[2024-01-24 14:55:26,904] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:26,906] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:26,906] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b245b92-5c8f-4324-8e72-082b0cc1c813/dqc_reference
[2024-01-24 14:55:28,276] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:28,277] [INFO] Task started: Prodigal
[2024-01-24 14:55:28,278] [INFO] Running command: gunzip -c /var/lib/cwl/stge170cfdd-c769-43e3-8b43-3cb8ea10792a/GCF_002355435.1_ASM235543v1_genomic.fna.gz | prodigal -d GCF_002355435.1_ASM235543v1_genomic.fna/cds.fna -a GCF_002355435.1_ASM235543v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:55,978] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:55,978] [INFO] Task started: HMMsearch
[2024-01-24 14:55:55,979] [INFO] Running command: hmmsearch --tblout GCF_002355435.1_ASM235543v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b245b92-5c8f-4324-8e72-082b0cc1c813/dqc_reference/reference_markers.hmm GCF_002355435.1_ASM235543v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:56,273] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:56,274] [INFO] Found 6/6 markers.
[2024-01-24 14:55:56,322] [INFO] Query marker FASTA was written to GCF_002355435.1_ASM235543v1_genomic.fna/markers.fasta
[2024-01-24 14:55:56,322] [INFO] Task started: Blastn
[2024-01-24 14:55:56,322] [INFO] Running command: blastn -query GCF_002355435.1_ASM235543v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b245b92-5c8f-4324-8e72-082b0cc1c813/dqc_reference/reference_markers.fasta -out GCF_002355435.1_ASM235543v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:56,933] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:56,936] [INFO] Selected 17 target genomes.
[2024-01-24 14:55:56,937] [INFO] Target genome list was writen to GCF_002355435.1_ASM235543v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:56,944] [INFO] Task started: fastANI
[2024-01-24 14:55:56,944] [INFO] Running command: fastANI --query /var/lib/cwl/stge170cfdd-c769-43e3-8b43-3cb8ea10792a/GCF_002355435.1_ASM235543v1_genomic.fna.gz --refList GCF_002355435.1_ASM235543v1_genomic.fna/target_genomes.txt --output GCF_002355435.1_ASM235543v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:14,966] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:14,967] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b245b92-5c8f-4324-8e72-082b0cc1c813/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:14,967] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b245b92-5c8f-4324-8e72-082b0cc1c813/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:14,981] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:56:14,981] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:14,981] [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 gotjawali	strain=SA3-7	GCA_002355435.1	1550579	1550579	type	True	100.0	2114	2114	95	conclusive
Mucilaginibacter gotjawali	strain=CECT 8628	GCA_014191635.1	1550579	1550579	type	True	99.9794	2077	2114	95	conclusive
Mucilaginibacter xinganensis	strain=BJC16-A31	GCA_002257585.1	1234841	1234841	type	True	78.4341	473	2114	95	below_threshold
Mucilaginibacter frigoritolerans	strain=ATCC BAA-1854	GCA_007830615.1	652788	652788	type	True	78.1354	489	2114	95	below_threshold
Mucilaginibacter mallensis	strain=MP1X4	GCA_900105165.1	652787	652787	type	True	77.9506	367	2114	95	below_threshold
Mucilaginibacter corticis	strain=MAH-19	GCA_007558865.1	2597670	2597670	type	True	77.7465	285	2114	95	below_threshold
Mucilaginibacter ginsenosidivorax	strain=KHI28	GCA_007971525.1	862126	862126	type	True	77.4335	407	2114	95	below_threshold
Mucilaginibacter pankratovii	strain=ZT4R22	GCA_014773265.1	2772110	2772110	type	True	77.4194	352	2114	95	below_threshold
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	77.4068	309	2114	95	below_threshold
Mucilaginibacter segetis	strain=SD-g	GCA_016522075.1	2793071	2793071	type	True	77.4014	242	2114	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	77.3914	321	2114	95	below_threshold
Mucilaginibacter kameinonensis	strain=SCK	GCA_003675385.1	452286	452286	type	True	77.2936	326	2114	95	below_threshold
Mucilaginibacter limnophilus	strain=YBJ-36	GCA_004005815.1	1932778	1932778	type	True	77.2536	201	2114	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	77.0571	212	2114	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	76.9727	250	2114	95	below_threshold
Mucilaginibacter ginsenosidivorans	strain=Gsoil 3017	GCA_007971025.1	398053	398053	type	True	76.892	346	2114	95	below_threshold
Pedobacter xinjiangensis	strain=CCTCC AB 208092	GCA_024436435.1	539206	539206	type	True	76.0937	59	2114	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:14,988] [INFO] DFAST Taxonomy check result was written to GCF_002355435.1_ASM235543v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:14,988] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:14,988] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:14,989] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b245b92-5c8f-4324-8e72-082b0cc1c813/dqc_reference/checkm_data
[2024-01-24 14:56:14,990] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:15,048] [INFO] Task started: CheckM
[2024-01-24 14:56:15,048] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002355435.1_ASM235543v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002355435.1_ASM235543v1_genomic.fna/checkm_input GCF_002355435.1_ASM235543v1_genomic.fna/checkm_result
[2024-01-24 14:57:29,758] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:29,759] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:29,776] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:29,777] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:29,777] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002355435.1_ASM235543v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:29,777] [INFO] Task started: Blastn
[2024-01-24 14:57:29,777] [INFO] Running command: blastn -query GCF_002355435.1_ASM235543v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b245b92-5c8f-4324-8e72-082b0cc1c813/dqc_reference/reference_markers_gtdb.fasta -out GCF_002355435.1_ASM235543v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:30,638] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:30,641] [INFO] Selected 13 target genomes.
[2024-01-24 14:57:30,641] [INFO] Target genome list was writen to GCF_002355435.1_ASM235543v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:30,650] [INFO] Task started: fastANI
[2024-01-24 14:57:30,650] [INFO] Running command: fastANI --query /var/lib/cwl/stge170cfdd-c769-43e3-8b43-3cb8ea10792a/GCF_002355435.1_ASM235543v1_genomic.fna.gz --refList GCF_002355435.1_ASM235543v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002355435.1_ASM235543v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:46,973] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:46,984] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:46,985] [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_002355435.1	s__Mucilaginibacter gotjawali	100.0	2114	2114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCA_903913935.1	s__Mucilaginibacter sp903913935	89.2769	1225	2114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013288235.1	s__Mucilaginibacter sp013288235	78.8629	506	2114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.30	99.08	0.67	0.66	3	-
GCA_002413785.1	s__Mucilaginibacter sp002413785	78.7685	627	2114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.87	99.70	0.98	0.97	4	-
GCF_002257585.1	s__Mucilaginibacter xinganensis	78.4057	472	2114	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	78.3766	606	2114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903864275.1	s__Mucilaginibacter sp903864275	78.2758	680	2114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	100.00	100.00	0.99	0.99	4	-
GCA_013288465.1	s__Mucilaginibacter sp013288465	77.7789	181	2114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013288685.1	s__Mucilaginibacter sp013288685	77.751	363	2114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013287375.1	s__Mucilaginibacter sp013287375	77.7329	168	2114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.48	99.44	0.60	0.60	3	-
GCF_007558865.1	s__Mucilaginibacter corticis	77.7326	287	2114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013286325.1	s__Mucilaginibacter sp013286325	77.6585	280	2114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200495.1	s__Mucilaginibacter sp014200495	77.5025	390	2114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:46,986] [INFO] GTDB search result was written to GCF_002355435.1_ASM235543v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:46,987] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:46,998] [INFO] DFAST_QC result json was written to GCF_002355435.1_ASM235543v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:46,998] [INFO] DFAST_QC completed!
[2024-01-24 14:57:46,999] [INFO] Total running time: 0h2m20s