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:28:34,539] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:28:34,539] [INFO] DQC Reference Directory: /var/lib/cwl/stg8bb9cb9c-4cb1-401f-bb97-74dbd06f3886/dqc_reference
[2024-01-24 12:28:35,727] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:28:35,728] [INFO] Task started: Prodigal
[2024-01-24 12:28:35,729] [INFO] Running command: gunzip -c /var/lib/cwl/stg1af1c8a0-fd8c-494c-8e62-1e228eadc6e9/GCF_014652355.1_ASM1465235v1_genomic.fna.gz | prodigal -d GCF_014652355.1_ASM1465235v1_genomic.fna/cds.fna -a GCF_014652355.1_ASM1465235v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:28:48,061] [INFO] Task succeeded: Prodigal
[2024-01-24 12:28:48,061] [INFO] Task started: HMMsearch
[2024-01-24 12:28:48,062] [INFO] Running command: hmmsearch --tblout GCF_014652355.1_ASM1465235v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8bb9cb9c-4cb1-401f-bb97-74dbd06f3886/dqc_reference/reference_markers.hmm GCF_014652355.1_ASM1465235v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:28:48,326] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:28:48,328] [INFO] Found 6/6 markers.
[2024-01-24 12:28:48,370] [INFO] Query marker FASTA was written to GCF_014652355.1_ASM1465235v1_genomic.fna/markers.fasta
[2024-01-24 12:28:48,370] [INFO] Task started: Blastn
[2024-01-24 12:28:48,371] [INFO] Running command: blastn -query GCF_014652355.1_ASM1465235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bb9cb9c-4cb1-401f-bb97-74dbd06f3886/dqc_reference/reference_markers.fasta -out GCF_014652355.1_ASM1465235v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:28:49,336] [INFO] Task succeeded: Blastn
[2024-01-24 12:28:49,340] [INFO] Selected 14 target genomes.
[2024-01-24 12:28:49,340] [INFO] Target genome list was writen to GCF_014652355.1_ASM1465235v1_genomic.fna/target_genomes.txt
[2024-01-24 12:28:49,388] [INFO] Task started: fastANI
[2024-01-24 12:28:49,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg1af1c8a0-fd8c-494c-8e62-1e228eadc6e9/GCF_014652355.1_ASM1465235v1_genomic.fna.gz --refList GCF_014652355.1_ASM1465235v1_genomic.fna/target_genomes.txt --output GCF_014652355.1_ASM1465235v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:01,195] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:01,196] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8bb9cb9c-4cb1-401f-bb97-74dbd06f3886/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:01,197] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8bb9cb9c-4cb1-401f-bb97-74dbd06f3886/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:01,220] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:29:01,220] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:01,221] [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
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	100.0	1320	1324	95	conclusive
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	82.6693	810	1324	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	81.8847	787	1324	95	below_threshold
Gemmobacter caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	81.5366	778	1324	95	below_threshold
Gemmobacter caeni	strain=CGMCC 1.7745	GCA_007830625.1	589035	589035	type	True	81.5313	789	1324	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	81.3987	783	1324	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	81.3742	784	1324	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	81.1797	695	1324	95	below_threshold
Gemmobacter aquaticus	strain=A1-9	GCA_007859075.1	490185	490185	type	True	81.0805	676	1324	95	below_threshold
Gemmobacter aquaticus	strain=CGMCC 1.7029	GCA_014645295.1	490185	490185	type	True	81.0172	686	1324	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	79.778	596	1324	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	79.7688	596	1324	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	79.5434	545	1324	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	79.3677	585	1324	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:01,222] [INFO] DFAST Taxonomy check result was written to GCF_014652355.1_ASM1465235v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:01,223] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:01,223] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:01,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8bb9cb9c-4cb1-401f-bb97-74dbd06f3886/dqc_reference/checkm_data
[2024-01-24 12:29:01,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:01,269] [INFO] Task started: CheckM
[2024-01-24 12:29:01,269] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652355.1_ASM1465235v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652355.1_ASM1465235v1_genomic.fna/checkm_input GCF_014652355.1_ASM1465235v1_genomic.fna/checkm_result
[2024-01-24 12:29:43,963] [INFO] Task succeeded: CheckM
[2024-01-24 12:29:43,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:29:43,987] [INFO] ===== Completeness check finished =====
[2024-01-24 12:29:43,987] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:29:43,988] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652355.1_ASM1465235v1_genomic.fna/markers.fasta)
[2024-01-24 12:29:43,988] [INFO] Task started: Blastn
[2024-01-24 12:29:43,988] [INFO] Running command: blastn -query GCF_014652355.1_ASM1465235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bb9cb9c-4cb1-401f-bb97-74dbd06f3886/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652355.1_ASM1465235v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:45,782] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:45,785] [INFO] Selected 10 target genomes.
[2024-01-24 12:29:45,785] [INFO] Target genome list was writen to GCF_014652355.1_ASM1465235v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:29:45,825] [INFO] Task started: fastANI
[2024-01-24 12:29:45,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg1af1c8a0-fd8c-494c-8e62-1e228eadc6e9/GCF_014652355.1_ASM1465235v1_genomic.fna.gz --refList GCF_014652355.1_ASM1465235v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652355.1_ASM1465235v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:29:54,911] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:54,929] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:29:54,930] [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_014652355.1	s__Gemmobacter lanyuensis	100.0	1320	1324	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008271655.1	s__Gemmobacter caeruleus	82.6457	811	1324	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110025.1	s__Gemmobacter aquatilis	81.8673	789	1324	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792925.1	s__Gemmobacter sp016792925	81.6296	645	1324	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054195.1	s__Gemmobacter caeni	81.5285	780	1324	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	98.77	98.23	0.88	0.79	5	-
GCF_003570715.1	s__Gemmobacter lutimaris	81.3955	783	1324	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018798885.1	s__Gemmobacter sp018798885	81.3877	783	1324	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008973825.1	s__Gemmobacter serpentinus	81.2047	692	1324	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859075.1	s__Gemmobacter aquaticus	81.0644	678	1324	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003509785.1	s__Gemmobacter sp003509785	81.0146	580	1324	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	99.39	99.26	0.82	0.79	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:29:54,932] [INFO] GTDB search result was written to GCF_014652355.1_ASM1465235v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:29:54,933] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:29:54,936] [INFO] DFAST_QC result json was written to GCF_014652355.1_ASM1465235v1_genomic.fna/dqc_result.json
[2024-01-24 12:29:54,936] [INFO] DFAST_QC completed!
[2024-01-24 12:29:54,936] [INFO] Total running time: 0h1m20s