[2024-01-25 19:11:51,011] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:51,013] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:51,013] [INFO] DQC Reference Directory: /var/lib/cwl/stg848ce7e2-030a-45be-a19d-7763693f8347/dqc_reference
[2024-01-25 19:11:52,186] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:52,187] [INFO] Task started: Prodigal
[2024-01-25 19:11:52,187] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5f5ba08-d646-4fa6-967d-9a4f38fe6130/GCF_003419895.1_ASM341989v1_genomic.fna.gz | prodigal -d GCF_003419895.1_ASM341989v1_genomic.fna/cds.fna -a GCF_003419895.1_ASM341989v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:12:14,130] [INFO] Task succeeded: Prodigal
[2024-01-25 19:12:14,131] [INFO] Task started: HMMsearch
[2024-01-25 19:12:14,131] [INFO] Running command: hmmsearch --tblout GCF_003419895.1_ASM341989v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg848ce7e2-030a-45be-a19d-7763693f8347/dqc_reference/reference_markers.hmm GCF_003419895.1_ASM341989v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:12:14,422] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:12:14,423] [INFO] Found 6/6 markers.
[2024-01-25 19:12:14,472] [INFO] Query marker FASTA was written to GCF_003419895.1_ASM341989v1_genomic.fna/markers.fasta
[2024-01-25 19:12:14,473] [INFO] Task started: Blastn
[2024-01-25 19:12:14,473] [INFO] Running command: blastn -query GCF_003419895.1_ASM341989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg848ce7e2-030a-45be-a19d-7763693f8347/dqc_reference/reference_markers.fasta -out GCF_003419895.1_ASM341989v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:15,017] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:15,020] [INFO] Selected 13 target genomes.
[2024-01-25 19:12:15,020] [INFO] Target genome list was writen to GCF_003419895.1_ASM341989v1_genomic.fna/target_genomes.txt
[2024-01-25 19:12:15,032] [INFO] Task started: fastANI
[2024-01-25 19:12:15,032] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5f5ba08-d646-4fa6-967d-9a4f38fe6130/GCF_003419895.1_ASM341989v1_genomic.fna.gz --refList GCF_003419895.1_ASM341989v1_genomic.fna/target_genomes.txt --output GCF_003419895.1_ASM341989v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:12:34,713] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:34,713] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg848ce7e2-030a-45be-a19d-7763693f8347/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:12:34,714] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg848ce7e2-030a-45be-a19d-7763693f8347/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:12:34,722] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:12:34,722] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:12:34,722] [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
Chitinophaga silvatica	strain=GDMCC 1.1288	GCA_003419895.1	2282649	2282649	type	True	100.0	2256	2257	95	conclusive
Chitinophaga terrae (ex Kim and Jung 2007)	strain=DSM 23920	GCA_900107795.1	408074	408074	type	True	80.6038	914	2257	95	below_threshold
Chitinophaga ginsengisegetis	strain=DSM 18108	GCA_900168065.1	393003	393003	type	True	79.3217	630	2257	95	below_threshold
Chitinophaga arvensicola	strain=DSM 3695	GCA_900110835.1	29529	29529	type	True	79.2341	658	2257	95	below_threshold
Chitinophaga hostae	strain=2R12	GCA_018224885.1	2831022	2831022	type	True	79.2239	642	2257	95	below_threshold
Chitinophaga niastensis	strain=DSM 24859	GCA_003014755.1	536980	536980	type	True	78.9961	583	2257	95	below_threshold
Chitinophaga dinghuensis	strain=DSM 29821	GCA_003259435.1	1539050	1539050	type	True	78.7971	461	2257	95	below_threshold
Chitinophaga flava	strain=GDMCC 1.1325	GCA_003308995.1	2259036	2259036	type	True	78.5972	476	2257	95	below_threshold
Chitinophaga eiseniae	strain=DSM 22224	GCA_900167135.1	634771	634771	type	True	78.4643	393	2257	95	below_threshold
Chitinophaga qingshengii	strain=JCM 30026	GCA_014529935.1	1569794	1569794	type	True	78.2596	474	2257	95	below_threshold
Chitinophaga tropicalis	strain=ysch24	GCA_009758205.1	2683588	2683588	type	True	77.2434	224	2257	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:12:34,723] [INFO] DFAST Taxonomy check result was written to GCF_003419895.1_ASM341989v1_genomic.fna/tc_result.tsv
[2024-01-25 19:12:34,726] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:12:34,726] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:12:34,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg848ce7e2-030a-45be-a19d-7763693f8347/dqc_reference/checkm_data
[2024-01-25 19:12:34,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:12:34,793] [INFO] Task started: CheckM
[2024-01-25 19:12:34,793] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003419895.1_ASM341989v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003419895.1_ASM341989v1_genomic.fna/checkm_input GCF_003419895.1_ASM341989v1_genomic.fna/checkm_result
[2024-01-25 19:13:35,755] [INFO] Task succeeded: CheckM
[2024-01-25 19:13:35,756] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:13:35,784] [INFO] ===== Completeness check finished =====
[2024-01-25 19:13:35,784] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:13:35,785] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003419895.1_ASM341989v1_genomic.fna/markers.fasta)
[2024-01-25 19:13:35,786] [INFO] Task started: Blastn
[2024-01-25 19:13:35,786] [INFO] Running command: blastn -query GCF_003419895.1_ASM341989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg848ce7e2-030a-45be-a19d-7763693f8347/dqc_reference/reference_markers_gtdb.fasta -out GCF_003419895.1_ASM341989v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:13:36,592] [INFO] Task succeeded: Blastn
[2024-01-25 19:13:36,595] [INFO] Selected 16 target genomes.
[2024-01-25 19:13:36,595] [INFO] Target genome list was writen to GCF_003419895.1_ASM341989v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:13:36,610] [INFO] Task started: fastANI
[2024-01-25 19:13:36,610] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5f5ba08-d646-4fa6-967d-9a4f38fe6130/GCF_003419895.1_ASM341989v1_genomic.fna.gz --refList GCF_003419895.1_ASM341989v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003419895.1_ASM341989v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:13:58,857] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:58,867] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:13:58,867] [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_003419895.1	s__Chitinophaga sp003419895	100.0	2256	2257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900107795.1	s__Chitinophaga terrae	80.6104	913	2257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	99.99	99.99	1.00	1.00	2	-
GCF_012726295.1	s__Chitinophaga sp012726295	79.4045	577	2257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	99.43	99.43	0.94	0.94	2	-
GCF_900168065.1	s__Chitinophaga ginsengisegetis	79.3292	629	2257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	98.27	98.27	0.94	0.94	3	-
GCF_007829335.1	s__Chitinophaga polysaccharea_B	79.2925	590	2257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110835.1	s__Chitinophaga arvensicola	79.2376	657	2257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641265.1	s__Chitinophaga eiseniae_A	79.2027	616	2257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902150045.1	s__Chitinophaga polysaccharea_A	79.1595	566	2257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	96.96	96.96	0.91	0.91	2	-
GCA_017745275.1	s__Chitinophaga sp017745275	79.1096	646	2257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014755.1	s__Chitinophaga niastensis	79.0076	582	2257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259435.1	s__Chitinophaga dinghuensis	78.7971	461	2257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018255755.1	s__Chitinophaga sp018255755	78.6407	451	2257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003308995.1	s__Chitinophaga flava	78.6212	474	2257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167135.1	s__Chitinophaga eiseniae	78.4532	392	2257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009758205.1	s__Chitinophaga sp009758205	77.273	220	2257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:13:58,869] [INFO] GTDB search result was written to GCF_003419895.1_ASM341989v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:13:58,870] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:13:58,872] [INFO] DFAST_QC result json was written to GCF_003419895.1_ASM341989v1_genomic.fna/dqc_result.json
[2024-01-25 19:13:58,872] [INFO] DFAST_QC completed!
[2024-01-25 19:13:58,873] [INFO] Total running time: 0h2m8s