[2024-01-24 14:22:31,121] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:31,123] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:31,123] [INFO] DQC Reference Directory: /var/lib/cwl/stga0a53bbd-4057-40a7-b51a-48d135ae58c1/dqc_reference
[2024-01-24 14:22:32,456] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:32,457] [INFO] Task started: Prodigal
[2024-01-24 14:22:32,457] [INFO] Running command: gunzip -c /var/lib/cwl/stgd84711f8-cdb6-4090-8b3a-085efb782b51/GCF_003259375.1_ASM325937v1_genomic.fna.gz | prodigal -d GCF_003259375.1_ASM325937v1_genomic.fna/cds.fna -a GCF_003259375.1_ASM325937v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:56,951] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:56,951] [INFO] Task started: HMMsearch
[2024-01-24 14:22:56,951] [INFO] Running command: hmmsearch --tblout GCF_003259375.1_ASM325937v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0a53bbd-4057-40a7-b51a-48d135ae58c1/dqc_reference/reference_markers.hmm GCF_003259375.1_ASM325937v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:57,285] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:57,288] [INFO] Found 6/6 markers.
[2024-01-24 14:22:57,397] [INFO] Query marker FASTA was written to GCF_003259375.1_ASM325937v1_genomic.fna/markers.fasta
[2024-01-24 14:22:57,398] [INFO] Task started: Blastn
[2024-01-24 14:22:57,398] [INFO] Running command: blastn -query GCF_003259375.1_ASM325937v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0a53bbd-4057-40a7-b51a-48d135ae58c1/dqc_reference/reference_markers.fasta -out GCF_003259375.1_ASM325937v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:58,055] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:58,059] [INFO] Selected 8 target genomes.
[2024-01-24 14:22:58,060] [INFO] Target genome list was writen to GCF_003259375.1_ASM325937v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:58,065] [INFO] Task started: fastANI
[2024-01-24 14:22:58,065] [INFO] Running command: fastANI --query /var/lib/cwl/stgd84711f8-cdb6-4090-8b3a-085efb782b51/GCF_003259375.1_ASM325937v1_genomic.fna.gz --refList GCF_003259375.1_ASM325937v1_genomic.fna/target_genomes.txt --output GCF_003259375.1_ASM325937v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:08,076] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:08,077] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0a53bbd-4057-40a7-b51a-48d135ae58c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:08,077] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0a53bbd-4057-40a7-b51a-48d135ae58c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:08,090] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:08,091] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:08,091] [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
Arenibacter echinorum	strain=DSM 23522	GCA_003259375.1	440515	440515	type	True	100.0	1717	1718	95	conclusive
Arenibacter algicola	strain=TG409	GCA_000733925.1	616991	616991	type	True	89.7972	1357	1718	95	below_threshold
Arenibacter palladensis	strain=DSM 17539	GCA_900129275.1	237373	237373	type	True	88.744	1393	1718	95	below_threshold
Arenibacter troitsensis	strain=DSM 19835	GCA_900177645.1	188872	188872	type	True	87.3812	1301	1718	95	below_threshold
Arenibacter arenosicollis	strain=BSSL-BM3	GCA_014397245.1	2762274	2762274	type	True	83.4956	1182	1718	95	below_threshold
Arenibacter hampyeongensis	strain=JCM 17788	GCA_002909255.1	1028743	1028743	type	True	83.3964	1203	1718	95	below_threshold
Arenibacter catalasegens	strain=P308H10	GCA_002909235.1	2056779	2056779	type	True	82.2184	1126	1718	95	below_threshold
Zhouia spongiae	strain=HN-Y44	GCA_022760175.1	2202721	2202721	type	True	76.2458	54	1718	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:08,093] [INFO] DFAST Taxonomy check result was written to GCF_003259375.1_ASM325937v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:08,093] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:08,093] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:08,094] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0a53bbd-4057-40a7-b51a-48d135ae58c1/dqc_reference/checkm_data
[2024-01-24 14:23:08,095] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:08,147] [INFO] Task started: CheckM
[2024-01-24 14:23:08,147] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003259375.1_ASM325937v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003259375.1_ASM325937v1_genomic.fna/checkm_input GCF_003259375.1_ASM325937v1_genomic.fna/checkm_result
[2024-01-24 14:24:15,677] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:15,681] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:15,731] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:15,732] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:15,732] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003259375.1_ASM325937v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:15,732] [INFO] Task started: Blastn
[2024-01-24 14:24:15,732] [INFO] Running command: blastn -query GCF_003259375.1_ASM325937v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0a53bbd-4057-40a7-b51a-48d135ae58c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_003259375.1_ASM325937v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:16,621] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:16,631] [INFO] Selected 8 target genomes.
[2024-01-24 14:24:16,632] [INFO] Target genome list was writen to GCF_003259375.1_ASM325937v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:16,640] [INFO] Task started: fastANI
[2024-01-24 14:24:16,641] [INFO] Running command: fastANI --query /var/lib/cwl/stgd84711f8-cdb6-4090-8b3a-085efb782b51/GCF_003259375.1_ASM325937v1_genomic.fna.gz --refList GCF_003259375.1_ASM325937v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003259375.1_ASM325937v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:27,555] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:27,566] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:27,567] [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_003259375.1	s__Arenibacter echinorum	100.0	1717	1718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018860365.1	s__Arenibacter algicola_B	90.2529	1412	1718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733925.1	s__Arenibacter algicola	89.7776	1358	1718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	98.04	97.34	0.85	0.81	5	-
GCF_900129275.1	s__Arenibacter palladensis	88.7358	1394	1718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	97.38	97.38	0.84	0.84	2	-
GCF_900177645.1	s__Arenibacter troitsensis	87.3848	1300	1718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201775.1	s__Arenibacter sp003201775	85.6727	1257	1718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014397245.1	s__Arenibacter arenosicollis	83.5106	1180	1718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002909235.1	s__Arenibacter catalasegens	82.2184	1126	1718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:27,568] [INFO] GTDB search result was written to GCF_003259375.1_ASM325937v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:27,569] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:27,573] [INFO] DFAST_QC result json was written to GCF_003259375.1_ASM325937v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:27,573] [INFO] DFAST_QC completed!
[2024-01-24 14:24:27,573] [INFO] Total running time: 0h1m56s