[2024-01-24 11:35:22,537] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:22,539] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:22,539] [INFO] DQC Reference Directory: /var/lib/cwl/stg2de527b4-3ea7-4487-8eb7-b12eaac0097c/dqc_reference
[2024-01-24 11:35:26,239] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,240] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,240] [INFO] Running command: gunzip -c /var/lib/cwl/stge35c766f-c93b-48b2-ba96-04b5eabc18bb/GCF_022809115.1_ASM2280911v1_genomic.fna.gz | prodigal -d GCF_022809115.1_ASM2280911v1_genomic.fna/cds.fna -a GCF_022809115.1_ASM2280911v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:37,780] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:37,781] [INFO] Task started: HMMsearch
[2024-01-24 11:35:37,781] [INFO] Running command: hmmsearch --tblout GCF_022809115.1_ASM2280911v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2de527b4-3ea7-4487-8eb7-b12eaac0097c/dqc_reference/reference_markers.hmm GCF_022809115.1_ASM2280911v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:38,119] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:38,121] [INFO] Found 6/6 markers.
[2024-01-24 11:35:38,152] [INFO] Query marker FASTA was written to GCF_022809115.1_ASM2280911v1_genomic.fna/markers.fasta
[2024-01-24 11:35:38,153] [INFO] Task started: Blastn
[2024-01-24 11:35:38,153] [INFO] Running command: blastn -query GCF_022809115.1_ASM2280911v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2de527b4-3ea7-4487-8eb7-b12eaac0097c/dqc_reference/reference_markers.fasta -out GCF_022809115.1_ASM2280911v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:38,791] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:38,795] [INFO] Selected 24 target genomes.
[2024-01-24 11:35:38,796] [INFO] Target genome list was writen to GCF_022809115.1_ASM2280911v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:38,809] [INFO] Task started: fastANI
[2024-01-24 11:35:38,810] [INFO] Running command: fastANI --query /var/lib/cwl/stge35c766f-c93b-48b2-ba96-04b5eabc18bb/GCF_022809115.1_ASM2280911v1_genomic.fna.gz --refList GCF_022809115.1_ASM2280911v1_genomic.fna/target_genomes.txt --output GCF_022809115.1_ASM2280911v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:57,253] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:57,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2de527b4-3ea7-4487-8eb7-b12eaac0097c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:57,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2de527b4-3ea7-4487-8eb7-b12eaac0097c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:57,273] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:57,273] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:57,273] [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 xixiisoli	strain=S27	GCA_005925365.1	1476464	1476464	type	True	78.0361	243	1095	95	below_threshold
Pedobacter xixiisoli	strain=CGMCC 1.12803	GCA_900215335.1	1476464	1476464	type	True	78.0167	241	1095	95	below_threshold
Pedobacter ureilyticus	strain=THG-T11	GCA_005925345.1	1393051	1393051	type	True	77.997	244	1095	95	below_threshold
Pedobacter namyangjuensis	strain=5G38	GCA_003313325.1	600626	600626	type	True	77.9694	208	1095	95	below_threshold
Pedobacter nanyangensis	strain=Q-4	GCA_003313505.1	1562389	1562389	type	True	77.9394	243	1095	95	below_threshold
Pedobacter planticolens	strain=LMG 31464	GCA_014172375.1	2679964	2679964	type	True	77.8046	237	1095	95	below_threshold
Pedobacter cryotolerans	strain=AR-2-6	GCA_005116475.1	2571270	2571270	type	True	77.7532	242	1095	95	below_threshold
Pedobacter insulae	strain=DSM 18684	GCA_900113525.1	414048	414048	type	True	77.7206	152	1095	95	below_threshold
Pedobacter chitinilyticus	strain=CM134L-2	GCA_003313385.1	2233776	2233776	type	True	77.7115	277	1095	95	below_threshold
Pedobacter chitinilyticus	strain=CM134L-2	GCA_004025525.1	2233776	2233776	type	True	77.706	276	1095	95	below_threshold
Pedobacter agri	strain=PB92	GCA_000258495.1	454586	454586	type	True	77.7034	143	1095	95	below_threshold
Pedobacter foliorum	strain=LMG 31463	GCA_013266735.1	2739058	2739058	type	True	77.6054	147	1095	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	77.595	132	1095	95	below_threshold
Pedobacter kyungheensis	strain=KACC 16221	GCA_000812965.1	1069985	1069985	type	True	77.3985	182	1095	95	below_threshold
Pedobacter frigoris	strain=RP-3-15	GCA_005116445.1	2571272	2571272	type	True	77.362	130	1095	95	below_threshold
Pedobacter polaris	strain=RP-3-22	GCA_005116505.1	2571273	2571273	type	True	77.3401	238	1095	95	below_threshold
Pedobacter caeni	strain=DSM 16990	GCA_900129215.1	288992	288992	type	True	77.2171	149	1095	95	below_threshold
Pedobacter mucosus	strain=Q8-18	GCA_022200785.1	2895286	2895286	type	True	77.1238	147	1095	95	below_threshold
Pedobacter rhizosphaerae	strain=DSM 18610	GCA_900111155.1	390241	390241	type	True	76.9855	168	1095	95	below_threshold
Pedobacter yulinensis	strain=YL28-9	GCA_003029735.1	2126353	2126353	type	True	76.8427	62	1095	95	below_threshold
Pedobacter segetis	strain=SD-b	GCA_016623585.1	2793069	2793069	type	True	76.3249	70	1095	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:57,275] [INFO] DFAST Taxonomy check result was written to GCF_022809115.1_ASM2280911v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:57,276] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:57,277] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:57,277] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2de527b4-3ea7-4487-8eb7-b12eaac0097c/dqc_reference/checkm_data
[2024-01-24 11:35:57,279] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:57,318] [INFO] Task started: CheckM
[2024-01-24 11:35:57,318] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022809115.1_ASM2280911v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022809115.1_ASM2280911v1_genomic.fna/checkm_input GCF_022809115.1_ASM2280911v1_genomic.fna/checkm_result
[2024-01-24 11:36:34,471] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:34,473] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:34,492] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:34,493] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:34,493] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022809115.1_ASM2280911v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:34,494] [INFO] Task started: Blastn
[2024-01-24 11:36:34,494] [INFO] Running command: blastn -query GCF_022809115.1_ASM2280911v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2de527b4-3ea7-4487-8eb7-b12eaac0097c/dqc_reference/reference_markers_gtdb.fasta -out GCF_022809115.1_ASM2280911v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:35,418] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:35,422] [INFO] Selected 22 target genomes.
[2024-01-24 11:36:35,423] [INFO] Target genome list was writen to GCF_022809115.1_ASM2280911v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:35,438] [INFO] Task started: fastANI
[2024-01-24 11:36:35,438] [INFO] Running command: fastANI --query /var/lib/cwl/stge35c766f-c93b-48b2-ba96-04b5eabc18bb/GCF_022809115.1_ASM2280911v1_genomic.fna.gz --refList GCF_022809115.1_ASM2280911v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022809115.1_ASM2280911v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:51,861] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:51,883] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:36:51,883] [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
GCA_002336465.1	s__Pedobacter sp002336465	86.7227	649	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005925325.1	s__Pedobacter helvus	78.2523	250	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003313335.1	s__Pedobacter zeaxanthinifaciens	78.2273	201	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215335.1	s__Pedobacter xixiisoli	78.0167	241	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005925345.1	s__Pedobacter ureilyticus	77.997	244	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003313325.1	s__Pedobacter namyangjuensis	77.9694	208	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003313505.1	s__Pedobacter nanyangensis	77.9394	243	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424305.1	s__Pedobacter sp001424305	77.8268	124	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001412215.1	s__Pedobacter sp001412215	77.8185	262	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428855.1	s__Pedobacter sp016428855	77.8179	278	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116475.1	s__Pedobacter sp005116475	77.7532	242	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003313385.1	s__Pedobacter chitinilyticus	77.7115	277	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	97.94	95.89	0.93	0.87	3	-
GCF_013204825.1	s__Pedobacter boryungensis	77.7093	237	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000258495.1	s__Pedobacter agri	77.7034	143	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	97.48	97.42	0.86	0.85	3	-
GCF_018492665.1	s__Pedobacter sp018492665	77.6739	152	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016429155.1	s__Pedobacter sp016429155	77.6432	177	1095	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	77.6013	148	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000812965.1	s__Pedobacter kyungheensis	77.3985	182	1095	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	77.362	130	1095	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	77.3175	240	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994015.1	s__Pedobacter terrae_A	77.2452	187	1095	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111155.1	s__Pedobacter rhizosphaerae	76.9855	168	1095	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 11:36:51,885] [INFO] GTDB search result was written to GCF_022809115.1_ASM2280911v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:51,885] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:51,889] [INFO] DFAST_QC result json was written to GCF_022809115.1_ASM2280911v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:51,890] [INFO] DFAST_QC completed!
[2024-01-24 11:36:51,890] [INFO] Total running time: 0h1m29s