[2024-01-24 15:26:36,845] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:36,847] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:36,847] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdba910e-7d0d-4a70-aeb3-c22c9b2f72bb/dqc_reference
[2024-01-24 15:26:39,059] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:39,061] [INFO] Task started: Prodigal
[2024-01-24 15:26:39,062] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ce85d2a-5894-49a4-9c3b-704fb21f31bb/GCF_004331695.1_ASM433169v1_genomic.fna.gz | prodigal -d GCF_004331695.1_ASM433169v1_genomic.fna/cds.fna -a GCF_004331695.1_ASM433169v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:01,777] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:01,778] [INFO] Task started: HMMsearch
[2024-01-24 15:27:01,778] [INFO] Running command: hmmsearch --tblout GCF_004331695.1_ASM433169v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdba910e-7d0d-4a70-aeb3-c22c9b2f72bb/dqc_reference/reference_markers.hmm GCF_004331695.1_ASM433169v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:02,090] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:02,091] [INFO] Found 6/6 markers.
[2024-01-24 15:27:02,135] [INFO] Query marker FASTA was written to GCF_004331695.1_ASM433169v1_genomic.fna/markers.fasta
[2024-01-24 15:27:02,136] [INFO] Task started: Blastn
[2024-01-24 15:27:02,136] [INFO] Running command: blastn -query GCF_004331695.1_ASM433169v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdba910e-7d0d-4a70-aeb3-c22c9b2f72bb/dqc_reference/reference_markers.fasta -out GCF_004331695.1_ASM433169v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:02,812] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:02,816] [INFO] Selected 18 target genomes.
[2024-01-24 15:27:02,817] [INFO] Target genome list was writen to GCF_004331695.1_ASM433169v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:02,825] [INFO] Task started: fastANI
[2024-01-24 15:27:02,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ce85d2a-5894-49a4-9c3b-704fb21f31bb/GCF_004331695.1_ASM433169v1_genomic.fna.gz --refList GCF_004331695.1_ASM433169v1_genomic.fna/target_genomes.txt --output GCF_004331695.1_ASM433169v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:19,281] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:19,282] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdba910e-7d0d-4a70-aeb3-c22c9b2f72bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:19,282] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdba910e-7d0d-4a70-aeb3-c22c9b2f72bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:19,294] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:19,294] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:19,294] [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 psychroterrae	strain=RP-1-14	GCA_004331695.1	2530453	2530453	type	True	100.0	1695	1695	95	conclusive
Pedobacter frigoris	strain=RP-3-15	GCA_005116445.1	2571272	2571272	type	True	79.3951	390	1695	95	below_threshold
Pedobacter panaciterrae	strain=LMG 23400	GCA_013204795.1	363849	363849	type	True	79.1851	410	1695	95	below_threshold
Pedobacter foliorum	strain=LMG 31463	GCA_013266735.1	2739058	2739058	type	True	79.0619	402	1695	95	below_threshold
Pedobacter hiemivivus	strain=RP-3-8	GCA_004331685.1	2530454	2530454	type	True	78.8625	322	1695	95	below_threshold
Pedobacter metabolipauper	strain=DSM 19035	GCA_004362715.1	425513	425513	type	True	78.8048	371	1695	95	below_threshold
Pedobacter heparinus	strain=DSM 2366	GCA_000410815.1	984	984	type	True	78.7717	359	1695	95	below_threshold
Pedobacter heparinus	strain=DSM 2366	GCA_000023825.1	984	984	type	True	78.7039	367	1695	95	below_threshold
Pedobacter schmidteae	strain=eg	GCA_900564155.1	2201271	2201271	type	True	78.619	325	1695	95	below_threshold
Pedobacter nyackensis	strain=DSM 19625	GCA_900176505.1	475255	475255	type	True	78.5608	353	1695	95	below_threshold
Pedobacter duraquae	strain=DSM 19034	GCA_004362245.1	425511	425511	type	True	78.2004	184	1695	95	below_threshold
Pedobacter endophyticus	strain=JBR3-12	GCA_015679185.1	2789740	2789740	type	True	77.4052	102	1695	95	below_threshold
Pedobacter aquae	strain=CJ43	GCA_008195825.1	2605747	2605747	type	True	76.452	62	1695	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:19,296] [INFO] DFAST Taxonomy check result was written to GCF_004331695.1_ASM433169v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:19,296] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:19,296] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:19,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdba910e-7d0d-4a70-aeb3-c22c9b2f72bb/dqc_reference/checkm_data
[2024-01-24 15:27:19,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:19,352] [INFO] Task started: CheckM
[2024-01-24 15:27:19,353] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004331695.1_ASM433169v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004331695.1_ASM433169v1_genomic.fna/checkm_input GCF_004331695.1_ASM433169v1_genomic.fna/checkm_result
[2024-01-24 15:28:22,057] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:22,059] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:22,081] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:22,081] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:22,082] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004331695.1_ASM433169v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:22,082] [INFO] Task started: Blastn
[2024-01-24 15:28:22,082] [INFO] Running command: blastn -query GCF_004331695.1_ASM433169v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdba910e-7d0d-4a70-aeb3-c22c9b2f72bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_004331695.1_ASM433169v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:22,899] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:22,903] [INFO] Selected 19 target genomes.
[2024-01-24 15:28:22,903] [INFO] Target genome list was writen to GCF_004331695.1_ASM433169v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:22,919] [INFO] Task started: fastANI
[2024-01-24 15:28:22,919] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ce85d2a-5894-49a4-9c3b-704fb21f31bb/GCF_004331695.1_ASM433169v1_genomic.fna.gz --refList GCF_004331695.1_ASM433169v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004331695.1_ASM433169v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:41,305] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:41,323] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:41,323] [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_004331695.1	s__Pedobacter sp004331695	100.0	1695	1695	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_005116445.1	s__Pedobacter sp005116445	79.4078	389	1695	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018492665.1	s__Pedobacter sp018492665	79.1922	394	1695	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013204795.1	s__Pedobacter panaciterrae	79.1734	411	1695	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	79.0822	430	1695	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	79.0689	401	1695	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	79.0605	411	1695	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002736205.1	s__Pedobacter ginsengisoli	79.0106	400	1695	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	78.8625	322	1695	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	78.8048	371	1695	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	78.7154	366	1695	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	99.29	98.59	0.94	0.88	3	-
GCF_900176535.1	s__Pedobacter africanus	78.6519	334	1695	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900564155.1	s__Pedobacter sp900564155	78.6318	324	1695	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	78.5608	353	1695	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	78.5358	326	1695	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	78.2004	184	1695	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	78.0047	257	1695	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015679185.1	s__Pedobacter sp015679185	77.3779	103	1695	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 15:28:41,326] [INFO] GTDB search result was written to GCF_004331695.1_ASM433169v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:41,327] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:41,332] [INFO] DFAST_QC result json was written to GCF_004331695.1_ASM433169v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:41,332] [INFO] DFAST_QC completed!
[2024-01-24 15:28:41,332] [INFO] Total running time: 0h2m4s