[2024-01-24 13:18:26,412] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:26,414] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:26,414] [INFO] DQC Reference Directory: /var/lib/cwl/stg29d2dab6-8ec5-4c5e-b25d-da059d57ba65/dqc_reference
[2024-01-24 13:18:27,559] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:27,560] [INFO] Task started: Prodigal
[2024-01-24 13:18:27,560] [INFO] Running command: gunzip -c /var/lib/cwl/stg15198cf9-ae1f-42be-8913-b4e4867d11b0/GCF_007830625.1_ASM783062v1_genomic.fna.gz | prodigal -d GCF_007830625.1_ASM783062v1_genomic.fna/cds.fna -a GCF_007830625.1_ASM783062v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:42,694] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:42,695] [INFO] Task started: HMMsearch
[2024-01-24 13:18:42,695] [INFO] Running command: hmmsearch --tblout GCF_007830625.1_ASM783062v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29d2dab6-8ec5-4c5e-b25d-da059d57ba65/dqc_reference/reference_markers.hmm GCF_007830625.1_ASM783062v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:42,931] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:42,933] [INFO] Found 6/6 markers.
[2024-01-24 13:18:42,994] [INFO] Query marker FASTA was written to GCF_007830625.1_ASM783062v1_genomic.fna/markers.fasta
[2024-01-24 13:18:42,995] [INFO] Task started: Blastn
[2024-01-24 13:18:42,995] [INFO] Running command: blastn -query GCF_007830625.1_ASM783062v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29d2dab6-8ec5-4c5e-b25d-da059d57ba65/dqc_reference/reference_markers.fasta -out GCF_007830625.1_ASM783062v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:43,905] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:43,910] [INFO] Selected 14 target genomes.
[2024-01-24 13:18:43,910] [INFO] Target genome list was writen to GCF_007830625.1_ASM783062v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:43,918] [INFO] Task started: fastANI
[2024-01-24 13:18:43,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg15198cf9-ae1f-42be-8913-b4e4867d11b0/GCF_007830625.1_ASM783062v1_genomic.fna.gz --refList GCF_007830625.1_ASM783062v1_genomic.fna/target_genomes.txt --output GCF_007830625.1_ASM783062v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:57,189] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:57,189] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29d2dab6-8ec5-4c5e-b25d-da059d57ba65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:57,190] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29d2dab6-8ec5-4c5e-b25d-da059d57ba65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:57,202] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:18:57,202] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:57,203] [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 caeni	strain=CGMCC 1.7745	GCA_007830625.1	589035	589035	type	True	100.0	1699	1704	95	conclusive
Gemmobacter caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	99.9615	1648	1704	95	conclusive
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	91.3925	1195	1704	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	83.2288	856	1704	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	81.6459	907	1704	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	81.4957	788	1704	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	81.195	753	1704	95	below_threshold
Gemmobacter aquaticus	strain=CGMCC 1.7029	GCA_014645295.1	490185	490185	type	True	80.3899	672	1704	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	79.8475	645	1704	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	79.8289	647	1704	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	79.6662	560	1704	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	79.3223	562	1704	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.2088	530	1704	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	78.9934	606	1704	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:57,205] [INFO] DFAST Taxonomy check result was written to GCF_007830625.1_ASM783062v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:57,205] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:57,205] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:57,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29d2dab6-8ec5-4c5e-b25d-da059d57ba65/dqc_reference/checkm_data
[2024-01-24 13:18:57,207] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:57,255] [INFO] Task started: CheckM
[2024-01-24 13:18:57,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830625.1_ASM783062v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830625.1_ASM783062v1_genomic.fna/checkm_input GCF_007830625.1_ASM783062v1_genomic.fna/checkm_result
[2024-01-24 13:19:50,795] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:50,796] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:50,812] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:50,813] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:50,813] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830625.1_ASM783062v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:50,813] [INFO] Task started: Blastn
[2024-01-24 13:19:50,814] [INFO] Running command: blastn -query GCF_007830625.1_ASM783062v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29d2dab6-8ec5-4c5e-b25d-da059d57ba65/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830625.1_ASM783062v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:52,535] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:52,539] [INFO] Selected 13 target genomes.
[2024-01-24 13:19:52,539] [INFO] Target genome list was writen to GCF_007830625.1_ASM783062v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:52,554] [INFO] Task started: fastANI
[2024-01-24 13:19:52,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg15198cf9-ae1f-42be-8913-b4e4867d11b0/GCF_007830625.1_ASM783062v1_genomic.fna.gz --refList GCF_007830625.1_ASM783062v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830625.1_ASM783062v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:05,099] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:05,110] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:05,110] [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_003054195.1	s__Gemmobacter caeni	99.9615	1648	1704	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	98.77	98.23	0.88	0.79	5	conclusive
GCF_003570715.1	s__Gemmobacter lutimaris	91.4032	1194	1704	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271655.1	s__Gemmobacter caeruleus	83.2017	857	1704	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	82.1245	846	1704	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	81.6448	651	1704	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	81.6276	906	1704	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014652355.1	s__Gemmobacter lanyuensis	81.4852	788	1704	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973825.1	s__Gemmobacter serpentinus	81.1675	758	1704	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003509785.1	s__Gemmobacter sp003509785	81.135	642	1704	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	99.39	99.26	0.82	0.79	4	-
GCF_007859075.1	s__Gemmobacter aquaticus	80.4094	674	1704	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004799285.1	s__Gemmobacter_D aestuarii	80.0562	664	1704	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765795.1	s__UBA1943 sp016765795	79.2001	596	1704	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336845.1	s__UBA1943 sp002336845	79.1345	572	1704	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:05,112] [INFO] GTDB search result was written to GCF_007830625.1_ASM783062v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:05,112] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:05,116] [INFO] DFAST_QC result json was written to GCF_007830625.1_ASM783062v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:05,116] [INFO] DFAST_QC completed!
[2024-01-24 13:20:05,116] [INFO] Total running time: 0h1m39s