[2024-01-24 11:12:40,053] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:40,057] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:40,058] [INFO] DQC Reference Directory: /var/lib/cwl/stg009b42bd-a50a-4b78-8999-a660184499a4/dqc_reference
[2024-01-24 11:12:41,393] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:41,395] [INFO] Task started: Prodigal
[2024-01-24 11:12:41,395] [INFO] Running command: gunzip -c /var/lib/cwl/stga644f3e6-eac3-4cd3-8ca1-7c6fb8232df6/GCF_008033385.1_ASM803338v1_genomic.fna.gz | prodigal -d GCF_008033385.1_ASM803338v1_genomic.fna/cds.fna -a GCF_008033385.1_ASM803338v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:54,302] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:54,302] [INFO] Task started: HMMsearch
[2024-01-24 11:12:54,303] [INFO] Running command: hmmsearch --tblout GCF_008033385.1_ASM803338v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg009b42bd-a50a-4b78-8999-a660184499a4/dqc_reference/reference_markers.hmm GCF_008033385.1_ASM803338v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:54,579] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:54,580] [INFO] Found 6/6 markers.
[2024-01-24 11:12:54,618] [INFO] Query marker FASTA was written to GCF_008033385.1_ASM803338v1_genomic.fna/markers.fasta
[2024-01-24 11:12:54,618] [INFO] Task started: Blastn
[2024-01-24 11:12:54,618] [INFO] Running command: blastn -query GCF_008033385.1_ASM803338v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg009b42bd-a50a-4b78-8999-a660184499a4/dqc_reference/reference_markers.fasta -out GCF_008033385.1_ASM803338v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:55,337] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:55,340] [INFO] Selected 13 target genomes.
[2024-01-24 11:12:55,340] [INFO] Target genome list was writen to GCF_008033385.1_ASM803338v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:55,346] [INFO] Task started: fastANI
[2024-01-24 11:12:55,346] [INFO] Running command: fastANI --query /var/lib/cwl/stga644f3e6-eac3-4cd3-8ca1-7c6fb8232df6/GCF_008033385.1_ASM803338v1_genomic.fna.gz --refList GCF_008033385.1_ASM803338v1_genomic.fna/target_genomes.txt --output GCF_008033385.1_ASM803338v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:05,127] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:05,128] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg009b42bd-a50a-4b78-8999-a660184499a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:05,128] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg009b42bd-a50a-4b78-8999-a660184499a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:05,139] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:05,139] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:05,139] [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
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	100.0	1363	1363	95	conclusive
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	82.7993	761	1363	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	79.1492	529	1363	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	79.1359	532	1363	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	79.1296	539	1363	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	79.0159	536	1363	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	78.774	375	1363	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.9406	335	1363	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	77.8261	282	1363	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.4614	203	1363	95	below_threshold
Lacinutrix jangbogonensis	strain=PAMC 27137	GCA_000797445.1	1469557	1469557	type	True	77.4455	255	1363	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.3237	230	1363	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	77.0929	202	1363	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:05,141] [INFO] DFAST Taxonomy check result was written to GCF_008033385.1_ASM803338v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:05,141] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:05,142] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:05,142] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg009b42bd-a50a-4b78-8999-a660184499a4/dqc_reference/checkm_data
[2024-01-24 11:13:05,143] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:05,185] [INFO] Task started: CheckM
[2024-01-24 11:13:05,186] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008033385.1_ASM803338v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008033385.1_ASM803338v1_genomic.fna/checkm_input GCF_008033385.1_ASM803338v1_genomic.fna/checkm_result
[2024-01-24 11:13:45,542] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:45,544] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:45,563] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:45,563] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:45,564] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008033385.1_ASM803338v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:45,564] [INFO] Task started: Blastn
[2024-01-24 11:13:45,564] [INFO] Running command: blastn -query GCF_008033385.1_ASM803338v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg009b42bd-a50a-4b78-8999-a660184499a4/dqc_reference/reference_markers_gtdb.fasta -out GCF_008033385.1_ASM803338v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:46,553] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:46,558] [INFO] Selected 10 target genomes.
[2024-01-24 11:13:46,558] [INFO] Target genome list was writen to GCF_008033385.1_ASM803338v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:46,569] [INFO] Task started: fastANI
[2024-01-24 11:13:46,569] [INFO] Running command: fastANI --query /var/lib/cwl/stga644f3e6-eac3-4cd3-8ca1-7c6fb8232df6/GCF_008033385.1_ASM803338v1_genomic.fna.gz --refList GCF_008033385.1_ASM803338v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008033385.1_ASM803338v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:55,956] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:55,971] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:55,971] [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_008033385.1	s__Algibacter pacificus	100.0	1363	1363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009796805.1	s__Algibacter sp009796805	83.3219	770	1363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796825.1	s__Algibacter sp009796825	82.8772	762	1363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900112395.1	s__Algibacter lectus	82.824	759	1363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	98.81	98.79	0.90	0.89	6	-
GCF_014202225.1	s__Algibacter_B amylolyticus	79.1388	537	1363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900112595.1	s__Algibacter_B pectinivorans	79.0324	535	1363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	78.9803	472	1363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015355625.1	s__Tamlana_A sp015355625	78.912	463	1363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	78.8923	454	1363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418015.1	s__Lacinutrix mariniflava	77.8286	283	1363	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:55,973] [INFO] GTDB search result was written to GCF_008033385.1_ASM803338v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:55,973] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:55,976] [INFO] DFAST_QC result json was written to GCF_008033385.1_ASM803338v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:55,977] [INFO] DFAST_QC completed!
[2024-01-24 11:13:55,977] [INFO] Total running time: 0h1m16s