[2024-01-24 15:26:33,204] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:33,205] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:33,205] [INFO] DQC Reference Directory: /var/lib/cwl/stg74374b73-c18e-48c6-8030-4713551c4bfa/dqc_reference
[2024-01-24 15:26:34,445] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:34,446] [INFO] Task started: Prodigal
[2024-01-24 15:26:34,446] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b5b3f82-2041-4203-bce5-89de60687597/GCF_007971025.1_ASM797102v1_genomic.fna.gz | prodigal -d GCF_007971025.1_ASM797102v1_genomic.fna/cds.fna -a GCF_007971025.1_ASM797102v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:59,757] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:59,758] [INFO] Task started: HMMsearch
[2024-01-24 15:26:59,758] [INFO] Running command: hmmsearch --tblout GCF_007971025.1_ASM797102v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74374b73-c18e-48c6-8030-4713551c4bfa/dqc_reference/reference_markers.hmm GCF_007971025.1_ASM797102v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:00,105] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:00,106] [INFO] Found 6/6 markers.
[2024-01-24 15:27:00,155] [INFO] Query marker FASTA was written to GCF_007971025.1_ASM797102v1_genomic.fna/markers.fasta
[2024-01-24 15:27:00,156] [INFO] Task started: Blastn
[2024-01-24 15:27:00,156] [INFO] Running command: blastn -query GCF_007971025.1_ASM797102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74374b73-c18e-48c6-8030-4713551c4bfa/dqc_reference/reference_markers.fasta -out GCF_007971025.1_ASM797102v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:00,802] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:00,807] [INFO] Selected 24 target genomes.
[2024-01-24 15:27:00,808] [INFO] Target genome list was writen to GCF_007971025.1_ASM797102v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:00,818] [INFO] Task started: fastANI
[2024-01-24 15:27:00,818] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b5b3f82-2041-4203-bce5-89de60687597/GCF_007971025.1_ASM797102v1_genomic.fna.gz --refList GCF_007971025.1_ASM797102v1_genomic.fna/target_genomes.txt --output GCF_007971025.1_ASM797102v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:21,522] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:21,523] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74374b73-c18e-48c6-8030-4713551c4bfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:21,523] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74374b73-c18e-48c6-8030-4713551c4bfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:21,552] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:21,552] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:21,553] [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 ginsenosidivorans	strain=Gsoil 3017	GCA_007971025.1	398053	398053	type	True	100.0	1784	1784	95	conclusive
Mucilaginibacter boryungensis	strain=KCTC 23157	GCA_015221995.1	768480	768480	type	True	78.9235	253	1784	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	77.3535	241	1784	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=CCM 8625	GCA_014635525.1	1812349	1812349	type	True	77.2486	239	1784	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=DSM 100995	GCA_014196695.1	1812349	1812349	type	True	77.2483	241	1784	95	below_threshold
Mucilaginibacter pedocola	strain=TBZ30	GCA_002013915.1	1792845	1792845	type	True	77.2405	233	1784	95	below_threshold
Mucilaginibacter limnophilus	strain=YBJ-36	GCA_004005815.1	1932778	1932778	type	True	77.2358	185	1784	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	77.1876	245	1784	95	below_threshold
Mucilaginibacter gossypiicola	strain=Gh-48	GCA_900110105.1	551995	551995	type	True	77.1873	228	1784	95	below_threshold
Mucilaginibacter gossypii	strain=Gh-67	GCA_900100945.1	551996	551996	type	True	77.1736	247	1784	95	below_threshold
Mucilaginibacter oryzae	strain=DSM 19975	GCA_003148845.1	468058	468058	type	True	77.1631	239	1784	95	below_threshold
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	77.1222	253	1784	95	below_threshold
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	77.0974	198	1784	95	below_threshold
Mucilaginibacter gotjawali	strain=SA3-7	GCA_002355435.1	1550579	1550579	type	True	77.0906	337	1784	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	77.0825	170	1784	95	below_threshold
Mucilaginibacter yixingensis	strain=DSM 26809	GCA_003050755.1	1295612	1295612	type	True	77.0782	180	1784	95	below_threshold
Mucilaginibacter pankratovii	strain=ZT4R22	GCA_014773265.1	2772110	2772110	type	True	77.0093	298	1784	95	below_threshold
Mucilaginibacter gotjawali	strain=CECT 8628	GCA_014191635.1	1550579	1550579	type	True	76.9571	335	1784	95	below_threshold
Mucilaginibacter rubeus	strain=CGMCC 1.15913	GCA_014643835.1	2027860	2027860	suspected-type	True	76.948	250	1784	95	below_threshold
Mucilaginibacter frigoritolerans	strain=ATCC BAA-1854	GCA_007830615.1	652788	652788	type	True	76.9462	212	1784	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	76.935	163	1784	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:21,554] [INFO] DFAST Taxonomy check result was written to GCF_007971025.1_ASM797102v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:21,555] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:21,555] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:21,555] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74374b73-c18e-48c6-8030-4713551c4bfa/dqc_reference/checkm_data
[2024-01-24 15:27:21,556] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:21,608] [INFO] Task started: CheckM
[2024-01-24 15:27:21,608] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007971025.1_ASM797102v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007971025.1_ASM797102v1_genomic.fna/checkm_input GCF_007971025.1_ASM797102v1_genomic.fna/checkm_result
[2024-01-24 15:28:31,214] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:31,215] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:31,238] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:31,238] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:31,238] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007971025.1_ASM797102v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:31,239] [INFO] Task started: Blastn
[2024-01-24 15:28:31,239] [INFO] Running command: blastn -query GCF_007971025.1_ASM797102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74374b73-c18e-48c6-8030-4713551c4bfa/dqc_reference/reference_markers_gtdb.fasta -out GCF_007971025.1_ASM797102v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:32,276] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:32,281] [INFO] Selected 17 target genomes.
[2024-01-24 15:28:32,281] [INFO] Target genome list was writen to GCF_007971025.1_ASM797102v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:32,296] [INFO] Task started: fastANI
[2024-01-24 15:28:32,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b5b3f82-2041-4203-bce5-89de60687597/GCF_007971025.1_ASM797102v1_genomic.fna.gz --refList GCF_007971025.1_ASM797102v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007971025.1_ASM797102v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:47,062] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:47,081] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:47,082] [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_007971025.1	s__Mucilaginibacter ginsenosidivorans	100.0	1783	1784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903863845.1	s__Mucilaginibacter sp903863845	78.0749	365	1784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.75	99.63	0.93	0.92	5	-
GCA_018266935.1	s__Mucilaginibacter sp018266935	78.0395	450	1784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903866915.1	s__Mucilaginibacter sp903866915	77.9354	340	1784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.75	99.75	0.86	0.86	2	-
GCA_018266915.1	s__Mucilaginibacter sp018266915	77.8206	399	1784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019235595.1	s__Mucilaginibacter sp019235595	77.7315	285	1784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903887275.1	s__Mucilaginibacter sp903887275	77.6825	376	1784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267005.1	s__Mucilaginibacter sp018267005	77.6635	418	1784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013286565.1	s__Mucilaginibacter sp013286565	77.5117	320	1784	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	77.1227	253	1784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355435.1	s__Mucilaginibacter gotjawali	77.083	338	1784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_903913935.1	s__Mucilaginibacter sp903913935	76.9336	249	1784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110415.1	s__Mucilaginibacter sp900110415	76.8235	259	1784	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	76.6656	164	1784	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.52	99.50	0.82	0.82	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:47,089] [INFO] GTDB search result was written to GCF_007971025.1_ASM797102v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:47,089] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:47,094] [INFO] DFAST_QC result json was written to GCF_007971025.1_ASM797102v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:47,094] [INFO] DFAST_QC completed!
[2024-01-24 15:28:47,094] [INFO] Total running time: 0h2m14s