[2024-01-25 17:34:07,121] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,126] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,126] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2a5a30b-1b2d-425b-896d-3e4830b176ba/dqc_reference
[2024-01-25 17:34:08,951] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:08,952] [INFO] Task started: Prodigal
[2024-01-25 17:34:08,952] [INFO] Running command: gunzip -c /var/lib/cwl/stg51933b0a-5984-4ce5-8fc4-d9dd4c761520/GCF_014773245.1_ASM1477324v1_genomic.fna.gz | prodigal -d GCF_014773245.1_ASM1477324v1_genomic.fna/cds.fna -a GCF_014773245.1_ASM1477324v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:25,380] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:25,380] [INFO] Task started: HMMsearch
[2024-01-25 17:34:25,380] [INFO] Running command: hmmsearch --tblout GCF_014773245.1_ASM1477324v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2a5a30b-1b2d-425b-896d-3e4830b176ba/dqc_reference/reference_markers.hmm GCF_014773245.1_ASM1477324v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:25,662] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:25,663] [INFO] Found 6/6 markers.
[2024-01-25 17:34:25,701] [INFO] Query marker FASTA was written to GCF_014773245.1_ASM1477324v1_genomic.fna/markers.fasta
[2024-01-25 17:34:25,701] [INFO] Task started: Blastn
[2024-01-25 17:34:25,702] [INFO] Running command: blastn -query GCF_014773245.1_ASM1477324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2a5a30b-1b2d-425b-896d-3e4830b176ba/dqc_reference/reference_markers.fasta -out GCF_014773245.1_ASM1477324v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:26,322] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:26,325] [INFO] Selected 15 target genomes.
[2024-01-25 17:34:26,325] [INFO] Target genome list was writen to GCF_014773245.1_ASM1477324v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:26,340] [INFO] Task started: fastANI
[2024-01-25 17:34:26,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg51933b0a-5984-4ce5-8fc4-d9dd4c761520/GCF_014773245.1_ASM1477324v1_genomic.fna.gz --refList GCF_014773245.1_ASM1477324v1_genomic.fna/target_genomes.txt --output GCF_014773245.1_ASM1477324v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:42,833] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:42,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2a5a30b-1b2d-425b-896d-3e4830b176ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:42,834] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2a5a30b-1b2d-425b-896d-3e4830b176ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:42,844] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:34:42,844] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:34:42,844] [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
Mucilaginibacter glaciei	strain=ZB1P21	GCA_014773245.1	2772109	2772109	type	True	100.0	1519	1520	95	conclusive
Mucilaginibacter phyllosphaerae	strain=CCM 8625	GCA_014635525.1	1812349	1812349	type	True	79.9613	657	1520	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	79.8803	659	1520	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=DSM 100995	GCA_014196695.1	1812349	1812349	type	True	79.8571	664	1520	95	below_threshold
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	79.2128	608	1520	95	below_threshold
Mucilaginibacter pankratovii	strain=ZT4R22	GCA_014773265.1	2772110	2772110	type	True	79.0966	619	1520	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	78.8714	613	1520	95	below_threshold
Mucilaginibacter pedocola	strain=TBZ30	GCA_002013915.1	1792845	1792845	type	True	78.2356	488	1520	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	78.2266	503	1520	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	77.8779	401	1520	95	below_threshold
Mucilaginibacter ginsenosidivorax	strain=KHI28	GCA_007971525.1	862126	862126	type	True	77.7943	376	1520	95	below_threshold
Mucilaginibacter gossypiicola	strain=Gh-48	GCA_900110105.1	551995	551995	type	True	77.5153	346	1520	95	below_threshold
Mucilaginibacter mallensis	strain=MP1X4	GCA_900105165.1	652787	652787	type	True	77.4389	298	1520	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	77.1149	260	1520	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:42,845] [INFO] DFAST Taxonomy check result was written to GCF_014773245.1_ASM1477324v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:42,846] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:42,846] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:42,846] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2a5a30b-1b2d-425b-896d-3e4830b176ba/dqc_reference/checkm_data
[2024-01-25 17:34:42,847] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:42,890] [INFO] Task started: CheckM
[2024-01-25 17:34:42,890] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014773245.1_ASM1477324v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014773245.1_ASM1477324v1_genomic.fna/checkm_input GCF_014773245.1_ASM1477324v1_genomic.fna/checkm_result
[2024-01-25 17:35:29,421] [INFO] Task succeeded: CheckM
[2024-01-25 17:35:29,422] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:29,441] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:29,442] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:29,442] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014773245.1_ASM1477324v1_genomic.fna/markers.fasta)
[2024-01-25 17:35:29,442] [INFO] Task started: Blastn
[2024-01-25 17:35:29,442] [INFO] Running command: blastn -query GCF_014773245.1_ASM1477324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2a5a30b-1b2d-425b-896d-3e4830b176ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_014773245.1_ASM1477324v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:30,420] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:30,423] [INFO] Selected 14 target genomes.
[2024-01-25 17:35:30,424] [INFO] Target genome list was writen to GCF_014773245.1_ASM1477324v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:30,431] [INFO] Task started: fastANI
[2024-01-25 17:35:30,432] [INFO] Running command: fastANI --query /var/lib/cwl/stg51933b0a-5984-4ce5-8fc4-d9dd4c761520/GCF_014773245.1_ASM1477324v1_genomic.fna.gz --refList GCF_014773245.1_ASM1477324v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014773245.1_ASM1477324v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:35:45,207] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:45,216] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:35:45,217] [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_014773245.1	s__Mucilaginibacter glaciei	100.0	1519	1520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004378255.1	s__Mucilaginibacter phyllosphaerae	79.8611	661	1520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001636615.1	s__Mucilaginibacter sp001636615	79.4215	627	1520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014773275.1	s__Mucilaginibacter rigui	79.3909	597	1520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003635105.1	s__Mucilaginibacter sp003635105	79.3357	605	1520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168255.1	s__Mucilaginibacter terrigena	79.2056	609	1520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938025.2	s__Mucilaginibacter sp005938025	79.0943	581	1520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004054195.1	s__Mucilaginibacter sp004054195	78.8619	615	1520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002013915.1	s__Mucilaginibacter pedocola	78.2356	488	1520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003432115.1	s__Mucilaginibacter sp003432115	78.2241	504	1520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007846095.1	s__Mucilaginibacter sp007846095	77.8854	400	1520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408825.1	s__Mucilaginibacter sp013408825	77.7447	251	1520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142915.1	s__Mucilaginibacter sp900142915	77.5582	312	1520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110105.1	s__Mucilaginibacter gossypiicola	77.514	346	1520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:35:45,218] [INFO] GTDB search result was written to GCF_014773245.1_ASM1477324v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:35:45,219] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:35:45,221] [INFO] DFAST_QC result json was written to GCF_014773245.1_ASM1477324v1_genomic.fna/dqc_result.json
[2024-01-25 17:35:45,222] [INFO] DFAST_QC completed!
[2024-01-25 17:35:45,222] [INFO] Total running time: 0h1m38s