[2024-01-24 13:49:19,353] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:19,358] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:19,358] [INFO] DQC Reference Directory: /var/lib/cwl/stg31e9e0a8-4830-4f78-86dc-45897b72bbe8/dqc_reference
[2024-01-24 13:49:20,772] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:20,773] [INFO] Task started: Prodigal
[2024-01-24 13:49:20,774] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3093016-57d2-4f2b-b290-31776495b6dc/GCF_008040165.1_ASM804016v1_genomic.fna.gz | prodigal -d GCF_008040165.1_ASM804016v1_genomic.fna/cds.fna -a GCF_008040165.1_ASM804016v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:38,647] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:38,648] [INFO] Task started: HMMsearch
[2024-01-24 13:49:38,648] [INFO] Running command: hmmsearch --tblout GCF_008040165.1_ASM804016v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31e9e0a8-4830-4f78-86dc-45897b72bbe8/dqc_reference/reference_markers.hmm GCF_008040165.1_ASM804016v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:38,927] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:38,928] [INFO] Found 6/6 markers.
[2024-01-24 13:49:38,962] [INFO] Query marker FASTA was written to GCF_008040165.1_ASM804016v1_genomic.fna/markers.fasta
[2024-01-24 13:49:38,963] [INFO] Task started: Blastn
[2024-01-24 13:49:38,963] [INFO] Running command: blastn -query GCF_008040165.1_ASM804016v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31e9e0a8-4830-4f78-86dc-45897b72bbe8/dqc_reference/reference_markers.fasta -out GCF_008040165.1_ASM804016v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:39,644] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:39,648] [INFO] Selected 20 target genomes.
[2024-01-24 13:49:39,648] [INFO] Target genome list was writen to GCF_008040165.1_ASM804016v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:39,655] [INFO] Task started: fastANI
[2024-01-24 13:49:39,656] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3093016-57d2-4f2b-b290-31776495b6dc/GCF_008040165.1_ASM804016v1_genomic.fna.gz --refList GCF_008040165.1_ASM804016v1_genomic.fna/target_genomes.txt --output GCF_008040165.1_ASM804016v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:53,740] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:53,741] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31e9e0a8-4830-4f78-86dc-45897b72bbe8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:53,741] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31e9e0a8-4830-4f78-86dc-45897b72bbe8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:53,761] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:49:53,761] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:49:53,761] [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 parva	strain=DSM 25885	GCA_900215465.1	1247520	1247520	type	True	79.1198	527	1294	95	below_threshold
Muricauda algicola	strain=AsT0115	GCA_005937185.1	2583815	2583815	type	True	78.4421	394	1294	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	78.295	401	1294	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	78.2584	413	1294	95	below_threshold
Muricauda flava	strain=DSM 22638	GCA_900129665.1	570519	570519	type	True	78.2034	399	1294	95	below_threshold
Muricauda nanhaiensis	strain=SM1704	GCA_003382275.1	2292706	2292706	type	True	77.953	343	1294	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	77.9295	371	1294	95	below_threshold
Muricauda ruestringensis	strain=DSM 13258	GCA_000224085.1	111501	111501	type	True	77.7736	242	1294	95	below_threshold
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	77.7395	266	1294	95	below_threshold
Muricauda ochracea	strain=JGD-17	GCA_009903685.1	2696472	2696472	type	True	77.7256	291	1294	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	77.6959	244	1294	95	below_threshold
Muricauda zhangzhouensis	strain=CGMCC 1.11028	GCA_900102925.1	1073328	1073328	type	True	77.6059	280	1294	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	77.5992	283	1294	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	77.463	271	1294	95	below_threshold
Maribacter sedimenticola	strain=DSM 19840	GCA_900188415.1	228956	228956	type	True	76.5814	117	1294	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	76.4151	119	1294	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.21	65	1294	95	below_threshold
Formosa algae	strain=KMM 3553	GCA_001439665.1	225843	225843	type	True	76.08	54	1294	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	75.8533	62	1294	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:53,768] [INFO] DFAST Taxonomy check result was written to GCF_008040165.1_ASM804016v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:53,769] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:53,769] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:53,770] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31e9e0a8-4830-4f78-86dc-45897b72bbe8/dqc_reference/checkm_data
[2024-01-24 13:49:53,772] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:53,814] [INFO] Task started: CheckM
[2024-01-24 13:49:53,814] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008040165.1_ASM804016v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008040165.1_ASM804016v1_genomic.fna/checkm_input GCF_008040165.1_ASM804016v1_genomic.fna/checkm_result
[2024-01-24 13:50:47,955] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:47,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:47,973] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:47,973] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:47,974] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008040165.1_ASM804016v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:47,974] [INFO] Task started: Blastn
[2024-01-24 13:50:47,975] [INFO] Running command: blastn -query GCF_008040165.1_ASM804016v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31e9e0a8-4830-4f78-86dc-45897b72bbe8/dqc_reference/reference_markers_gtdb.fasta -out GCF_008040165.1_ASM804016v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:48,818] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:48,822] [INFO] Selected 12 target genomes.
[2024-01-24 13:50:48,822] [INFO] Target genome list was writen to GCF_008040165.1_ASM804016v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:48,845] [INFO] Task started: fastANI
[2024-01-24 13:50:48,846] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3093016-57d2-4f2b-b290-31776495b6dc/GCF_008040165.1_ASM804016v1_genomic.fna.gz --refList GCF_008040165.1_ASM804016v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008040165.1_ASM804016v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:58,359] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:58,374] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:58,375] [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_008040165.1	s__Muricauda hymeniacidonis	100.0	1294	1294	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_010993855.1	s__Muricauda sp010993855	81.9005	785	1294	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149745.1	s__Muricauda koreensis	81.3561	715	1294	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001413955.1	s__Muricauda eckloniae	80.2258	553	1294	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215465.1	s__Muricauda pacifica_A	79.124	526	1294	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698935.1	s__Muricauda sp014698935	78.8424	491	1294	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449435.1	s__Muricauda sp018449435	78.6954	454	1294	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993815.1	s__Muricauda sp010993815	78.4791	438	1294	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003269425.1	s__Muricauda maritima	78.2584	413	1294	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129665.1	s__Muricauda flava	78.2036	399	1294	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003581615.1	s__Muricauda lutimaris	77.7347	267	1294	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112245.1	s__Maribacter stanieri	76.4151	119	1294	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:58,376] [INFO] GTDB search result was written to GCF_008040165.1_ASM804016v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:58,376] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:58,380] [INFO] DFAST_QC result json was written to GCF_008040165.1_ASM804016v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:58,380] [INFO] DFAST_QC completed!
[2024-01-24 13:50:58,380] [INFO] Total running time: 0h1m39s