[2024-01-24 15:32:05,624] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:32:05,627] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:32:05,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ea2054d-f889-46e7-82d0-ac75a0719af0/dqc_reference
[2024-01-24 15:32:06,862] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:32:06,863] [INFO] Task started: Prodigal
[2024-01-24 15:32:06,864] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b36bf24-33bb-4a9b-b848-dd53b524ce19/GCF_004331685.1_ASM433168v1_genomic.fna.gz | prodigal -d GCF_004331685.1_ASM433168v1_genomic.fna/cds.fna -a GCF_004331685.1_ASM433168v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:32:32,567] [INFO] Task succeeded: Prodigal
[2024-01-24 15:32:32,567] [INFO] Task started: HMMsearch
[2024-01-24 15:32:32,567] [INFO] Running command: hmmsearch --tblout GCF_004331685.1_ASM433168v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ea2054d-f889-46e7-82d0-ac75a0719af0/dqc_reference/reference_markers.hmm GCF_004331685.1_ASM433168v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:32:32,905] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:32:32,907] [INFO] Found 6/6 markers.
[2024-01-24 15:32:32,968] [INFO] Query marker FASTA was written to GCF_004331685.1_ASM433168v1_genomic.fna/markers.fasta
[2024-01-24 15:32:32,969] [INFO] Task started: Blastn
[2024-01-24 15:32:32,969] [INFO] Running command: blastn -query GCF_004331685.1_ASM433168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ea2054d-f889-46e7-82d0-ac75a0719af0/dqc_reference/reference_markers.fasta -out GCF_004331685.1_ASM433168v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:32:33,599] [INFO] Task succeeded: Blastn
[2024-01-24 15:32:33,603] [INFO] Selected 15 target genomes.
[2024-01-24 15:32:33,604] [INFO] Target genome list was writen to GCF_004331685.1_ASM433168v1_genomic.fna/target_genomes.txt
[2024-01-24 15:32:33,630] [INFO] Task started: fastANI
[2024-01-24 15:32:33,631] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b36bf24-33bb-4a9b-b848-dd53b524ce19/GCF_004331685.1_ASM433168v1_genomic.fna.gz --refList GCF_004331685.1_ASM433168v1_genomic.fna/target_genomes.txt --output GCF_004331685.1_ASM433168v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:32:48,712] [INFO] Task succeeded: fastANI
[2024-01-24 15:32:48,713] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ea2054d-f889-46e7-82d0-ac75a0719af0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:32:48,713] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ea2054d-f889-46e7-82d0-ac75a0719af0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:32:48,735] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:32:48,735] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:32:48,735] [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 hiemivivus	strain=RP-3-8	GCA_004331685.1	2530454	2530454	type	True	100.0	2158	2161	95	conclusive
Pedobacter nyackensis	strain=DSM 19625	GCA_900176505.1	475255	475255	type	True	82.4996	975	2161	95	below_threshold
Pedobacter schmidteae	strain=eg	GCA_900564155.1	2201271	2201271	type	True	80.3779	780	2161	95	below_threshold
Pedobacter heparinus	strain=DSM 2366	GCA_000410815.1	984	984	type	True	79.9645	641	2161	95	below_threshold
Pedobacter heparinus	strain=DSM 2366	GCA_000023825.1	984	984	type	True	79.9411	649	2161	95	below_threshold
Pedobacter foliorum	strain=LMG 31463	GCA_013266735.1	2739058	2739058	type	True	79.4193	491	2161	95	below_threshold
Pedobacter panaciterrae	strain=LMG 23400	GCA_013204795.1	363849	363849	type	True	79.3785	457	2161	95	below_threshold
Pedobacter steynii	strain=DSM 19110	GCA_900103665.1	430522	430522	type	True	79.3543	493	2161	95	below_threshold
Pedobacter frigoris	strain=RP-3-15	GCA_005116445.1	2571272	2571272	type	True	79.1021	403	2161	95	below_threshold
Pedobacter gandavensis	strain=LMG 31462	GCA_014172405.1	2679963	2679963	type	True	79.0452	417	2161	95	below_threshold
Pedobacter mucosus	strain=Q8-18	GCA_022200785.1	2895286	2895286	type	True	77.5637	177	2161	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	77.5292	199	2161	95	below_threshold
Mucilaginibacter robiniae	strain=F39-2	GCA_012849215.1	2728022	2728022	type	True	76.8032	63	2161	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	76.7135	66	2161	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	76.6223	67	2161	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:32:48,737] [INFO] DFAST Taxonomy check result was written to GCF_004331685.1_ASM433168v1_genomic.fna/tc_result.tsv
[2024-01-24 15:32:48,737] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:32:48,738] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:32:48,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ea2054d-f889-46e7-82d0-ac75a0719af0/dqc_reference/checkm_data
[2024-01-24 15:32:48,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:32:48,805] [INFO] Task started: CheckM
[2024-01-24 15:32:48,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004331685.1_ASM433168v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004331685.1_ASM433168v1_genomic.fna/checkm_input GCF_004331685.1_ASM433168v1_genomic.fna/checkm_result
[2024-01-24 15:33:59,578] [INFO] Task succeeded: CheckM
[2024-01-24 15:33:59,580] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:33:59,605] [INFO] ===== Completeness check finished =====
[2024-01-24 15:33:59,605] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:33:59,606] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004331685.1_ASM433168v1_genomic.fna/markers.fasta)
[2024-01-24 15:33:59,606] [INFO] Task started: Blastn
[2024-01-24 15:33:59,606] [INFO] Running command: blastn -query GCF_004331685.1_ASM433168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ea2054d-f889-46e7-82d0-ac75a0719af0/dqc_reference/reference_markers_gtdb.fasta -out GCF_004331685.1_ASM433168v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:34:00,404] [INFO] Task succeeded: Blastn
[2024-01-24 15:34:00,407] [INFO] Selected 12 target genomes.
[2024-01-24 15:34:00,407] [INFO] Target genome list was writen to GCF_004331685.1_ASM433168v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:34:00,442] [INFO] Task started: fastANI
[2024-01-24 15:34:00,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b36bf24-33bb-4a9b-b848-dd53b524ce19/GCF_004331685.1_ASM433168v1_genomic.fna.gz --refList GCF_004331685.1_ASM433168v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004331685.1_ASM433168v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:34:14,607] [INFO] Task succeeded: fastANI
[2024-01-24 15:34:14,628] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:34:14,628] [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_004331685.1	s__Pedobacter sp004331685	100.0	2158	2161	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	97.88	97.88	0.86	0.86	2	conclusive
GCF_900100435.1	s__Pedobacter sp900100435	88.5444	1418	2161	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900176505.1	s__Pedobacter nyackensis	82.5051	974	2161	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	80.3822	779	2161	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	79.966	648	2161	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	99.29	98.59	0.94	0.88	3	-
GCF_015223055.1	s__Pedobacter sp015223055	79.6639	551	2161	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	79.4838	479	2161	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	79.4059	493	2161	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	79.349	496	2161	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003852525.1	s__Pedobacter sp003852525	79.1829	453	2161	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	79.1611	471	2161	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	78.9884	451	2161	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 15:34:14,630] [INFO] GTDB search result was written to GCF_004331685.1_ASM433168v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:34:14,631] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:34:14,637] [INFO] DFAST_QC result json was written to GCF_004331685.1_ASM433168v1_genomic.fna/dqc_result.json
[2024-01-24 15:34:14,637] [INFO] DFAST_QC completed!
[2024-01-24 15:34:14,637] [INFO] Total running time: 0h2m9s