[2024-01-24 12:14:33,872] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,874] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,874] [INFO] DQC Reference Directory: /var/lib/cwl/stg16f553cb-579e-4300-b77a-009694fce938/dqc_reference
[2024-01-24 12:14:35,148] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,148] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,149] [INFO] Running command: gunzip -c /var/lib/cwl/stg51d2cd46-c596-4de8-b8c2-34ef71d90b7d/GCF_003992675.1_ASM399267v1_genomic.fna.gz | prodigal -d GCF_003992675.1_ASM399267v1_genomic.fna/cds.fna -a GCF_003992675.1_ASM399267v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:55,876] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:55,877] [INFO] Task started: HMMsearch
[2024-01-24 12:14:55,877] [INFO] Running command: hmmsearch --tblout GCF_003992675.1_ASM399267v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16f553cb-579e-4300-b77a-009694fce938/dqc_reference/reference_markers.hmm GCF_003992675.1_ASM399267v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:56,177] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:56,178] [INFO] Found 6/6 markers.
[2024-01-24 12:14:56,210] [INFO] Query marker FASTA was written to GCF_003992675.1_ASM399267v1_genomic.fna/markers.fasta
[2024-01-24 12:14:56,211] [INFO] Task started: Blastn
[2024-01-24 12:14:56,211] [INFO] Running command: blastn -query GCF_003992675.1_ASM399267v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16f553cb-579e-4300-b77a-009694fce938/dqc_reference/reference_markers.fasta -out GCF_003992675.1_ASM399267v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:56,895] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:56,898] [INFO] Selected 14 target genomes.
[2024-01-24 12:14:56,899] [INFO] Target genome list was writen to GCF_003992675.1_ASM399267v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:56,910] [INFO] Task started: fastANI
[2024-01-24 12:14:56,910] [INFO] Running command: fastANI --query /var/lib/cwl/stg51d2cd46-c596-4de8-b8c2-34ef71d90b7d/GCF_003992675.1_ASM399267v1_genomic.fna.gz --refList GCF_003992675.1_ASM399267v1_genomic.fna/target_genomes.txt --output GCF_003992675.1_ASM399267v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:08,257] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:08,258] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16f553cb-579e-4300-b77a-009694fce938/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:08,258] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16f553cb-579e-4300-b77a-009694fce938/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:08,269] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:08,270] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:08,270] [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
Muricauda aquimarina	strain=JCM11811	GCA_003992675.1	254955	254955	type	True	100.0	1127	1129	95	conclusive
Muricauda oceani	strain=501str8	GCA_011068285.1	2698672	2698672	type	True	81.5923	706	1129	95	below_threshold
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	81.577	686	1129	95	below_threshold
Muricauda ruestringensis	strain=DSM 13258	GCA_000224085.1	111501	111501	type	True	81.1919	660	1129	95	below_threshold
Muricauda oceanensis	strain=40DY170	GCA_003992595.1	2499163	2499163	type	True	81.1246	686	1129	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	81.0098	660	1129	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	80.9347	673	1129	95	below_threshold
Muricauda chongwuensis	strain=HICW	GCA_013376415.1	2697365	2697365	type	True	80.6407	633	1129	95	below_threshold
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	80.5769	658	1129	95	below_threshold
Muricauda brasiliensis	strain=K001	GCA_003057865.1	2162892	2162892	type	True	80.526	615	1129	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	79.1152	525	1129	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	78.999	447	1129	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	78.8496	477	1129	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	76.9638	221	1129	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:08,272] [INFO] DFAST Taxonomy check result was written to GCF_003992675.1_ASM399267v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:08,273] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:08,273] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:08,273] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16f553cb-579e-4300-b77a-009694fce938/dqc_reference/checkm_data
[2024-01-24 12:15:08,275] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:08,320] [INFO] Task started: CheckM
[2024-01-24 12:15:08,320] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003992675.1_ASM399267v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003992675.1_ASM399267v1_genomic.fna/checkm_input GCF_003992675.1_ASM399267v1_genomic.fna/checkm_result
[2024-01-24 12:16:05,847] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:05,849] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:05,871] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:05,871] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:05,872] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003992675.1_ASM399267v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:05,872] [INFO] Task started: Blastn
[2024-01-24 12:16:05,873] [INFO] Running command: blastn -query GCF_003992675.1_ASM399267v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16f553cb-579e-4300-b77a-009694fce938/dqc_reference/reference_markers_gtdb.fasta -out GCF_003992675.1_ASM399267v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:06,678] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:06,682] [INFO] Selected 11 target genomes.
[2024-01-24 12:16:06,682] [INFO] Target genome list was writen to GCF_003992675.1_ASM399267v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:06,689] [INFO] Task started: fastANI
[2024-01-24 12:16:06,690] [INFO] Running command: fastANI --query /var/lib/cwl/stg51d2cd46-c596-4de8-b8c2-34ef71d90b7d/GCF_003992675.1_ASM399267v1_genomic.fna.gz --refList GCF_003992675.1_ASM399267v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003992675.1_ASM399267v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:15,514] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:15,527] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:15,527] [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_003992675.1	s__Muricauda aquimarina	100.0	1128	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013407935.1	s__Muricauda sp013407935	89.4269	953	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.58	96.50	0.87	0.86	8	-
GCF_011068285.1	s__Muricauda sp011068285	81.5966	705	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010468565.1	s__Muricauda sp010468565	81.5704	695	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224085.1	s__Muricauda ruestringensis	81.1816	661	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911645.1	s__Muricauda sp013911645	81.1273	697	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992595.1	s__Muricauda sp002452975	81.1262	684	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.01	99.01	0.89	0.89	2	-
GCF_017313785.1	s__Muricauda sp002711825	81.0098	660	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.76	98.31	0.81	0.77	4	-
GCF_017313105.1	s__Muricauda sp017313105	80.9918	653	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313275.1	s__Muricauda lutimaris_A	80.9347	673	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813125.1	s__Muricauda sp002813125	80.7133	661	1129	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:15,528] [INFO] GTDB search result was written to GCF_003992675.1_ASM399267v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:15,529] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:15,532] [INFO] DFAST_QC result json was written to GCF_003992675.1_ASM399267v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:15,532] [INFO] DFAST_QC completed!
[2024-01-24 12:16:15,533] [INFO] Total running time: 0h1m42s