[2023-06-13 15:45:10,436] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:45:10,439] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:45:10,439] [INFO] DQC Reference Directory: /var/lib/cwl/stgb08fd86e-4a32-422e-87ba-ada86bb2bd45/dqc_reference
[2023-06-13 15:45:11,744] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:45:11,744] [INFO] Task started: Prodigal
[2023-06-13 15:45:11,745] [INFO] Running command: gunzip -c /var/lib/cwl/stg381c6eb3-9b0c-42b9-ab24-45e018d7426d/GCA_022825025.1_ASM2282502v1_genomic.fna.gz | prodigal -d GCA_022825025.1_ASM2282502v1_genomic.fna/cds.fna -a GCA_022825025.1_ASM2282502v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:45:25,275] [INFO] Task succeeded: Prodigal
[2023-06-13 15:45:25,276] [INFO] Task started: HMMsearch
[2023-06-13 15:45:25,276] [INFO] Running command: hmmsearch --tblout GCA_022825025.1_ASM2282502v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb08fd86e-4a32-422e-87ba-ada86bb2bd45/dqc_reference/reference_markers.hmm GCA_022825025.1_ASM2282502v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:45:25,625] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:45:25,627] [INFO] Found 6/6 markers.
[2023-06-13 15:45:25,693] [INFO] Query marker FASTA was written to GCA_022825025.1_ASM2282502v1_genomic.fna/markers.fasta
[2023-06-13 15:45:25,694] [INFO] Task started: Blastn
[2023-06-13 15:45:25,694] [INFO] Running command: blastn -query GCA_022825025.1_ASM2282502v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb08fd86e-4a32-422e-87ba-ada86bb2bd45/dqc_reference/reference_markers.fasta -out GCA_022825025.1_ASM2282502v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:45:26,390] [INFO] Task succeeded: Blastn
[2023-06-13 15:45:26,395] [INFO] Selected 30 target genomes.
[2023-06-13 15:45:26,395] [INFO] Target genome list was writen to GCA_022825025.1_ASM2282502v1_genomic.fna/target_genomes.txt
[2023-06-13 15:45:26,429] [INFO] Task started: fastANI
[2023-06-13 15:45:26,430] [INFO] Running command: fastANI --query /var/lib/cwl/stg381c6eb3-9b0c-42b9-ab24-45e018d7426d/GCA_022825025.1_ASM2282502v1_genomic.fna.gz --refList GCA_022825025.1_ASM2282502v1_genomic.fna/target_genomes.txt --output GCA_022825025.1_ASM2282502v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:45:51,222] [INFO] Task succeeded: fastANI
[2023-06-13 15:45:51,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb08fd86e-4a32-422e-87ba-ada86bb2bd45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:45:51,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb08fd86e-4a32-422e-87ba-ada86bb2bd45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:45:51,244] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 15:45:51,244] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 15:45:51,245] [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
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	75.8367	124	1537	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.8272	125	1537	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.8271	125	1537	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	75.3294	152	1537	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	75.0433	70	1537	95	below_threshold
Halorhodospira neutriphila	strain=DSM 15116	GCA_016584055.1	168379	168379	type	True	75.0042	51	1537	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	74.9264	61	1537	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	74.8897	76	1537	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	74.8705	79	1537	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	74.8435	128	1537	95	below_threshold
Actinoplanes atraurantiacus	strain=CGMCC 4.6857	GCA_900215205.1	1036182	1036182	type	True	74.8143	123	1537	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	74.8075	99	1537	95	below_threshold
Geodermatophilus tzadiensis	strain=DSM 45416	GCA_003002915.1	1137988	1137988	type	True	74.7589	105	1537	95	below_threshold
Geodermatophilus telluris	strain=DSM 45421	GCA_900102745.1	1190417	1190417	type	True	74.755	102	1537	95	below_threshold
Rathayibacter oskolensis	strain=VKM Ac-2121	GCA_900177245.1	1891671	1891671	type	True	74.7276	56	1537	95	below_threshold
Agromyces tardus	strain=SJ-23	GCA_003710805.1	2583849	2583849	type	True	74.691	60	1537	95	below_threshold
Agromyces allii	strain=JCM 13584	GCA_009749385.1	393607	393607	type	True	74.6367	74	1537	95	below_threshold
Saccharopolyspora spinosa	strain=NRRL 18395	GCA_000194155.1	60894	60894	type	True	74.6218	76	1537	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 15:45:51,251] [INFO] DFAST Taxonomy check result was written to GCA_022825025.1_ASM2282502v1_genomic.fna/tc_result.tsv
[2023-06-13 15:45:51,252] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:45:51,253] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:45:51,253] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb08fd86e-4a32-422e-87ba-ada86bb2bd45/dqc_reference/checkm_data
[2023-06-13 15:45:51,254] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:45:51,341] [INFO] Task started: CheckM
[2023-06-13 15:45:51,341] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022825025.1_ASM2282502v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022825025.1_ASM2282502v1_genomic.fna/checkm_input GCA_022825025.1_ASM2282502v1_genomic.fna/checkm_result
[2023-06-13 15:46:33,320] [INFO] Task succeeded: CheckM
[2023-06-13 15:46:33,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 15:46:33,351] [INFO] ===== Completeness check finished =====
[2023-06-13 15:46:33,352] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:46:33,352] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022825025.1_ASM2282502v1_genomic.fna/markers.fasta)
[2023-06-13 15:46:33,353] [INFO] Task started: Blastn
[2023-06-13 15:46:33,353] [INFO] Running command: blastn -query GCA_022825025.1_ASM2282502v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb08fd86e-4a32-422e-87ba-ada86bb2bd45/dqc_reference/reference_markers_gtdb.fasta -out GCA_022825025.1_ASM2282502v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:46:34,370] [INFO] Task succeeded: Blastn
[2023-06-13 15:46:34,375] [INFO] Selected 16 target genomes.
[2023-06-13 15:46:34,376] [INFO] Target genome list was writen to GCA_022825025.1_ASM2282502v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:46:34,381] [INFO] Task started: fastANI
[2023-06-13 15:46:34,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg381c6eb3-9b0c-42b9-ab24-45e018d7426d/GCA_022825025.1_ASM2282502v1_genomic.fna.gz --refList GCA_022825025.1_ASM2282502v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022825025.1_ASM2282502v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:46:45,318] [INFO] Task succeeded: fastANI
[2023-06-13 15:46:45,337] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 15:46:45,338] [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_009841475.1	s__Bin94 sp009841475	84.5052	849	1537	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__Bin94	95.0	99.08	98.52	0.89	0.85	6	-
GCA_009843625.1	s__BD2-11 sp009843625	81.5152	293	1537	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__BD2-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840525.1	s__BD2-11 sp009840525	81.4535	346	1537	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__BD2-11	95.0	96.09	95.11	0.90	0.85	6	-
GCA_002238605.1	s__BD2-11 sp002238605	80.9634	379	1537	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__BD2-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009838975.1	s__Bin94 sp009838975	80.2689	605	1537	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__Bin94	95.0	99.37	98.63	0.95	0.92	5	-
GCA_009841165.1	s__Bin94 sp009841165	80.1193	575	1537	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__Bin94	95.0	99.63	99.39	0.93	0.90	5	-
GCA_009840215.1	s__Bin94 sp009840215	80.0714	529	1537	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__Bin94	95.0	99.38	99.00	0.93	0.91	6	-
GCA_009844885.1	s__Bin94 sp009844885	79.4965	528	1537	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__Bin94	95.0	99.84	99.84	0.89	0.89	3	-
GCA_002238865.1	s__Bin94 sp002238865	79.0724	561	1537	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__Bin94	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003695865.1	s__J028 sp003695865	76.6481	123	1537	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__J028	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007132965.1	s__PWLA01 sp007132965	76.1792	83	1537	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__PWLA01	95.0	99.78	99.76	0.93	0.93	3	-
GCA_007130605.1	s__SLBA01 sp007130605	76.1103	74	1537	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SLBA01	95.0	99.40	99.31	0.83	0.83	4	-
GCA_003222235.1	s__AG12 sp003222235	75.339	55	1537	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__AG12	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 15:46:45,340] [INFO] GTDB search result was written to GCA_022825025.1_ASM2282502v1_genomic.fna/result_gtdb.tsv
[2023-06-13 15:46:45,341] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:46:45,346] [INFO] DFAST_QC result json was written to GCA_022825025.1_ASM2282502v1_genomic.fna/dqc_result.json
[2023-06-13 15:46:45,346] [INFO] DFAST_QC completed!
[2023-06-13 15:46:45,347] [INFO] Total running time: 0h1m35s