[2024-01-24 11:13:04,350] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:04,352] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:04,352] [INFO] DQC Reference Directory: /var/lib/cwl/stgaad20c2c-a15e-4f00-8bd9-da7c2418dc6b/dqc_reference
[2024-01-24 11:13:05,621] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:05,621] [INFO] Task started: Prodigal
[2024-01-24 11:13:05,622] [INFO] Running command: gunzip -c /var/lib/cwl/stg75b8cca6-bd86-40fd-8efe-ca502bccee07/GCF_019457905.1_ASM1945790v1_genomic.fna.gz | prodigal -d GCF_019457905.1_ASM1945790v1_genomic.fna/cds.fna -a GCF_019457905.1_ASM1945790v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:30,128] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:30,128] [INFO] Task started: HMMsearch
[2024-01-24 11:13:30,129] [INFO] Running command: hmmsearch --tblout GCF_019457905.1_ASM1945790v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaad20c2c-a15e-4f00-8bd9-da7c2418dc6b/dqc_reference/reference_markers.hmm GCF_019457905.1_ASM1945790v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:30,438] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:30,439] [INFO] Found 6/6 markers.
[2024-01-24 11:13:30,478] [INFO] Query marker FASTA was written to GCF_019457905.1_ASM1945790v1_genomic.fna/markers.fasta
[2024-01-24 11:13:30,478] [INFO] Task started: Blastn
[2024-01-24 11:13:30,478] [INFO] Running command: blastn -query GCF_019457905.1_ASM1945790v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaad20c2c-a15e-4f00-8bd9-da7c2418dc6b/dqc_reference/reference_markers.fasta -out GCF_019457905.1_ASM1945790v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:31,110] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:31,114] [INFO] Selected 9 target genomes.
[2024-01-24 11:13:31,114] [INFO] Target genome list was writen to GCF_019457905.1_ASM1945790v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:31,119] [INFO] Task started: fastANI
[2024-01-24 11:13:31,119] [INFO] Running command: fastANI --query /var/lib/cwl/stg75b8cca6-bd86-40fd-8efe-ca502bccee07/GCF_019457905.1_ASM1945790v1_genomic.fna.gz --refList GCF_019457905.1_ASM1945790v1_genomic.fna/target_genomes.txt --output GCF_019457905.1_ASM1945790v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:38,525] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:38,526] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaad20c2c-a15e-4f00-8bd9-da7c2418dc6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:38,526] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaad20c2c-a15e-4f00-8bd9-da7c2418dc6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:38,535] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:13:38,535] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:13:38,535] [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 aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	93.6712	1141	1427	95	below_threshold
Muricauda chongwuensis	strain=HICW	GCA_013376415.1	2697365	2697365	type	True	90.2951	1039	1427	95	below_threshold
Muricauda brasiliensis	strain=K001	GCA_003057865.1	2162892	2162892	type	True	90.23	1040	1427	95	below_threshold
Muricauda oceani	strain=501str8	GCA_011068285.1	2698672	2698672	type	True	86.1025	928	1427	95	below_threshold
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	86.06	916	1427	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	81.8946	769	1427	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	78.8892	513	1427	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:38,537] [INFO] DFAST Taxonomy check result was written to GCF_019457905.1_ASM1945790v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:38,538] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:38,538] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:38,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaad20c2c-a15e-4f00-8bd9-da7c2418dc6b/dqc_reference/checkm_data
[2024-01-24 11:13:38,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:38,579] [INFO] Task started: CheckM
[2024-01-24 11:13:38,579] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019457905.1_ASM1945790v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019457905.1_ASM1945790v1_genomic.fna/checkm_input GCF_019457905.1_ASM1945790v1_genomic.fna/checkm_result
[2024-01-24 11:14:47,245] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:47,247] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:47,266] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:47,266] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:47,266] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019457905.1_ASM1945790v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:47,267] [INFO] Task started: Blastn
[2024-01-24 11:14:47,267] [INFO] Running command: blastn -query GCF_019457905.1_ASM1945790v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaad20c2c-a15e-4f00-8bd9-da7c2418dc6b/dqc_reference/reference_markers_gtdb.fasta -out GCF_019457905.1_ASM1945790v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:48,101] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:48,104] [INFO] Selected 11 target genomes.
[2024-01-24 11:14:48,105] [INFO] Target genome list was writen to GCF_019457905.1_ASM1945790v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:48,117] [INFO] Task started: fastANI
[2024-01-24 11:14:48,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg75b8cca6-bd86-40fd-8efe-ca502bccee07/GCF_019457905.1_ASM1945790v1_genomic.fna.gz --refList GCF_019457905.1_ASM1945790v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019457905.1_ASM1945790v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:57,836] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:57,856] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:14:57,856] [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_017313785.1	s__Muricauda sp002711825	93.6543	1142	1427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.76	98.31	0.81	0.77	4	-
GCF_003057865.1	s__Muricauda brasiliensis	90.2256	1041	1427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.90	96.90	0.89	0.89	2	-
GCF_011068285.1	s__Muricauda sp011068285	86.0926	929	1427	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	83.1859	811	1427	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	83.1281	876	1427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.01	99.01	0.89	0.89	2	-
GCA_013911645.1	s__Muricauda sp013911645	82.9227	813	1427	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	82.5459	800	1427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313105.1	s__Muricauda sp017313105	82.0522	717	1427	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	81.8946	769	1427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167435.2	s__Muricauda sp002167435	81.41	681	1427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222835.1	s__Muricauda sp018222835	80.8056	610	1427	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 11:14:57,858] [INFO] GTDB search result was written to GCF_019457905.1_ASM1945790v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:57,859] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:57,863] [INFO] DFAST_QC result json was written to GCF_019457905.1_ASM1945790v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:57,863] [INFO] DFAST_QC completed!
[2024-01-24 11:14:57,863] [INFO] Total running time: 0h1m54s