[2024-01-24 11:58:55,605] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:55,607] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:55,607] [INFO] DQC Reference Directory: /var/lib/cwl/stg4090a313-0332-4661-b4ab-503e61c377b1/dqc_reference
[2024-01-24 11:58:56,963] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:56,964] [INFO] Task started: Prodigal
[2024-01-24 11:58:56,964] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ee17181-cb85-41a6-9653-a8392409812b/GCF_018798885.1_ASM1879888v1_genomic.fna.gz | prodigal -d GCF_018798885.1_ASM1879888v1_genomic.fna/cds.fna -a GCF_018798885.1_ASM1879888v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:11,935] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:11,935] [INFO] Task started: HMMsearch
[2024-01-24 11:59:11,935] [INFO] Running command: hmmsearch --tblout GCF_018798885.1_ASM1879888v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4090a313-0332-4661-b4ab-503e61c377b1/dqc_reference/reference_markers.hmm GCF_018798885.1_ASM1879888v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:12,259] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:12,261] [INFO] Found 6/6 markers.
[2024-01-24 11:59:12,303] [INFO] Query marker FASTA was written to GCF_018798885.1_ASM1879888v1_genomic.fna/markers.fasta
[2024-01-24 11:59:12,304] [INFO] Task started: Blastn
[2024-01-24 11:59:12,304] [INFO] Running command: blastn -query GCF_018798885.1_ASM1879888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4090a313-0332-4661-b4ab-503e61c377b1/dqc_reference/reference_markers.fasta -out GCF_018798885.1_ASM1879888v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:13,286] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:13,290] [INFO] Selected 15 target genomes.
[2024-01-24 11:59:13,290] [INFO] Target genome list was writen to GCF_018798885.1_ASM1879888v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:13,295] [INFO] Task started: fastANI
[2024-01-24 11:59:13,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ee17181-cb85-41a6-9653-a8392409812b/GCF_018798885.1_ASM1879888v1_genomic.fna.gz --refList GCF_018798885.1_ASM1879888v1_genomic.fna/target_genomes.txt --output GCF_018798885.1_ASM1879888v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:27,327] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:27,328] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4090a313-0332-4661-b4ab-503e61c377b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:27,328] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4090a313-0332-4661-b4ab-503e61c377b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:27,342] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:27,342] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:27,342] [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 fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	100.0	1551	1556	95	conclusive
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	83.6759	926	1556	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	82.1228	847	1556	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	81.8816	895	1556	95	below_threshold
Gemmobacter caeni	strain=CGMCC 1.7745	GCA_007830625.1	589035	589035	type	True	81.8169	887	1556	95	below_threshold
Gemmobacter caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	81.7576	891	1556	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	81.3477	784	1556	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	81.2522	775	1556	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	79.7525	618	1556	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	79.748	619	1556	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	79.7337	581	1556	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	79.7318	618	1556	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	79.7024	649	1556	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	79.5228	645	1556	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	79.2828	568	1556	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:27,344] [INFO] DFAST Taxonomy check result was written to GCF_018798885.1_ASM1879888v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:27,346] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:27,347] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:27,347] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4090a313-0332-4661-b4ab-503e61c377b1/dqc_reference/checkm_data
[2024-01-24 11:59:27,349] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:27,399] [INFO] Task started: CheckM
[2024-01-24 11:59:27,399] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018798885.1_ASM1879888v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018798885.1_ASM1879888v1_genomic.fna/checkm_input GCF_018798885.1_ASM1879888v1_genomic.fna/checkm_result
[2024-01-24 12:00:30,110] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:30,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:30,134] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:30,134] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:30,135] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018798885.1_ASM1879888v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:30,135] [INFO] Task started: Blastn
[2024-01-24 12:00:30,135] [INFO] Running command: blastn -query GCF_018798885.1_ASM1879888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4090a313-0332-4661-b4ab-503e61c377b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_018798885.1_ASM1879888v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:31,950] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:31,954] [INFO] Selected 14 target genomes.
[2024-01-24 12:00:31,954] [INFO] Target genome list was writen to GCF_018798885.1_ASM1879888v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:31,962] [INFO] Task started: fastANI
[2024-01-24 12:00:31,962] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ee17181-cb85-41a6-9653-a8392409812b/GCF_018798885.1_ASM1879888v1_genomic.fna.gz --refList GCF_018798885.1_ASM1879888v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018798885.1_ASM1879888v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:45,515] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:45,531] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:45,532] [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
GCA_018798885.1	s__Gemmobacter sp018798885	100.0	1551	1556	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900110025.1	s__Gemmobacter aquatilis	83.6732	928	1556	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	82.123	846	1556	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	82.0697	701	1556	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	99.39	99.26	0.82	0.79	4	-
GCF_003570715.1	s__Gemmobacter lutimaris	81.8924	894	1556	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	81.7643	689	1556	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	81.7292	895	1556	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	98.77	98.23	0.88	0.79	5	-
GCF_014652355.1	s__Gemmobacter lanyuensis	81.35	782	1556	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	81.2695	773	1556	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176015.1	s__Pseudorhodobacter_B sp000176015	80.5545	662	1556	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009380135.2	s__Fertoeibacter niger	80.4076	738	1556	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fertoeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034985.1	s__Cereibacter changlensis	79.7237	619	1556	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter	95.0	98.07	96.18	0.89	0.78	3	-
GCF_004799285.1	s__Gemmobacter_D aestuarii	79.4674	679	1556	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_000429765.1	s__Wagnerdoeblera nectariphila	79.2915	567	1556	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wagnerdoeblera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:45,533] [INFO] GTDB search result was written to GCF_018798885.1_ASM1879888v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:45,534] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:45,537] [INFO] DFAST_QC result json was written to GCF_018798885.1_ASM1879888v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:45,538] [INFO] DFAST_QC completed!
[2024-01-24 12:00:45,538] [INFO] Total running time: 0h1m50s