[2024-01-25 20:16:05,488] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:16:05,496] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:16:05,496] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e8f4e22-c898-45cc-a67f-95275c5aef27/dqc_reference
[2024-01-25 20:16:06,641] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:16:06,642] [INFO] Task started: Prodigal
[2024-01-25 20:16:06,642] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c24e3ac-453c-4d34-96a3-6d3adfd127d7/GCF_021215455.1_ASM2121545v1_genomic.fna.gz | prodigal -d GCF_021215455.1_ASM2121545v1_genomic.fna/cds.fna -a GCF_021215455.1_ASM2121545v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:16:22,237] [INFO] Task succeeded: Prodigal
[2024-01-25 20:16:22,237] [INFO] Task started: HMMsearch
[2024-01-25 20:16:22,237] [INFO] Running command: hmmsearch --tblout GCF_021215455.1_ASM2121545v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e8f4e22-c898-45cc-a67f-95275c5aef27/dqc_reference/reference_markers.hmm GCF_021215455.1_ASM2121545v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:16:22,493] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:16:22,494] [INFO] Found 6/6 markers.
[2024-01-25 20:16:22,532] [INFO] Query marker FASTA was written to GCF_021215455.1_ASM2121545v1_genomic.fna/markers.fasta
[2024-01-25 20:16:22,532] [INFO] Task started: Blastn
[2024-01-25 20:16:22,532] [INFO] Running command: blastn -query GCF_021215455.1_ASM2121545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e8f4e22-c898-45cc-a67f-95275c5aef27/dqc_reference/reference_markers.fasta -out GCF_021215455.1_ASM2121545v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:23,156] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:23,159] [INFO] Selected 19 target genomes.
[2024-01-25 20:16:23,160] [INFO] Target genome list was writen to GCF_021215455.1_ASM2121545v1_genomic.fna/target_genomes.txt
[2024-01-25 20:16:23,166] [INFO] Task started: fastANI
[2024-01-25 20:16:23,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c24e3ac-453c-4d34-96a3-6d3adfd127d7/GCF_021215455.1_ASM2121545v1_genomic.fna.gz --refList GCF_021215455.1_ASM2121545v1_genomic.fna/target_genomes.txt --output GCF_021215455.1_ASM2121545v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:16:40,665] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:40,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e8f4e22-c898-45cc-a67f-95275c5aef27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:16:40,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e8f4e22-c898-45cc-a67f-95275c5aef27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:16:40,677] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:16:40,677] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:16:40,677] [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 roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	100.0	1392	1392	95	conclusive
Mucilaginibacter limnophilus	strain=YBJ-36	GCA_004005815.1	1932778	1932778	type	True	78.4717	410	1392	95	below_threshold
Mucilaginibacter hurinus	strain=ZR32	GCA_003324525.1	2201324	2201324	type	True	77.8483	289	1392	95	below_threshold
Mucilaginibacter gossypiicola	strain=Gh-48	GCA_900110105.1	551995	551995	type	True	77.7169	283	1392	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	77.6552	256	1392	95	below_threshold
Mucilaginibacter rubeus	strain=CGMCC 1.15913	GCA_014643835.1	2027860	2027860	suspected-type	True	77.5389	277	1392	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	77.5372	248	1392	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	77.5055	204	1392	95	below_threshold
Mucilaginibacter gossypii	strain=Gh-67	GCA_900100945.1	551996	551996	type	True	77.4228	291	1392	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=CCM 8625	GCA_014635525.1	1812349	1812349	type	True	77.4025	282	1392	95	below_threshold
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	77.3952	269	1392	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	77.3785	286	1392	95	below_threshold
Mucilaginibacter segetis	strain=SD-g	GCA_016522075.1	2793071	2793071	type	True	77.3752	197	1392	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=DSM 100995	GCA_014196695.1	1812349	1812349	type	True	77.3713	290	1392	95	below_threshold
Mucilaginibacter psychrotolerans	strain=NH7-4	GCA_004519315.1	1524096	1524096	type	True	77.2762	221	1392	95	below_threshold
Mucilaginibacter lappiensis	strain=ATCC BAA-1855	GCA_900155965.1	354630	354630	type	True	77.1259	278	1392	95	below_threshold
Mucilaginibacter paludis	strain=DSM 18603	GCA_000166195.3	423351	423351	type	True	76.8995	218	1392	95	below_threshold
Pedobacter aquae	strain=CJ43	GCA_008195825.1	2605747	2605747	type	True	76.3745	50	1392	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:16:40,679] [INFO] DFAST Taxonomy check result was written to GCF_021215455.1_ASM2121545v1_genomic.fna/tc_result.tsv
[2024-01-25 20:16:40,679] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:16:40,679] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:16:40,679] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e8f4e22-c898-45cc-a67f-95275c5aef27/dqc_reference/checkm_data
[2024-01-25 20:16:40,680] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:16:40,721] [INFO] Task started: CheckM
[2024-01-25 20:16:40,721] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021215455.1_ASM2121545v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021215455.1_ASM2121545v1_genomic.fna/checkm_input GCF_021215455.1_ASM2121545v1_genomic.fna/checkm_result
[2024-01-25 20:17:25,367] [INFO] Task succeeded: CheckM
[2024-01-25 20:17:25,368] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:17:25,393] [INFO] ===== Completeness check finished =====
[2024-01-25 20:17:25,393] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:17:25,394] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021215455.1_ASM2121545v1_genomic.fna/markers.fasta)
[2024-01-25 20:17:25,394] [INFO] Task started: Blastn
[2024-01-25 20:17:25,394] [INFO] Running command: blastn -query GCF_021215455.1_ASM2121545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e8f4e22-c898-45cc-a67f-95275c5aef27/dqc_reference/reference_markers_gtdb.fasta -out GCF_021215455.1_ASM2121545v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:26,269] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:26,274] [INFO] Selected 23 target genomes.
[2024-01-25 20:17:26,274] [INFO] Target genome list was writen to GCF_021215455.1_ASM2121545v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:17:26,314] [INFO] Task started: fastANI
[2024-01-25 20:17:26,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c24e3ac-453c-4d34-96a3-6d3adfd127d7/GCF_021215455.1_ASM2121545v1_genomic.fna.gz --refList GCF_021215455.1_ASM2121545v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021215455.1_ASM2121545v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:17:45,890] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:45,903] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:17:45,904] [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_015223065.1	s__Mucilaginibacter sp015223065	83.2252	936	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005815.1	s__Mucilaginibacter limnophilus	78.4813	409	1392	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	77.9081	234	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003324525.1	s__Mucilaginibacter hurinus	77.8599	288	1392	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	77.6946	285	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007846085.1	s__Mucilaginibacter sp007846085	77.6436	257	1392	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	77.6242	300	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003208075.1	s__Mucilaginibacter sp003208075	77.6133	275	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015221995.1	s__Mucilaginibacter boryungensis	77.612	211	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002288635.1	s__Mucilaginibacter sp002288635	77.6097	263	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013149275.1	s__Mucilaginibacter sp013149275	77.6015	270	1392	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	77.5787	322	1392	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	77.5372	248	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643835.1	s__Mucilaginibacter rubeus	77.5174	279	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	97.62	97.51	0.93	0.92	3	-
GCF_014200575.1	s__Mucilaginibacter sp014200575	77.4785	260	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101875.1	s__Mucilaginibacter pineti	77.4369	276	1392	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	77.3952	269	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004378255.1	s__Mucilaginibacter phyllosphaerae	77.3657	288	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCA_013288465.1	s__Mucilaginibacter sp013288465	77.3624	101	1392	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	77.319	273	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403905.1	s__Mucilaginibacter sp002403905	76.9753	169	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.52	99.50	0.82	0.82	3	-
GCA_013286325.1	s__Mucilaginibacter sp013286325	76.7663	112	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903885865.1	s__Mucilaginibacter sp903885865	76.6024	122	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.00	99.00	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:17:45,906] [INFO] GTDB search result was written to GCF_021215455.1_ASM2121545v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:17:45,906] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:17:45,913] [INFO] DFAST_QC result json was written to GCF_021215455.1_ASM2121545v1_genomic.fna/dqc_result.json
[2024-01-25 20:17:45,913] [INFO] DFAST_QC completed!
[2024-01-25 20:17:45,913] [INFO] Total running time: 0h1m40s