[2024-01-24 13:33:10,078] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:33:10,080] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:33:10,080] [INFO] DQC Reference Directory: /var/lib/cwl/stg948b1414-6bc6-47a8-94c5-e61761576394/dqc_reference
[2024-01-24 13:33:11,235] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:33:11,235] [INFO] Task started: Prodigal
[2024-01-24 13:33:11,236] [INFO] Running command: gunzip -c /var/lib/cwl/stg43064711-7d9b-486d-8f50-211c73bc81b4/GCF_003412465.1_ASM341246v1_genomic.fna.gz | prodigal -d GCF_003412465.1_ASM341246v1_genomic.fna/cds.fna -a GCF_003412465.1_ASM341246v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:52,276] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:52,277] [INFO] Task started: HMMsearch
[2024-01-24 13:33:52,277] [INFO] Running command: hmmsearch --tblout GCF_003412465.1_ASM341246v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg948b1414-6bc6-47a8-94c5-e61761576394/dqc_reference/reference_markers.hmm GCF_003412465.1_ASM341246v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:52,658] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:52,660] [INFO] Found 6/6 markers.
[2024-01-24 13:33:52,726] [INFO] Query marker FASTA was written to GCF_003412465.1_ASM341246v1_genomic.fna/markers.fasta
[2024-01-24 13:33:52,726] [INFO] Task started: Blastn
[2024-01-24 13:33:52,726] [INFO] Running command: blastn -query GCF_003412465.1_ASM341246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg948b1414-6bc6-47a8-94c5-e61761576394/dqc_reference/reference_markers.fasta -out GCF_003412465.1_ASM341246v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:53,304] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:53,307] [INFO] Selected 15 target genomes.
[2024-01-24 13:33:53,307] [INFO] Target genome list was writen to GCF_003412465.1_ASM341246v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:53,313] [INFO] Task started: fastANI
[2024-01-24 13:33:53,313] [INFO] Running command: fastANI --query /var/lib/cwl/stg43064711-7d9b-486d-8f50-211c73bc81b4/GCF_003412465.1_ASM341246v1_genomic.fna.gz --refList GCF_003412465.1_ASM341246v1_genomic.fna/target_genomes.txt --output GCF_003412465.1_ASM341246v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:34:14,503] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:14,504] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg948b1414-6bc6-47a8-94c5-e61761576394/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:34:14,505] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg948b1414-6bc6-47a8-94c5-e61761576394/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:34:14,524] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:34:14,525] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:34:14,525] [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 silvisoli	strain=K20C18050901	GCA_003412465.1	2291814	2291814	type	True	100.0	2748	2753	95	conclusive
Chitinophaga sancti	strain=DSM 784	GCA_900119105.1	1004	1004	type	True	86.7588	1998	2753	95	below_threshold
Chitinophaga ginsengisoli	strain=DSM 18107	GCA_003014595.1	363837	363837	type	True	79.0245	644	2753	95	below_threshold
Chitinophaga filiformis	strain=DSM 527	GCA_900102545.1	104663	104663	type	True	78.9242	619	2753	95	below_threshold
Chitinophaga rhizophila	strain=B61	GCA_019492185.1	2866212	2866212	type	True	78.8613	516	2753	95	below_threshold
Chitinophaga pinensis	strain=DSM 2588	GCA_000024005.1	79329	79329	type	True	78.801	676	2753	95	below_threshold
Chitinophaga tropicalis	strain=ysch24	GCA_009758205.1	2683588	2683588	type	True	78.6033	639	2753	95	below_threshold
Chitinophaga oryziterrae	strain=JCM 16595	GCA_009758125.1	1031224	1031224	type	True	78.4676	624	2753	95	below_threshold
Chitinophaga hostae	strain=2R12	GCA_018224885.1	2831022	2831022	type	True	77.6354	281	2753	95	below_threshold
Chitinophaga dinghuensis	strain=DSM 29821	GCA_003259435.1	1539050	1539050	type	True	77.5964	275	2753	95	below_threshold
Chitinophaga solisilvae	strain=O9	GCA_009928525.1	1233460	1233460	type	True	77.4597	272	2753	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:34:14,527] [INFO] DFAST Taxonomy check result was written to GCF_003412465.1_ASM341246v1_genomic.fna/tc_result.tsv
[2024-01-24 13:34:14,528] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:34:14,528] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:34:14,528] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg948b1414-6bc6-47a8-94c5-e61761576394/dqc_reference/checkm_data
[2024-01-24 13:34:14,529] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:34:14,602] [INFO] Task started: CheckM
[2024-01-24 13:34:14,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003412465.1_ASM341246v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003412465.1_ASM341246v1_genomic.fna/checkm_input GCF_003412465.1_ASM341246v1_genomic.fna/checkm_result
[2024-01-24 13:36:05,922] [INFO] Task succeeded: CheckM
[2024-01-24 13:36:05,924] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:36:05,946] [INFO] ===== Completeness check finished =====
[2024-01-24 13:36:05,946] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:36:05,946] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003412465.1_ASM341246v1_genomic.fna/markers.fasta)
[2024-01-24 13:36:05,947] [INFO] Task started: Blastn
[2024-01-24 13:36:05,947] [INFO] Running command: blastn -query GCF_003412465.1_ASM341246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg948b1414-6bc6-47a8-94c5-e61761576394/dqc_reference/reference_markers_gtdb.fasta -out GCF_003412465.1_ASM341246v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:06,714] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:06,718] [INFO] Selected 5 target genomes.
[2024-01-24 13:36:06,718] [INFO] Target genome list was writen to GCF_003412465.1_ASM341246v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:36:06,739] [INFO] Task started: fastANI
[2024-01-24 13:36:06,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg43064711-7d9b-486d-8f50-211c73bc81b4/GCF_003412465.1_ASM341246v1_genomic.fna.gz --refList GCF_003412465.1_ASM341246v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003412465.1_ASM341246v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:36:17,171] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:17,179] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:36:17,179] [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_003412465.1	s__Chitinophaga silvisoli	100.0	2748	2753	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_014190745.1	s__Chitinophaga sancti_A	87.114	2133	2753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	99.26	99.26	0.97	0.97	2	-
GCF_900119105.1	s__Chitinophaga sancti	86.7698	1997	2753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994035.1	s__Chitinophaga pinensis_B	86.0088	2073	2753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975825.1	s__Chitinophaga sp001975825	85.6927	1936	2753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	98.88	98.88	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:36:17,181] [INFO] GTDB search result was written to GCF_003412465.1_ASM341246v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:36:17,181] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:36:17,184] [INFO] DFAST_QC result json was written to GCF_003412465.1_ASM341246v1_genomic.fna/dqc_result.json
[2024-01-24 13:36:17,184] [INFO] DFAST_QC completed!
[2024-01-24 13:36:17,184] [INFO] Total running time: 0h3m7s