[2024-01-24 12:14:09,509] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:09,515] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:09,518] [INFO] DQC Reference Directory: /var/lib/cwl/stgca413759-8b1b-4cb7-93e1-98067c39b7bd/dqc_reference
[2024-01-24 12:14:10,978] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:10,979] [INFO] Task started: Prodigal
[2024-01-24 12:14:10,979] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c6d6085-a072-438f-8b4b-4f3e0acaeeae/GCF_004362715.1_ASM436271v1_genomic.fna.gz | prodigal -d GCF_004362715.1_ASM436271v1_genomic.fna/cds.fna -a GCF_004362715.1_ASM436271v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:33,003] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:33,004] [INFO] Task started: HMMsearch
[2024-01-24 12:14:33,004] [INFO] Running command: hmmsearch --tblout GCF_004362715.1_ASM436271v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca413759-8b1b-4cb7-93e1-98067c39b7bd/dqc_reference/reference_markers.hmm GCF_004362715.1_ASM436271v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:33,428] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:33,429] [INFO] Found 6/6 markers.
[2024-01-24 12:14:33,480] [INFO] Query marker FASTA was written to GCF_004362715.1_ASM436271v1_genomic.fna/markers.fasta
[2024-01-24 12:14:33,481] [INFO] Task started: Blastn
[2024-01-24 12:14:33,481] [INFO] Running command: blastn -query GCF_004362715.1_ASM436271v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca413759-8b1b-4cb7-93e1-98067c39b7bd/dqc_reference/reference_markers.fasta -out GCF_004362715.1_ASM436271v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:34,144] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:34,148] [INFO] Selected 23 target genomes.
[2024-01-24 12:14:34,148] [INFO] Target genome list was writen to GCF_004362715.1_ASM436271v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:34,171] [INFO] Task started: fastANI
[2024-01-24 12:14:34,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c6d6085-a072-438f-8b4b-4f3e0acaeeae/GCF_004362715.1_ASM436271v1_genomic.fna.gz --refList GCF_004362715.1_ASM436271v1_genomic.fna/target_genomes.txt --output GCF_004362715.1_ASM436271v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:59,292] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:59,293] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca413759-8b1b-4cb7-93e1-98067c39b7bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:59,294] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca413759-8b1b-4cb7-93e1-98067c39b7bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:59,314] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:59,314] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:59,315] [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 metabolipauper	strain=DSM 19035	GCA_004362715.1	425513	425513	type	True	100.0	1743	1744	95	conclusive
Pedobacter foliorum	strain=LMG 31463	GCA_013266735.1	2739058	2739058	type	True	78.9868	419	1744	95	below_threshold
Pedobacter hiemivivus	strain=RP-3-8	GCA_004331685.1	2530454	2530454	type	True	78.9575	348	1744	95	below_threshold
Pedobacter panaciterrae	strain=LMG 23400	GCA_013204795.1	363849	363849	type	True	78.912	441	1744	95	below_threshold
Pedobacter psychroterrae	strain=RP-1-14	GCA_004331695.1	2530453	2530453	type	True	78.8634	366	1744	95	below_threshold
Pedobacter frigoris	strain=RP-3-15	GCA_005116445.1	2571272	2571272	type	True	78.858	407	1744	95	below_threshold
Pedobacter nyackensis	strain=DSM 19625	GCA_900176505.1	475255	475255	type	True	78.6747	370	1744	95	below_threshold
Pedobacter steynii	strain=DSM 19110	GCA_900103665.1	430522	430522	type	True	78.6641	414	1744	95	below_threshold
Pedobacter heparinus	strain=DSM 2366	GCA_000410815.1	984	984	type	True	78.6401	364	1744	95	below_threshold
Pedobacter schmidteae	strain=eg	GCA_900564155.1	2201271	2201271	type	True	78.6255	344	1744	95	below_threshold
Pedobacter heparinus	strain=DSM 2366	GCA_000023825.1	984	984	type	True	78.6211	363	1744	95	below_threshold
Pedobacter hartonius	strain=DSM 19033	GCA_900107535.1	425514	425514	type	True	78.6153	271	1744	95	below_threshold
Pedobacter caeni	strain=DSM 16990	GCA_900129215.1	288992	288992	type	True	78.5878	407	1744	95	below_threshold
Pedobacter africanus	strain=DSM 12126	GCA_900176535.1	151894	151894	type	True	78.481	343	1744	95	below_threshold
Pedobacter mucosus	strain=Q8-18	GCA_022200785.1	2895286	2895286	type	True	77.9662	121	1744	95	below_threshold
Pedobacter polaris	strain=RP-3-22	GCA_005116505.1	2571273	2571273	type	True	77.9575	178	1744	95	below_threshold
Mucilaginibacter ginsenosidivorax	strain=KHI28	GCA_007971525.1	862126	862126	type	True	76.5576	71	1744	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	76.0582	69	1744	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:59,317] [INFO] DFAST Taxonomy check result was written to GCF_004362715.1_ASM436271v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:59,317] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:59,318] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:59,318] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca413759-8b1b-4cb7-93e1-98067c39b7bd/dqc_reference/checkm_data
[2024-01-24 12:14:59,319] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:59,367] [INFO] Task started: CheckM
[2024-01-24 12:14:59,368] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004362715.1_ASM436271v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004362715.1_ASM436271v1_genomic.fna/checkm_input GCF_004362715.1_ASM436271v1_genomic.fna/checkm_result
[2024-01-24 12:15:59,781] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:59,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:59,802] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:59,802] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:59,802] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004362715.1_ASM436271v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:59,803] [INFO] Task started: Blastn
[2024-01-24 12:15:59,803] [INFO] Running command: blastn -query GCF_004362715.1_ASM436271v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca413759-8b1b-4cb7-93e1-98067c39b7bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_004362715.1_ASM436271v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:00,635] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:00,642] [INFO] Selected 20 target genomes.
[2024-01-24 12:16:00,642] [INFO] Target genome list was writen to GCF_004362715.1_ASM436271v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:00,660] [INFO] Task started: fastANI
[2024-01-24 12:16:00,661] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c6d6085-a072-438f-8b4b-4f3e0acaeeae/GCF_004362715.1_ASM436271v1_genomic.fna.gz --refList GCF_004362715.1_ASM436271v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004362715.1_ASM436271v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:20,869] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:20,888] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:20,888] [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_004362715.1	s__Pedobacter metabolipauper	100.0	1743	1744	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_000523515.1	s__Pedobacter sp000523515	79.2253	412	1744	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	79.2158	413	1744	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	79.0368	415	1744	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	78.9575	348	1744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	97.88	97.88	0.86	0.86	2	-
GCF_013204795.1	s__Pedobacter panaciterrae	78.9183	439	1744	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	78.858	407	1744	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	78.8455	418	1744	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	78.8053	342	1744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001721645.1	s__Pedobacter steynii_A	78.7666	408	1744	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	78.7165	421	1744	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	78.6979	353	1744	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	78.6738	413	1744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900564155.1	s__Pedobacter sp900564155	78.6309	343	1744	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	78.6211	363	1744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	99.29	98.59	0.94	0.88	3	-
GCF_900107535.1	s__Pedobacter hartonius	78.6153	271	1744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129215.1	s__Pedobacter caeni	78.5878	407	1744	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	78.481	343	1744	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	78.2468	316	1744	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116505.1	s__Pedobacter sp005116505	77.9575	178	1744	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 12:16:20,890] [INFO] GTDB search result was written to GCF_004362715.1_ASM436271v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:20,890] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:20,895] [INFO] DFAST_QC result json was written to GCF_004362715.1_ASM436271v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:20,895] [INFO] DFAST_QC completed!
[2024-01-24 12:16:20,895] [INFO] Total running time: 0h2m11s