[2024-01-24 14:30:34,481] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:34,483] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:34,483] [INFO] DQC Reference Directory: /var/lib/cwl/stg39db0a14-61b0-46b0-88a6-033d4efbc575/dqc_reference
[2024-01-24 14:30:35,955] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:35,956] [INFO] Task started: Prodigal
[2024-01-24 14:30:35,956] [INFO] Running command: gunzip -c /var/lib/cwl/stg78734d5e-49d7-4e3b-a08d-08bdb713f300/GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna.gz | prodigal -d GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna/cds.fna -a GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:48,857] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:48,857] [INFO] Task started: HMMsearch
[2024-01-24 14:30:48,857] [INFO] Running command: hmmsearch --tblout GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39db0a14-61b0-46b0-88a6-033d4efbc575/dqc_reference/reference_markers.hmm GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:49,127] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:49,128] [INFO] Found 6/6 markers.
[2024-01-24 14:30:49,165] [INFO] Query marker FASTA was written to GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta
[2024-01-24 14:30:49,165] [INFO] Task started: Blastn
[2024-01-24 14:30:49,165] [INFO] Running command: blastn -query GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta -db /var/lib/cwl/stg39db0a14-61b0-46b0-88a6-033d4efbc575/dqc_reference/reference_markers.fasta -out GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:49,937] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:49,941] [INFO] Selected 17 target genomes.
[2024-01-24 14:30:49,941] [INFO] Target genome list was writen to GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna/target_genomes.txt
[2024-01-24 14:30:49,948] [INFO] Task started: fastANI
[2024-01-24 14:30:49,948] [INFO] Running command: fastANI --query /var/lib/cwl/stg78734d5e-49d7-4e3b-a08d-08bdb713f300/GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna.gz --refList GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna/target_genomes.txt --output GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:03,008] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:03,008] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39db0a14-61b0-46b0-88a6-033d4efbc575/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:03,009] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39db0a14-61b0-46b0-88a6-033d4efbc575/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:03,023] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:03,023] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:03,024] [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
Thioclava indica	strain=DT23-4	GCA_000714545.1	1353528	1353528	type	True	100.0	1219	1222	95	conclusive
Thioclava dalianensis	strain=DLFJ1-1	GCA_000715505.1	1185766	1185766	type	True	81.3354	693	1222	95	below_threshold
Thioclava dalianensis	strain=CGMCC 1.12325	GCA_900115035.1	1185766	1185766	type	True	81.3155	710	1222	95	below_threshold
Thioclava electrotropha	strain=Elox9	GCA_002085925.2	1549850	1549850	type	True	80.3647	687	1222	95	below_threshold
Thioclava pacifica	strain=DSM 10166	GCA_000714535.1	285109	285109	type	True	80.3528	649	1222	95	below_threshold
Thioclava marina	strain=11.10-0-13	GCA_002020135.1	1915077	1915077	type	True	80.194	666	1222	95	below_threshold
Thioclava sediminum	strain=TAW-CT134	GCA_002020355.1	1915319	1915319	type	True	80.0813	676	1222	95	below_threshold
Thioclava nitratireducens	strain=25B10_4	GCA_001940525.2	1915078	1915078	type	True	79.9263	637	1222	95	below_threshold
Thioclava atlantica	strain=13D2W-2	GCA_000737065.1	1317124	1317124	type	True	79.8834	622	1222	95	below_threshold
Rhodobacter capsulatus	strain=DSM 1710	GCA_003254295.1	1061	1061	type	True	78.2687	415	1222	95	below_threshold
Rhodobacter aestuarii	strain=DSM 19945	GCA_900156655.1	453582	453582	type	True	77.9002	359	1222	95	below_threshold
Rhodobacter aestuarii	strain=JA296	GCA_003053525.1	453582	453582	type	True	77.8545	368	1222	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	77.5937	258	1222	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	77.5252	345	1222	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.4445	240	1222	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	77.4016	287	1222	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	77.337	249	1222	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:03,026] [INFO] DFAST Taxonomy check result was written to GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna/tc_result.tsv
[2024-01-24 14:31:03,027] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:03,027] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:03,027] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39db0a14-61b0-46b0-88a6-033d4efbc575/dqc_reference/checkm_data
[2024-01-24 14:31:03,028] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:03,071] [INFO] Task started: CheckM
[2024-01-24 14:31:03,071] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna/checkm_input GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna/checkm_result
[2024-01-24 14:31:43,651] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:43,652] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:43,674] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:43,675] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:43,675] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta)
[2024-01-24 14:31:43,676] [INFO] Task started: Blastn
[2024-01-24 14:31:43,676] [INFO] Running command: blastn -query GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta -db /var/lib/cwl/stg39db0a14-61b0-46b0-88a6-033d4efbc575/dqc_reference/reference_markers_gtdb.fasta -out GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:44,868] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:44,874] [INFO] Selected 12 target genomes.
[2024-01-24 14:31:44,874] [INFO] Target genome list was writen to GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:44,883] [INFO] Task started: fastANI
[2024-01-24 14:31:44,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg78734d5e-49d7-4e3b-a08d-08bdb713f300/GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna.gz --refList GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna/target_genomes_gtdb.txt --output GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:54,313] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:54,327] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:54,327] [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_000714545.1	s__Thioclava indica	100.0	1219	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016937195.1	s__Thioclava sp016937195	89.1596	733	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000715505.1	s__Thioclava dalianensis	81.3492	692	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009296265.1	s__Thioclava sp009296265	80.4631	672	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2474	N/A	N/A	N/A	N/A	1	-
GCF_000714535.1	s__Thioclava pacifica	80.3565	649	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002085925.2	s__Thioclava electrotropha	80.3559	688	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2561	N/A	N/A	N/A	N/A	1	-
GCF_002563775.1	s__Thioclava sp002563775	80.3378	675	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0406	95.45	95.45	0.86	0.86	2	-
GCF_002020135.1	s__Thioclava marina	80.1985	665	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	98.70	98.47	0.89	0.86	6	-
GCF_002020355.1	s__Thioclava sediminum	80.0815	676	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2561	96.53	96.29	0.92	0.90	8	-
GCF_000737065.1	s__Thioclava atlantica	79.9051	619	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452815.1	s__UBA6796 sp002452815	79.2195	508	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA6796	95.0	97.98	97.98	0.95	0.95	2	-
GCF_002358085.1	s__Thioclava arenosa	79.127	495	1222	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:54,329] [INFO] GTDB search result was written to GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:54,330] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:54,334] [INFO] DFAST_QC result json was written to GCF_000714545.1_SOAPdenovo_v1.05_genomic.fna/dqc_result.json
[2024-01-24 14:31:54,334] [INFO] DFAST_QC completed!
[2024-01-24 14:31:54,334] [INFO] Total running time: 0h1m20s