[2024-01-24 13:19:01,503] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:01,505] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:01,506] [INFO] DQC Reference Directory: /var/lib/cwl/stg967d968a-91de-4f50-b7bd-52fb0b066431/dqc_reference
[2024-01-24 13:19:02,897] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:02,897] [INFO] Task started: Prodigal
[2024-01-24 13:19:02,898] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5a2eee7-d98a-4f8b-ab21-1d1b4c6baf1d/GCF_021532615.1_ASM2153261v1_genomic.fna.gz | prodigal -d GCF_021532615.1_ASM2153261v1_genomic.fna/cds.fna -a GCF_021532615.1_ASM2153261v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:16,518] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:16,518] [INFO] Task started: HMMsearch
[2024-01-24 13:19:16,518] [INFO] Running command: hmmsearch --tblout GCF_021532615.1_ASM2153261v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg967d968a-91de-4f50-b7bd-52fb0b066431/dqc_reference/reference_markers.hmm GCF_021532615.1_ASM2153261v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:16,840] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:16,841] [INFO] Found 6/6 markers.
[2024-01-24 13:19:16,877] [INFO] Query marker FASTA was written to GCF_021532615.1_ASM2153261v1_genomic.fna/markers.fasta
[2024-01-24 13:19:16,877] [INFO] Task started: Blastn
[2024-01-24 13:19:16,877] [INFO] Running command: blastn -query GCF_021532615.1_ASM2153261v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg967d968a-91de-4f50-b7bd-52fb0b066431/dqc_reference/reference_markers.fasta -out GCF_021532615.1_ASM2153261v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:17,807] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:17,811] [INFO] Selected 16 target genomes.
[2024-01-24 13:19:17,811] [INFO] Target genome list was writen to GCF_021532615.1_ASM2153261v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:17,823] [INFO] Task started: fastANI
[2024-01-24 13:19:17,824] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5a2eee7-d98a-4f8b-ab21-1d1b4c6baf1d/GCF_021532615.1_ASM2153261v1_genomic.fna.gz --refList GCF_021532615.1_ASM2153261v1_genomic.fna/target_genomes.txt --output GCF_021532615.1_ASM2153261v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:31,834] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:31,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg967d968a-91de-4f50-b7bd-52fb0b066431/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:31,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg967d968a-91de-4f50-b7bd-52fb0b066431/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:31,856] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:31,856] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:31,856] [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
Octadecabacter ascidiaceicola	strain=CECT 8868	GCA_900185015.1	1655543	1655543	type	True	79.364	518	1240	95	below_threshold
Octadecabacter temperatus	strain=SB1	GCA_001187845.1	1458307	1458307	type	True	79.2149	484	1240	95	below_threshold
Octadecabacter temperatus	strain=DSM 26878	GCA_900142425.1	1458307	1458307	type	True	79.2031	494	1240	95	below_threshold
Octadecabacter antarcticus	strain=307	GCA_000155675.2	1217908	1217908	type	True	79.0958	534	1240	95	below_threshold
Octadecabacter arcticus	strain=238	GCA_000155735.2	53946	53946	type	True	79.0024	547	1240	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	78.1351	368	1240	95	below_threshold
Yoonia maritima	strain=DSM 101533	GCA_003003285.1	1435347	1435347	type	True	77.2746	153	1240	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	77.0088	236	1240	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.7667	146	1240	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.5002	151	1240	95	below_threshold
Puniceibacterium antarcticum	strain=SM1211	GCA_002760615.1	1206336	1206336	type	True	76.4845	151	1240	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.4475	99	1240	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	76.4387	140	1240	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	76.4052	134	1240	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.3841	126	1240	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	76.1273	163	1240	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:31,859] [INFO] DFAST Taxonomy check result was written to GCF_021532615.1_ASM2153261v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:31,860] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:31,860] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:31,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg967d968a-91de-4f50-b7bd-52fb0b066431/dqc_reference/checkm_data
[2024-01-24 13:19:31,862] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:31,908] [INFO] Task started: CheckM
[2024-01-24 13:19:31,909] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021532615.1_ASM2153261v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021532615.1_ASM2153261v1_genomic.fna/checkm_input GCF_021532615.1_ASM2153261v1_genomic.fna/checkm_result
[2024-01-24 13:20:14,085] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:14,087] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:14,186] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:14,187] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:14,187] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021532615.1_ASM2153261v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:14,188] [INFO] Task started: Blastn
[2024-01-24 13:20:14,188] [INFO] Running command: blastn -query GCF_021532615.1_ASM2153261v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg967d968a-91de-4f50-b7bd-52fb0b066431/dqc_reference/reference_markers_gtdb.fasta -out GCF_021532615.1_ASM2153261v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:15,580] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:15,583] [INFO] Selected 10 target genomes.
[2024-01-24 13:20:15,583] [INFO] Target genome list was writen to GCF_021532615.1_ASM2153261v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:15,612] [INFO] Task started: fastANI
[2024-01-24 13:20:15,612] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5a2eee7-d98a-4f8b-ab21-1d1b4c6baf1d/GCF_021532615.1_ASM2153261v1_genomic.fna.gz --refList GCF_021532615.1_ASM2153261v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021532615.1_ASM2153261v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:22,234] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:22,245] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:20:22,246] [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_018608045.1	s__Octadecabacter sp018608045	81.2438	592	1240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	98.68	98.68	0.85	0.85	2	-
GCA_018500005.1	s__Octadecabacter sp018500005	79.4119	358	1240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900185015.1	s__Octadecabacter ascidiaceicola	79.364	518	1240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187845.1	s__Octadecabacter temperatus	79.2247	483	1240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017886375.1	s__Octadecabacter sp017886375	79.1565	521	1240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	99.96	99.96	0.97	0.97	2	-
GCF_000155675.2	s__Octadecabacter antarcticus	79.1001	533	1240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000155735.2	s__Octadecabacter arcticus	79.0105	546	1240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	96.73	96.73	0.93	0.93	2	-
GCF_018861045.1	s__Octadecabacter sp018861045	78.7319	469	1240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003533975.1	s__Octadecabacter sp003533975	78.3265	316	1240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072065.1	s__Thalassorhabdomicrobium marinisediminis	78.1351	368	1240	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassorhabdomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:22,248] [INFO] GTDB search result was written to GCF_021532615.1_ASM2153261v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:22,249] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:22,255] [INFO] DFAST_QC result json was written to GCF_021532615.1_ASM2153261v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:22,256] [INFO] DFAST_QC completed!
[2024-01-24 13:20:22,256] [INFO] Total running time: 0h1m21s