[2024-01-24 13:41:40,818] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:40,820] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:40,820] [INFO] DQC Reference Directory: /var/lib/cwl/stg237a43d6-bced-4383-88c1-08ae03cdb48b/dqc_reference
[2024-01-24 13:41:42,155] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:42,156] [INFO] Task started: Prodigal
[2024-01-24 13:41:42,157] [INFO] Running command: gunzip -c /var/lib/cwl/stg3cfe1e15-8746-4dcc-9421-a505d7865982/GCF_002909255.1_ASM290925v1_genomic.fna.gz | prodigal -d GCF_002909255.1_ASM290925v1_genomic.fna/cds.fna -a GCF_002909255.1_ASM290925v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:42:07,303] [INFO] Task succeeded: Prodigal
[2024-01-24 13:42:07,304] [INFO] Task started: HMMsearch
[2024-01-24 13:42:07,304] [INFO] Running command: hmmsearch --tblout GCF_002909255.1_ASM290925v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg237a43d6-bced-4383-88c1-08ae03cdb48b/dqc_reference/reference_markers.hmm GCF_002909255.1_ASM290925v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:42:07,680] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:42:07,682] [INFO] Found 6/6 markers.
[2024-01-24 13:42:07,729] [INFO] Query marker FASTA was written to GCF_002909255.1_ASM290925v1_genomic.fna/markers.fasta
[2024-01-24 13:42:07,730] [INFO] Task started: Blastn
[2024-01-24 13:42:07,730] [INFO] Running command: blastn -query GCF_002909255.1_ASM290925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg237a43d6-bced-4383-88c1-08ae03cdb48b/dqc_reference/reference_markers.fasta -out GCF_002909255.1_ASM290925v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:08,365] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:08,368] [INFO] Selected 10 target genomes.
[2024-01-24 13:42:08,368] [INFO] Target genome list was writen to GCF_002909255.1_ASM290925v1_genomic.fna/target_genomes.txt
[2024-01-24 13:42:08,372] [INFO] Task started: fastANI
[2024-01-24 13:42:08,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cfe1e15-8746-4dcc-9421-a505d7865982/GCF_002909255.1_ASM290925v1_genomic.fna.gz --refList GCF_002909255.1_ASM290925v1_genomic.fna/target_genomes.txt --output GCF_002909255.1_ASM290925v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:18,447] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:18,447] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg237a43d6-bced-4383-88c1-08ae03cdb48b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:18,448] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg237a43d6-bced-4383-88c1-08ae03cdb48b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:18,458] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:42:18,458] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:18,458] [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 hampyeongensis	strain=JCM 17788	GCA_002909255.1	1028743	1028743	type	True	100.0	1798	1798	95	conclusive
Arenibacter arenosicollis	strain=BSSL-BM3	GCA_014397245.1	2762274	2762274	type	True	88.9551	1368	1798	95	below_threshold
Arenibacter catalasegens	strain=P308H10	GCA_002909235.1	2056779	2056779	type	True	85.785	1364	1798	95	below_threshold
Arenibacter echinorum	strain=DSM 23522	GCA_003259375.1	440515	440515	type	True	83.3347	1222	1798	95	below_threshold
Arenibacter palladensis	strain=DSM 17539	GCA_900129275.1	237373	237373	type	True	82.2546	1173	1798	95	below_threshold
Arenibacter algicola	strain=TG409	GCA_000733925.1	616991	616991	type	True	82.1457	1191	1798	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	76.1141	114	1798	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	75.7602	53	1798	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:18,461] [INFO] DFAST Taxonomy check result was written to GCF_002909255.1_ASM290925v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:18,461] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:18,462] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:18,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg237a43d6-bced-4383-88c1-08ae03cdb48b/dqc_reference/checkm_data
[2024-01-24 13:42:18,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:18,516] [INFO] Task started: CheckM
[2024-01-24 13:42:18,517] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002909255.1_ASM290925v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002909255.1_ASM290925v1_genomic.fna/checkm_input GCF_002909255.1_ASM290925v1_genomic.fna/checkm_result
[2024-01-24 13:43:26,029] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:26,030] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:26,054] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:26,054] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:26,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002909255.1_ASM290925v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:26,055] [INFO] Task started: Blastn
[2024-01-24 13:43:26,055] [INFO] Running command: blastn -query GCF_002909255.1_ASM290925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg237a43d6-bced-4383-88c1-08ae03cdb48b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002909255.1_ASM290925v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:26,870] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:26,875] [INFO] Selected 7 target genomes.
[2024-01-24 13:43:26,875] [INFO] Target genome list was writen to GCF_002909255.1_ASM290925v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:26,907] [INFO] Task started: fastANI
[2024-01-24 13:43:26,908] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cfe1e15-8746-4dcc-9421-a505d7865982/GCF_002909255.1_ASM290925v1_genomic.fna.gz --refList GCF_002909255.1_ASM290925v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002909255.1_ASM290925v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:35,887] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:35,901] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:35,902] [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_002909255.1	s__Arenibacter hampyeongensis	100.0	1798	1798	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_014397245.1	s__Arenibacter arenosicollis	88.9526	1368	1798	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	85.7903	1363	1798	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860365.1	s__Arenibacter algicola_B	83.8224	1239	1798	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259375.1	s__Arenibacter echinorum	83.3364	1222	1798	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	82.2336	1124	1798	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	82.1531	1189	1798	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	98.04	97.34	0.85	0.81	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:35,904] [INFO] GTDB search result was written to GCF_002909255.1_ASM290925v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:35,904] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:35,909] [INFO] DFAST_QC result json was written to GCF_002909255.1_ASM290925v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:35,909] [INFO] DFAST_QC completed!
[2024-01-24 13:43:35,909] [INFO] Total running time: 0h1m55s