[2024-01-24 13:17:13,822] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:13,823] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:13,824] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a6832b3-09d9-43b3-b475-b6f9cdb5a7f3/dqc_reference
[2024-01-24 13:17:15,239] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:15,239] [INFO] Task started: Prodigal
[2024-01-24 13:17:15,240] [INFO] Running command: gunzip -c /var/lib/cwl/stg71bd838c-8230-4fa8-acad-a1f217ab5279/GCF_024436395.1_ASM2443639v1_genomic.fna.gz | prodigal -d GCF_024436395.1_ASM2443639v1_genomic.fna/cds.fna -a GCF_024436395.1_ASM2443639v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:33,370] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:33,371] [INFO] Task started: HMMsearch
[2024-01-24 13:17:33,371] [INFO] Running command: hmmsearch --tblout GCF_024436395.1_ASM2443639v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a6832b3-09d9-43b3-b475-b6f9cdb5a7f3/dqc_reference/reference_markers.hmm GCF_024436395.1_ASM2443639v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:33,704] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:33,706] [INFO] Found 6/6 markers.
[2024-01-24 13:17:33,753] [INFO] Query marker FASTA was written to GCF_024436395.1_ASM2443639v1_genomic.fna/markers.fasta
[2024-01-24 13:17:33,754] [INFO] Task started: Blastn
[2024-01-24 13:17:33,754] [INFO] Running command: blastn -query GCF_024436395.1_ASM2443639v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a6832b3-09d9-43b3-b475-b6f9cdb5a7f3/dqc_reference/reference_markers.fasta -out GCF_024436395.1_ASM2443639v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:34,423] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:34,427] [INFO] Selected 28 target genomes.
[2024-01-24 13:17:34,427] [INFO] Target genome list was writen to GCF_024436395.1_ASM2443639v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:34,446] [INFO] Task started: fastANI
[2024-01-24 13:17:34,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg71bd838c-8230-4fa8-acad-a1f217ab5279/GCF_024436395.1_ASM2443639v1_genomic.fna.gz --refList GCF_024436395.1_ASM2443639v1_genomic.fna/target_genomes.txt --output GCF_024436395.1_ASM2443639v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:58,149] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:58,150] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a6832b3-09d9-43b3-b475-b6f9cdb5a7f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:58,150] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a6832b3-09d9-43b3-b475-b6f9cdb5a7f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:58,172] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:58,173] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:58,173] [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
Pedobacter mongoliensis	strain=KCTC 52859	GCA_024436395.1	2100740	2100740	type	True	100.0	1514	1514	95	conclusive
Arcticibacter tournemirensis	strain=DSM 23085	GCA_006716645.1	699437	699437	type	True	77.702	92	1514	95	below_threshold
Pedobacter xinjiangensis	strain=CCTCC AB 208092	GCA_024436435.1	539206	539206	type	True	77.6121	126	1514	95	below_threshold
Arcticibacter tournemirensis	strain=TF5-37.2-LB10	GCA_008690275.1	699437	699437	type	True	77.5003	90	1514	95	below_threshold
Pedobacter planticolens	strain=LMG 31464	GCA_014172375.1	2679964	2679964	type	True	77.2322	56	1514	95	below_threshold
Arcticibacter pallidicorallinus	strain=CGMCC 1.9313	GCA_003002875.1	1259464	1259464	type	True	77.152	90	1514	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	77.0316	71	1514	95	below_threshold
Mucilaginibacter gracilis	strain=DSM 18602	GCA_003633615.1	423350	423350	type	True	77.0256	54	1514	95	below_threshold
Pedobacter glucosidilyticus	strain=DSM 23534	GCA_000425145.1	1122941	1122941	type	True	76.9414	67	1514	95	below_threshold
Mucilaginibacter corticis	strain=MAH-19	GCA_007558865.1	2597670	2597670	type	True	76.9198	56	1514	95	below_threshold
Pedobacter ureilyticus	strain=THG-T11	GCA_005925345.1	1393051	1393051	type	True	76.8858	61	1514	95	below_threshold
Pedobacter cryophilus	strain=AR-3-17	GCA_005116455.1	2571271	2571271	type	True	76.8787	67	1514	95	below_threshold
Mucilaginibacter celer	strain=HYN0043	GCA_003576455.2	2305508	2305508	type	True	76.8697	63	1514	95	below_threshold
Pedobacter nototheniae	strain=36B243	GCA_004335085.1	2488994	2488994	type	True	76.8661	69	1514	95	below_threshold
Pedobacter foliorum	strain=LMG 31463	GCA_013266735.1	2739058	2739058	type	True	76.8569	57	1514	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	76.8368	51	1514	95	below_threshold
Pelobium manganitolerans	strain=YS-25	GCA_003609575.1	1842495	1842495	type	True	76.8303	54	1514	95	below_threshold
Pararcticibacter amylolyticus	strain=FJ4-8	GCA_003130405.1	2173175	2173175	type	True	76.808	98	1514	95	below_threshold
Mucilaginibacter pineti	strain=47C3B	GCA_900101875.1	1391627	1391627	type	True	76.771	66	1514	95	below_threshold
Pedobacter yonginense	strain=KCTC22721	GCA_003173595.1	651869	651869	type	True	76.7262	50	1514	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	76.7099	79	1514	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	76.6764	50	1514	95	below_threshold
Pedobacter agri	strain=PB92	GCA_000258495.1	454586	454586	type	True	76.6466	62	1514	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	76.4218	65	1514	95	below_threshold
Pedobacter nyackensis	strain=DSM 19625	GCA_900176505.1	475255	475255	type	True	76.3775	76	1514	95	below_threshold
Pedobacter cryoconitis	strain=DSM 14825	GCA_003259615.1	188932	188932	suspected-type	True	76.2181	57	1514	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:58,174] [INFO] DFAST Taxonomy check result was written to GCF_024436395.1_ASM2443639v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:58,175] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:58,175] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:58,176] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a6832b3-09d9-43b3-b475-b6f9cdb5a7f3/dqc_reference/checkm_data
[2024-01-24 13:17:58,177] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:58,221] [INFO] Task started: CheckM
[2024-01-24 13:17:58,221] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024436395.1_ASM2443639v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024436395.1_ASM2443639v1_genomic.fna/checkm_input GCF_024436395.1_ASM2443639v1_genomic.fna/checkm_result
[2024-01-24 13:18:53,574] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:53,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:53,599] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:53,600] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:53,600] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024436395.1_ASM2443639v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:53,600] [INFO] Task started: Blastn
[2024-01-24 13:18:53,601] [INFO] Running command: blastn -query GCF_024436395.1_ASM2443639v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a6832b3-09d9-43b3-b475-b6f9cdb5a7f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_024436395.1_ASM2443639v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:54,439] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:54,444] [INFO] Selected 30 target genomes.
[2024-01-24 13:18:54,445] [INFO] Target genome list was writen to GCF_024436395.1_ASM2443639v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:54,471] [INFO] Task started: fastANI
[2024-01-24 13:18:54,472] [INFO] Running command: fastANI --query /var/lib/cwl/stg71bd838c-8230-4fa8-acad-a1f217ab5279/GCF_024436395.1_ASM2443639v1_genomic.fna.gz --refList GCF_024436395.1_ASM2443639v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024436395.1_ASM2443639v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:19,454] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:19,484] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:19:19,484] [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
GCA_014380615.1	s__JACMJM01 sp014380615	79.3764	414	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__JACMJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834875.1	s__HMF7647 sp009834875	77.9178	77	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__HMF7647	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716645.1	s__Pararcticibacter tournemirensis	77.702	92	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pararcticibacter	95.0	98.22	96.45	0.92	0.83	3	-
GCF_017355855.1	s__SYSU-D00535 sp017355855	77.5242	140	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__SYSU-D00535	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355785.1	s__SYSU-D00535 sp017355785	77.3028	110	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__SYSU-D00535	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001027745.1	s__Pedobacter sp001027745	77.2051	52	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355835.1	s__SYSU-D00535 sp017355835	77.195	111	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__SYSU-D00535	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422545.1	s__Pedobacter sp001422545	77.1129	59	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633615.1	s__Mucilaginibacter gracilis	77.0256	54	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007558865.1	s__Mucilaginibacter corticis	76.9207	55	1514	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	76.8881	64	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005925345.1	s__Pedobacter ureilyticus	76.8858	61	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130405.1	s__Pararcticibacter amylolyticus	76.808	98	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pararcticibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002257025.1	s__Daejeonella sp002257025	76.7712	70	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900101875.1	s__Mucilaginibacter pineti	76.733	66	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200575.1	s__Mucilaginibacter sp014200575	76.7093	65	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752175.1	s__Pedobacter sp015752175	76.6763	61	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765875.1	s__Pedobacter sp009765875	76.6553	69	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008274585.1	s__BS3 sp008274585	76.6488	83	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__BS3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000258495.1	s__Pedobacter agri	76.6139	61	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	97.48	97.42	0.86	0.85	3	-
GCF_015221995.1	s__Mucilaginibacter boryungensis	76.5983	68	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176505.1	s__Pedobacter nyackensis	76.402	75	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200595.1	s__Pedobacter cryoconitis_C	76.2377	61	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.76	98.76	0.93	0.93	2	-
GCF_003259615.1	s__Pedobacter cryoconitis	76.2004	56	1514	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:19,487] [INFO] GTDB search result was written to GCF_024436395.1_ASM2443639v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:19,487] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:19,495] [INFO] DFAST_QC result json was written to GCF_024436395.1_ASM2443639v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:19,495] [INFO] DFAST_QC completed!
[2024-01-24 13:19:19,496] [INFO] Total running time: 0h2m6s