[2024-01-24 12:22:34,152] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:34,153] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:34,153] [INFO] DQC Reference Directory: /var/lib/cwl/stgb423b4d7-9f18-4c95-ae38-4866525f6887/dqc_reference
[2024-01-24 12:22:35,579] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:35,580] [INFO] Task started: Prodigal
[2024-01-24 12:22:35,581] [INFO] Running command: gunzip -c /var/lib/cwl/stg57eda16d-a8b2-4b22-9e68-14905e77508d/GCF_009754905.2_ASM975490v2_genomic.fna.gz | prodigal -d GCF_009754905.2_ASM975490v2_genomic.fna/cds.fna -a GCF_009754905.2_ASM975490v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:53,215] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:53,216] [INFO] Task started: HMMsearch
[2024-01-24 12:22:53,216] [INFO] Running command: hmmsearch --tblout GCF_009754905.2_ASM975490v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb423b4d7-9f18-4c95-ae38-4866525f6887/dqc_reference/reference_markers.hmm GCF_009754905.2_ASM975490v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:53,511] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:53,512] [INFO] Found 6/6 markers.
[2024-01-24 12:22:53,546] [INFO] Query marker FASTA was written to GCF_009754905.2_ASM975490v2_genomic.fna/markers.fasta
[2024-01-24 12:22:53,547] [INFO] Task started: Blastn
[2024-01-24 12:22:53,547] [INFO] Running command: blastn -query GCF_009754905.2_ASM975490v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb423b4d7-9f18-4c95-ae38-4866525f6887/dqc_reference/reference_markers.fasta -out GCF_009754905.2_ASM975490v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:54,163] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:54,166] [INFO] Selected 18 target genomes.
[2024-01-24 12:22:54,166] [INFO] Target genome list was writen to GCF_009754905.2_ASM975490v2_genomic.fna/target_genomes.txt
[2024-01-24 12:22:54,182] [INFO] Task started: fastANI
[2024-01-24 12:22:54,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg57eda16d-a8b2-4b22-9e68-14905e77508d/GCF_009754905.2_ASM975490v2_genomic.fna.gz --refList GCF_009754905.2_ASM975490v2_genomic.fna/target_genomes.txt --output GCF_009754905.2_ASM975490v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:09,705] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:09,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb423b4d7-9f18-4c95-ae38-4866525f6887/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:09,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb423b4d7-9f18-4c95-ae38-4866525f6887/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:09,720] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:09,720] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:09,720] [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 ginkgonis	strain=HMF7856	GCA_009754905.2	2682091	2682091	type	True	100.0	1231	1232	95	conclusive
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	79.3542	265	1232	95	below_threshold
Mucilaginibacter limnophilus	strain=YBJ-36	GCA_004005815.1	1932778	1932778	type	True	77.6699	124	1232	95	below_threshold
Mucilaginibacter polytrichastri	strain=RG4-7	GCA_001911425.1	1302689	1302689	type	True	77.5793	267	1232	95	below_threshold
Mucilaginibacter polytrichastri	strain=DSM 26907	GCA_900116355.1	1302689	1302689	type	True	77.5627	261	1232	95	below_threshold
Mucilaginibacter mali	strain=G2-14	GCA_013283875.1	2740462	2740462	type	True	77.5163	177	1232	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	77.3594	156	1232	95	below_threshold
Mucilaginibacter aquatilis	strain=HME9299	GCA_009755275.1	1517760	1517760	type	True	77.2866	131	1232	95	below_threshold
Mucilaginibacter pedocola	strain=TBZ30	GCA_002013915.1	1792845	1792845	type	True	77.2643	175	1232	95	below_threshold
Mucilaginibacter myungsuensis	strain=KCTC 22746	GCA_015222005.1	649104	649104	type	True	77.1226	145	1232	95	below_threshold
Mucilaginibacter glaciei	strain=ZB1P21	GCA_014773245.1	2772109	2772109	type	True	77.1137	171	1232	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.1097	182	1232	95	below_threshold
Mucilaginibacter kameinonensis	strain=SCK	GCA_003675385.1	452286	452286	type	True	77.0357	163	1232	95	below_threshold
Mucilaginibacter psychrotolerans	strain=NH7-4	GCA_004519315.1	1524096	1524096	type	True	76.8946	143	1232	95	below_threshold
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	76.8516	158	1232	95	below_threshold
Pedobacter psychrodurus	strain=RP-3-21	GCA_004331735.1	2530456	2530456	type	True	76.4768	56	1232	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	76.2269	57	1232	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:09,723] [INFO] DFAST Taxonomy check result was written to GCF_009754905.2_ASM975490v2_genomic.fna/tc_result.tsv
[2024-01-24 12:23:09,724] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:09,724] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:09,724] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb423b4d7-9f18-4c95-ae38-4866525f6887/dqc_reference/checkm_data
[2024-01-24 12:23:09,725] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:09,767] [INFO] Task started: CheckM
[2024-01-24 12:23:09,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009754905.2_ASM975490v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009754905.2_ASM975490v2_genomic.fna/checkm_input GCF_009754905.2_ASM975490v2_genomic.fna/checkm_result
[2024-01-24 12:23:57,820] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:57,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:57,845] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:57,845] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:57,845] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009754905.2_ASM975490v2_genomic.fna/markers.fasta)
[2024-01-24 12:23:57,846] [INFO] Task started: Blastn
[2024-01-24 12:23:57,846] [INFO] Running command: blastn -query GCF_009754905.2_ASM975490v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb423b4d7-9f18-4c95-ae38-4866525f6887/dqc_reference/reference_markers_gtdb.fasta -out GCF_009754905.2_ASM975490v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:58,621] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:58,625] [INFO] Selected 22 target genomes.
[2024-01-24 12:23:58,625] [INFO] Target genome list was writen to GCF_009754905.2_ASM975490v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:58,643] [INFO] Task started: fastANI
[2024-01-24 12:23:58,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg57eda16d-a8b2-4b22-9e68-14905e77508d/GCF_009754905.2_ASM975490v2_genomic.fna.gz --refList GCF_009754905.2_ASM975490v2_genomic.fna/target_genomes_gtdb.txt --output GCF_009754905.2_ASM975490v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:17,176] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:17,199] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:17,200] [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_009754905.2	s__Mucilaginibacter ginkgonis	100.0	1231	1232	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_009928685.1	s__Mucilaginibacter sp009928685	79.3542	265	1232	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	77.6699	124	1232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001911425.1	s__Mucilaginibacter polytrichastri	77.5674	268	1232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_001898335.1	s__Mucilaginibacter sp001898335	77.4619	170	1232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.32	99.30	0.92	0.89	3	-
GCF_007846095.1	s__Mucilaginibacter sp007846095	77.3764	155	1232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755275.1	s__Mucilaginibacter aquatilis	77.2866	131	1232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576455.2	s__Mucilaginibacter celer	77.283	164	1232	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	77.2744	176	1232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664165.1	s__Mucilaginibacter sp003664165	77.2574	165	1232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223065.1	s__Mucilaginibacter sp015223065	77.2204	156	1232	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	77.1903	163	1232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014773245.1	s__Mucilaginibacter glaciei	77.1137	171	1232	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	77.1099	182	1232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636615.1	s__Mucilaginibacter sp001636615	77.0377	193	1232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675385.1	s__Mucilaginibacter kameinonensis	77.0203	164	1232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	95.21	95.21	0.87	0.87	2	-
GCA_903644075.1	s__Mucilaginibacter sp903644075	76.9965	232	1232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390515.1	s__Mucilaginibacter sp018390515	76.9562	153	1232	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	76.9181	159	1232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103125.1	s__Mucilaginibacter sp900103125	76.9123	172	1232	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013286235.1	s__Mucilaginibacter sp013286235	76.144	80	1232	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 12:24:17,201] [INFO] GTDB search result was written to GCF_009754905.2_ASM975490v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:17,202] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:17,206] [INFO] DFAST_QC result json was written to GCF_009754905.2_ASM975490v2_genomic.fna/dqc_result.json
[2024-01-24 12:24:17,206] [INFO] DFAST_QC completed!
[2024-01-24 12:24:17,206] [INFO] Total running time: 0h1m43s