[2024-01-24 15:03:14,477] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:14,479] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:14,479] [INFO] DQC Reference Directory: /var/lib/cwl/stgaaf4e337-6b42-45b4-9628-cdef6f0d3bdf/dqc_reference
[2024-01-24 15:03:15,886] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:15,887] [INFO] Task started: Prodigal
[2024-01-24 15:03:15,888] [INFO] Running command: gunzip -c /var/lib/cwl/stg61111074-d2d0-40cf-927c-85ea4db18b47/GCF_005116445.1_ASM511644v1_genomic.fna.gz | prodigal -d GCF_005116445.1_ASM511644v1_genomic.fna/cds.fna -a GCF_005116445.1_ASM511644v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:36,396] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:36,396] [INFO] Task started: HMMsearch
[2024-01-24 15:03:36,396] [INFO] Running command: hmmsearch --tblout GCF_005116445.1_ASM511644v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaaf4e337-6b42-45b4-9628-cdef6f0d3bdf/dqc_reference/reference_markers.hmm GCF_005116445.1_ASM511644v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:36,760] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:36,761] [INFO] Found 6/6 markers.
[2024-01-24 15:03:36,804] [INFO] Query marker FASTA was written to GCF_005116445.1_ASM511644v1_genomic.fna/markers.fasta
[2024-01-24 15:03:36,805] [INFO] Task started: Blastn
[2024-01-24 15:03:36,805] [INFO] Running command: blastn -query GCF_005116445.1_ASM511644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaaf4e337-6b42-45b4-9628-cdef6f0d3bdf/dqc_reference/reference_markers.fasta -out GCF_005116445.1_ASM511644v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:37,445] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:37,450] [INFO] Selected 21 target genomes.
[2024-01-24 15:03:37,450] [INFO] Target genome list was writen to GCF_005116445.1_ASM511644v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:37,463] [INFO] Task started: fastANI
[2024-01-24 15:03:37,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg61111074-d2d0-40cf-927c-85ea4db18b47/GCF_005116445.1_ASM511644v1_genomic.fna.gz --refList GCF_005116445.1_ASM511644v1_genomic.fna/target_genomes.txt --output GCF_005116445.1_ASM511644v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:57,614] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:57,615] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaaf4e337-6b42-45b4-9628-cdef6f0d3bdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:57,615] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaaf4e337-6b42-45b4-9628-cdef6f0d3bdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:57,630] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:57,630] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:57,630] [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 frigoris	strain=RP-3-15	GCA_005116445.1	2571272	2571272	type	True	100.0	1548	1551	95	conclusive
Pedobacter panaciterrae	strain=LMG 23400	GCA_013204795.1	363849	363849	type	True	79.6642	447	1551	95	below_threshold
Pedobacter foliorum	strain=LMG 31463	GCA_013266735.1	2739058	2739058	type	True	79.5161	457	1551	95	below_threshold
Pedobacter psychroterrae	strain=RP-1-14	GCA_004331695.1	2530453	2530453	type	True	79.3875	388	1551	95	below_threshold
Pedobacter nyackensis	strain=DSM 19625	GCA_900176505.1	475255	475255	type	True	79.0264	400	1551	95	below_threshold
Pedobacter hiemivivus	strain=RP-3-8	GCA_004331685.1	2530454	2530454	type	True	78.9917	415	1551	95	below_threshold
Pedobacter heparinus	strain=DSM 2366	GCA_000410815.1	984	984	type	True	78.9798	376	1551	95	below_threshold
Pedobacter metabolipauper	strain=DSM 19035	GCA_004362715.1	425513	425513	type	True	78.9527	404	1551	95	below_threshold
Pedobacter heparinus	strain=DSM 2366	GCA_000023825.1	984	984	type	True	78.8916	382	1551	95	below_threshold
Pedobacter schmidteae	strain=eg	GCA_900564155.1	2201271	2201271	type	True	78.8431	380	1551	95	below_threshold
Pedobacter steynii	strain=DSM 19110	GCA_900103665.1	430522	430522	type	True	78.7986	399	1551	95	below_threshold
Pedobacter caeni	strain=DSM 16990	GCA_900129215.1	288992	288992	type	True	78.7744	412	1551	95	below_threshold
Pedobacter westerhofensis	strain=DSM 19036	GCA_900182595.1	425512	425512	type	True	78.5455	237	1551	95	below_threshold
Pedobacter duraquae	strain=DSM 19034	GCA_004362245.1	425511	425511	type	True	78.2788	222	1551	95	below_threshold
Pedobacter cryoconitis	strain=DSM 14825	GCA_003259615.1	188932	188932	suspected-type	True	78.2511	237	1551	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	77.3385	173	1551	95	below_threshold
Mucilaginibacter segetis	strain=SD-g	GCA_016522075.1	2793071	2793071	type	True	77.0958	51	1551	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	76.6872	52	1551	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	76.2286	62	1551	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:57,632] [INFO] DFAST Taxonomy check result was written to GCF_005116445.1_ASM511644v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:57,633] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:57,633] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:57,633] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaaf4e337-6b42-45b4-9628-cdef6f0d3bdf/dqc_reference/checkm_data
[2024-01-24 15:03:57,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:57,683] [INFO] Task started: CheckM
[2024-01-24 15:03:57,683] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005116445.1_ASM511644v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005116445.1_ASM511644v1_genomic.fna/checkm_input GCF_005116445.1_ASM511644v1_genomic.fna/checkm_result
[2024-01-24 15:04:56,620] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:56,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:56,644] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:56,645] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:56,645] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005116445.1_ASM511644v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:56,646] [INFO] Task started: Blastn
[2024-01-24 15:04:56,646] [INFO] Running command: blastn -query GCF_005116445.1_ASM511644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaaf4e337-6b42-45b4-9628-cdef6f0d3bdf/dqc_reference/reference_markers_gtdb.fasta -out GCF_005116445.1_ASM511644v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:57,554] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:57,558] [INFO] Selected 21 target genomes.
[2024-01-24 15:04:57,558] [INFO] Target genome list was writen to GCF_005116445.1_ASM511644v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:57,576] [INFO] Task started: fastANI
[2024-01-24 15:04:57,576] [INFO] Running command: fastANI --query /var/lib/cwl/stg61111074-d2d0-40cf-927c-85ea4db18b47/GCF_005116445.1_ASM511644v1_genomic.fna.gz --refList GCF_005116445.1_ASM511644v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005116445.1_ASM511644v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:20,668] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:20,685] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:20,686] [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_005116445.1	s__Pedobacter sp005116445	100.0	1548	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018492665.1	s__Pedobacter sp018492665	79.6862	444	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054115.1	s__Pedobacter sp003054115	79.5449	459	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013266735.1	s__Pedobacter foliorum	79.5258	455	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636695.1	s__Pedobacter panaciterrae_A	79.5233	457	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000523515.1	s__Pedobacter sp000523515	79.3943	468	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331695.1	s__Pedobacter sp004331695	79.3942	387	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001721645.1	s__Pedobacter steynii_A	79.1288	387	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100435.1	s__Pedobacter sp900100435	79.1148	370	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003852525.1	s__Pedobacter sp003852525	79.0334	380	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176505.1	s__Pedobacter nyackensis	79.0216	401	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331685.1	s__Pedobacter sp004331685	78.9917	415	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	97.88	97.88	0.86	0.86	2	-
GCF_004362715.1	s__Pedobacter metabolipauper	78.975	402	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223055.1	s__Pedobacter sp015223055	78.907	380	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023825.1	s__Pedobacter heparinus	78.8916	382	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	99.29	98.59	0.94	0.88	3	-
GCF_900564155.1	s__Pedobacter sp900564155	78.8426	380	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103665.1	s__Pedobacter steynii	78.8093	398	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014377665.1	s__Pedobacter sp014377665	78.6544	197	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364225.1	s__Pedobacter sp004364225	78.6258	277	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362245.1	s__Pedobacter duraquae	78.2788	222	1551	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442625.1	s__Pedobacter ginsenosidimutans	77.3457	172	1551	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 15:05:20,688] [INFO] GTDB search result was written to GCF_005116445.1_ASM511644v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:20,688] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:20,697] [INFO] DFAST_QC result json was written to GCF_005116445.1_ASM511644v1_genomic.fna/dqc_result.json
[2024-01-24 15:05:20,697] [INFO] DFAST_QC completed!
[2024-01-24 15:05:20,697] [INFO] Total running time: 0h2m6s