[2024-01-25 18:33:20,621] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:33:20,622] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:33:20,623] [INFO] DQC Reference Directory: /var/lib/cwl/stg11a17e85-404c-4c67-98f3-a69a38a21661/dqc_reference
[2024-01-25 18:33:21,885] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:33:21,886] [INFO] Task started: Prodigal
[2024-01-25 18:33:21,886] [INFO] Running command: gunzip -c /var/lib/cwl/stg05e3ccce-6b6a-4b1c-be13-3b3ef08b8274/GCF_030244015.1_ASM3024401v1_genomic.fna.gz | prodigal -d GCF_030244015.1_ASM3024401v1_genomic.fna/cds.fna -a GCF_030244015.1_ASM3024401v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:33:40,108] [INFO] Task succeeded: Prodigal
[2024-01-25 18:33:40,109] [INFO] Task started: HMMsearch
[2024-01-25 18:33:40,109] [INFO] Running command: hmmsearch --tblout GCF_030244015.1_ASM3024401v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11a17e85-404c-4c67-98f3-a69a38a21661/dqc_reference/reference_markers.hmm GCF_030244015.1_ASM3024401v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:33:40,387] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:33:40,389] [INFO] Found 6/6 markers.
[2024-01-25 18:33:40,429] [INFO] Query marker FASTA was written to GCF_030244015.1_ASM3024401v1_genomic.fna/markers.fasta
[2024-01-25 18:33:40,430] [INFO] Task started: Blastn
[2024-01-25 18:33:40,430] [INFO] Running command: blastn -query GCF_030244015.1_ASM3024401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11a17e85-404c-4c67-98f3-a69a38a21661/dqc_reference/reference_markers.fasta -out GCF_030244015.1_ASM3024401v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:33:40,996] [INFO] Task succeeded: Blastn
[2024-01-25 18:33:40,999] [INFO] Selected 20 target genomes.
[2024-01-25 18:33:40,999] [INFO] Target genome list was writen to GCF_030244015.1_ASM3024401v1_genomic.fna/target_genomes.txt
[2024-01-25 18:33:41,028] [INFO] Task started: fastANI
[2024-01-25 18:33:41,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg05e3ccce-6b6a-4b1c-be13-3b3ef08b8274/GCF_030244015.1_ASM3024401v1_genomic.fna.gz --refList GCF_030244015.1_ASM3024401v1_genomic.fna/target_genomes.txt --output GCF_030244015.1_ASM3024401v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:33:58,947] [INFO] Task succeeded: fastANI
[2024-01-25 18:33:58,947] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11a17e85-404c-4c67-98f3-a69a38a21661/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:33:58,948] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11a17e85-404c-4c67-98f3-a69a38a21661/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:33:58,957] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:33:58,957] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:33:58,957] [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	78.8811	422	1607	95	below_threshold
Pedobacter frigoris	strain=RP-3-15	GCA_005116445.1	2571272	2571272	type	True	78.7211	390	1607	95	below_threshold
Pedobacter nyackensis	strain=DSM 19625	GCA_900176505.1	475255	475255	type	True	78.5946	283	1607	95	below_threshold
Pedobacter panaciterrae	strain=LMG 23400	GCA_013204795.1	363849	363849	type	True	78.5933	430	1607	95	below_threshold
Pedobacter foliorum	strain=LMG 31463	GCA_013266735.1	2739058	2739058	type	True	78.5546	382	1607	95	below_threshold
Pedobacter schmidteae	strain=eg	GCA_900564155.1	2201271	2201271	type	True	78.5017	314	1607	95	below_threshold
Pedobacter hiemivivus	strain=RP-3-8	GCA_004331685.1	2530454	2530454	type	True	78.4203	307	1607	95	below_threshold
Pedobacter steynii	strain=DSM 19110	GCA_900103665.1	430522	430522	type	True	78.3051	321	1607	95	below_threshold
Pedobacter africanus	strain=DSM 12126	GCA_900176535.1	151894	151894	type	True	78.305	360	1607	95	below_threshold
Pedobacter lusitanus	strain=NL19	GCA_000832545.1	1503925	1503925	type	True	78.1044	184	1607	95	below_threshold
Pedobacter gandavensis	strain=LMG 31462	GCA_014172405.1	2679963	2679963	type	True	78.1003	238	1607	95	below_threshold
Pedobacter caeni	strain=DSM 16990	GCA_900129215.1	288992	288992	type	True	78.0491	321	1607	95	below_threshold
Pedobacter hartonius	strain=DSM 19033	GCA_900107535.1	425514	425514	type	True	77.9502	209	1607	95	below_threshold
Pedobacter cryoconitis	strain=DSM 14825	GCA_003259615.1	188932	188932	suspected-type	True	77.6923	203	1607	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:33:58,960] [INFO] DFAST Taxonomy check result was written to GCF_030244015.1_ASM3024401v1_genomic.fna/tc_result.tsv
[2024-01-25 18:33:58,961] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:33:58,961] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:33:58,962] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11a17e85-404c-4c67-98f3-a69a38a21661/dqc_reference/checkm_data
[2024-01-25 18:33:58,962] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:33:59,007] [INFO] Task started: CheckM
[2024-01-25 18:33:59,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030244015.1_ASM3024401v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030244015.1_ASM3024401v1_genomic.fna/checkm_input GCF_030244015.1_ASM3024401v1_genomic.fna/checkm_result
[2024-01-25 18:34:51,822] [INFO] Task succeeded: CheckM
[2024-01-25 18:34:51,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 18:34:51,846] [INFO] ===== Completeness check finished =====
[2024-01-25 18:34:51,847] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:34:51,848] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030244015.1_ASM3024401v1_genomic.fna/markers.fasta)
[2024-01-25 18:34:51,848] [INFO] Task started: Blastn
[2024-01-25 18:34:51,848] [INFO] Running command: blastn -query GCF_030244015.1_ASM3024401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11a17e85-404c-4c67-98f3-a69a38a21661/dqc_reference/reference_markers_gtdb.fasta -out GCF_030244015.1_ASM3024401v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:34:52,767] [INFO] Task succeeded: Blastn
[2024-01-25 18:34:52,770] [INFO] Selected 19 target genomes.
[2024-01-25 18:34:52,771] [INFO] Target genome list was writen to GCF_030244015.1_ASM3024401v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:34:52,828] [INFO] Task started: fastANI
[2024-01-25 18:34:52,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg05e3ccce-6b6a-4b1c-be13-3b3ef08b8274/GCF_030244015.1_ASM3024401v1_genomic.fna.gz --refList GCF_030244015.1_ASM3024401v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030244015.1_ASM3024401v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:35:12,731] [INFO] Task succeeded: fastANI
[2024-01-25 18:35:12,743] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:35:12,743] [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	78.8706	423	1607	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	78.759	389	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116445.1	s__Pedobacter sp005116445	78.7211	390	1607	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	78.6217	409	1607	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	78.6129	379	1607	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	78.6027	429	1607	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	78.5546	382	1607	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	78.536	384	1607	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	78.5017	314	1607	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	78.4932	297	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015223055.1	s__Pedobacter sp015223055	78.3908	308	1607	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	78.352	331	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176535.1	s__Pedobacter africanus	78.3157	359	1607	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	78.3051	321	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003208655.1	s__Pedobacter nutrimenti	78.283	234	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000832545.1	s__Pedobacter lusitanus	78.1044	184	1607	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	77.9506	280	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200605.1	s__Pedobacter cryoconitis_B	77.8625	194	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.88	98.88	0.94	0.94	2	-
GCF_003061025.1	s__Pedobacter sp003061025	77.7749	219	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:35:12,744] [INFO] GTDB search result was written to GCF_030244015.1_ASM3024401v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:35:12,745] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:35:12,748] [INFO] DFAST_QC result json was written to GCF_030244015.1_ASM3024401v1_genomic.fna/dqc_result.json
[2024-01-25 18:35:12,748] [INFO] DFAST_QC completed!
[2024-01-25 18:35:12,749] [INFO] Total running time: 0h1m52s