[2024-01-25 20:27:20,930] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:27:20,932] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:27:20,932] [INFO] DQC Reference Directory: /var/lib/cwl/stg07d25f6d-a7df-4cd6-8cbf-425184e4d16e/dqc_reference
[2024-01-25 20:27:22,143] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:27:22,143] [INFO] Task started: Prodigal
[2024-01-25 20:27:22,144] [INFO] Running command: gunzip -c /var/lib/cwl/stg85abb9a0-fc88-41a4-a8db-3dc80d1501c9/GCF_000403135.1_ArSv1_genomic.fna.gz | prodigal -d GCF_000403135.1_ArSv1_genomic.fna/cds.fna -a GCF_000403135.1_ArSv1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:27:36,263] [INFO] Task succeeded: Prodigal
[2024-01-25 20:27:36,263] [INFO] Task started: HMMsearch
[2024-01-25 20:27:36,263] [INFO] Running command: hmmsearch --tblout GCF_000403135.1_ArSv1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07d25f6d-a7df-4cd6-8cbf-425184e4d16e/dqc_reference/reference_markers.hmm GCF_000403135.1_ArSv1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:27:36,554] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:27:36,555] [INFO] Found 6/6 markers.
[2024-01-25 20:27:36,603] [INFO] Query marker FASTA was written to GCF_000403135.1_ArSv1_genomic.fna/markers.fasta
[2024-01-25 20:27:36,603] [INFO] Task started: Blastn
[2024-01-25 20:27:36,603] [INFO] Running command: blastn -query GCF_000403135.1_ArSv1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07d25f6d-a7df-4cd6-8cbf-425184e4d16e/dqc_reference/reference_markers.fasta -out GCF_000403135.1_ArSv1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:37,165] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:37,168] [INFO] Selected 20 target genomes.
[2024-01-25 20:27:37,168] [INFO] Target genome list was writen to GCF_000403135.1_ArSv1_genomic.fna/target_genomes.txt
[2024-01-25 20:27:37,186] [INFO] Task started: fastANI
[2024-01-25 20:27:37,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg85abb9a0-fc88-41a4-a8db-3dc80d1501c9/GCF_000403135.1_ArSv1_genomic.fna.gz --refList GCF_000403135.1_ArSv1_genomic.fna/target_genomes.txt --output GCF_000403135.1_ArSv1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:27:52,966] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:52,966] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07d25f6d-a7df-4cd6-8cbf-425184e4d16e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:27:52,967] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07d25f6d-a7df-4cd6-8cbf-425184e4d16e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:27:52,976] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:27:52,976] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:27:52,976] [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
Arcticibacter svalbardensis	strain=MN12-7	GCA_000403135.1	1288027	1288027	type	True	100.0	1481	1488	95	conclusive
Arcticibacter eurypsychrophilus	strain=MJ9-5	GCA_001730525.1	1434752	1434752	type	True	89.1102	1024	1488	95	below_threshold
Arcticibacter pallidicorallinus	strain=CGMCC 1.9313	GCA_003002875.1	1259464	1259464	type	True	78.2837	202	1488	95	below_threshold
Arcticibacter tournemirensis	strain=DSM 23085	GCA_006716645.1	699437	699437	type	True	77.4122	121	1488	95	below_threshold
Arcticibacter tournemirensis	strain=TF5-37.2-LB10	GCA_008690275.1	699437	699437	type	True	77.315	123	1488	95	below_threshold
Pedobacter xinjiangensis	strain=CCTCC AB 208092	GCA_024436435.1	539206	539206	type	True	76.8587	93	1488	95	below_threshold
Pedobacter frigoris	strain=RP-3-15	GCA_005116445.1	2571272	2571272	type	True	76.7484	58	1488	95	below_threshold
Pedobacter cryophilus	strain=AR-3-17	GCA_005116455.1	2571271	2571271	type	True	76.5995	71	1488	95	below_threshold
Pedobacter panaciterrae	strain=LMG 23400	GCA_013204795.1	363849	363849	type	True	76.487	68	1488	95	below_threshold
Daejeonella oryzae	strain=DSM 19973	GCA_000422945.1	1122943	1122943	type	True	76.4822	62	1488	95	below_threshold
Pedobacter aquae	strain=CJ43	GCA_008195825.1	2605747	2605747	type	True	76.3611	70	1488	95	below_threshold
Pedobacter nutrimenti	strain=DSM 27372	GCA_003208655.1	1241337	1241337	type	True	76.2022	66	1488	95	below_threshold
Pedobacter steynii	strain=DSM 19110	GCA_900103665.1	430522	430522	type	True	76.1696	81	1488	95	below_threshold
Pedobacter rhizosphaerae	strain=DSM 18610	GCA_900111155.1	390241	390241	type	True	76.1469	55	1488	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:27:52,978] [INFO] DFAST Taxonomy check result was written to GCF_000403135.1_ArSv1_genomic.fna/tc_result.tsv
[2024-01-25 20:27:52,978] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:27:52,978] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:27:52,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07d25f6d-a7df-4cd6-8cbf-425184e4d16e/dqc_reference/checkm_data
[2024-01-25 20:27:52,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:27:53,027] [INFO] Task started: CheckM
[2024-01-25 20:27:53,027] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000403135.1_ArSv1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000403135.1_ArSv1_genomic.fna/checkm_input GCF_000403135.1_ArSv1_genomic.fna/checkm_result
[2024-01-25 20:28:35,494] [INFO] Task succeeded: CheckM
[2024-01-25 20:28:35,496] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:28:35,516] [INFO] ===== Completeness check finished =====
[2024-01-25 20:28:35,517] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:28:35,518] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000403135.1_ArSv1_genomic.fna/markers.fasta)
[2024-01-25 20:28:35,518] [INFO] Task started: Blastn
[2024-01-25 20:28:35,518] [INFO] Running command: blastn -query GCF_000403135.1_ArSv1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07d25f6d-a7df-4cd6-8cbf-425184e4d16e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000403135.1_ArSv1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:28:36,283] [INFO] Task succeeded: Blastn
[2024-01-25 20:28:36,287] [INFO] Selected 22 target genomes.
[2024-01-25 20:28:36,287] [INFO] Target genome list was writen to GCF_000403135.1_ArSv1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:28:36,312] [INFO] Task started: fastANI
[2024-01-25 20:28:36,312] [INFO] Running command: fastANI --query /var/lib/cwl/stg85abb9a0-fc88-41a4-a8db-3dc80d1501c9/GCF_000403135.1_ArSv1_genomic.fna.gz --refList GCF_000403135.1_ArSv1_genomic.fna/target_genomes_gtdb.txt --output GCF_000403135.1_ArSv1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:28:55,314] [INFO] Task succeeded: fastANI
[2024-01-25 20:28:55,332] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:28:55,333] [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_000403135.1	s__Arcticibacter svalbardensis	100.0	1481	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Arcticibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001730525.1	s__Arcticibacter eurypsychrophilus	89.084	1026	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Arcticibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002875.1	s__Arcticibacter pallidicorallinus	78.2824	201	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Arcticibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716645.1	s__Pararcticibacter tournemirensis	77.4348	120	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pararcticibacter	95.0	98.22	96.45	0.92	0.83	3	-
GCF_000302595.1	s__Pelobium arcticum	77.0279	52	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130405.1	s__Pararcticibacter amylolyticus	76.9843	101	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pararcticibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004354365.1	s__Pedobacter changchengzhani	76.61	53	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799115.1	s__Pelobium glucosidilyticum_A	76.5145	61	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	97.72	97.72	0.84	0.84	2	-
GCF_013204795.1	s__Pedobacter panaciterrae	76.487	68	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422945.1	s__Daejeonella oryzae	76.4822	62	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003061025.1	s__Pedobacter sp003061025	76.4351	63	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054145.1	s__Pedobacter sp003054145	76.3349	72	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001412655.1	s__Pedobacter sp001412655	76.2206	74	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111155.1	s__Pedobacter rhizosphaerae	76.1469	55	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014378705.1	s__Daejeonella sp014378705	75.8435	50	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:28:55,334] [INFO] GTDB search result was written to GCF_000403135.1_ArSv1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:28:55,335] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:28:55,338] [INFO] DFAST_QC result json was written to GCF_000403135.1_ArSv1_genomic.fna/dqc_result.json
[2024-01-25 20:28:55,338] [INFO] DFAST_QC completed!
[2024-01-25 20:28:55,338] [INFO] Total running time: 0h1m34s