[2024-01-25 17:39:35,584] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:39:35,586] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:39:35,586] [INFO] DQC Reference Directory: /var/lib/cwl/stga7eb8820-3aa6-48a5-b137-b90298c9f78d/dqc_reference
[2024-01-25 17:39:36,717] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:39:36,718] [INFO] Task started: Prodigal
[2024-01-25 17:39:36,718] [INFO] Running command: gunzip -c /var/lib/cwl/stg69b6cf55-905c-4d10-a50e-ec350d6be872/GCF_003807585.1_ASM380758v1_genomic.fna.gz | prodigal -d GCF_003807585.1_ASM380758v1_genomic.fna/cds.fna -a GCF_003807585.1_ASM380758v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:10,947] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:10,947] [INFO] Task started: HMMsearch
[2024-01-25 17:40:10,947] [INFO] Running command: hmmsearch --tblout GCF_003807585.1_ASM380758v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7eb8820-3aa6-48a5-b137-b90298c9f78d/dqc_reference/reference_markers.hmm GCF_003807585.1_ASM380758v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:11,225] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:11,226] [INFO] Found 6/6 markers.
[2024-01-25 17:40:11,277] [INFO] Query marker FASTA was written to GCF_003807585.1_ASM380758v1_genomic.fna/markers.fasta
[2024-01-25 17:40:11,278] [INFO] Task started: Blastn
[2024-01-25 17:40:11,278] [INFO] Running command: blastn -query GCF_003807585.1_ASM380758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7eb8820-3aa6-48a5-b137-b90298c9f78d/dqc_reference/reference_markers.fasta -out GCF_003807585.1_ASM380758v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:11,836] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:11,838] [INFO] Selected 15 target genomes.
[2024-01-25 17:40:11,839] [INFO] Target genome list was writen to GCF_003807585.1_ASM380758v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:11,853] [INFO] Task started: fastANI
[2024-01-25 17:40:11,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg69b6cf55-905c-4d10-a50e-ec350d6be872/GCF_003807585.1_ASM380758v1_genomic.fna.gz --refList GCF_003807585.1_ASM380758v1_genomic.fna/target_genomes.txt --output GCF_003807585.1_ASM380758v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:30,035] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:30,035] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7eb8820-3aa6-48a5-b137-b90298c9f78d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:30,035] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7eb8820-3aa6-48a5-b137-b90298c9f78d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:30,043] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:40:30,043] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:40:30,043] [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 barathri	strain=YLT18	GCA_003807585.1	1647451	1647451	type	True	100.0	2268	2270	95	conclusive
Chitinophaga barathri	strain=YLT18	GCA_003614855.1	1647451	1647451	type	True	99.9997	2267	2270	95	conclusive
Chitinophaga chungangae	strain=MAH-28	GCA_017742215.1	2821488	2821488	type	True	84.566	1516	2270	95	below_threshold
Chitinophaga lutea	strain=ZY74	GCA_003813775.1	2488634	2488634	type	True	80.0843	940	2270	95	below_threshold
Chitinophaga alhagiae	strain=T22	GCA_003177275.1	2203219	2203219	suspected-type	True	80.0564	448	2270	95	below_threshold
Chitinophaga alhagiae	strain=T22	GCA_003568665.1	2203219	2203219	suspected-type	True	79.7834	874	2270	95	below_threshold
Chitinophaga rhizosphaerae	strain=T16R-86	GCA_003958645.1	1864947	1864947	type	True	79.1421	762	2270	95	below_threshold
Chitinophaga deserti	strain=XJ-2	GCA_003149455.1	2164099	2164099	type	True	78.8785	689	2270	95	below_threshold
Chitinophaga fulva	strain=G-6-1-13	GCA_012927205.1	2728842	2728842	type	True	77.1791	333	2270	95	below_threshold
Chitinophaga filiformis	strain=DSM 527	GCA_900102545.1	104663	104663	type	True	76.8009	240	2270	95	below_threshold
Chitinophaga rhizophila	strain=B61	GCA_019492185.1	2866212	2866212	type	True	76.7501	148	2270	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:30,044] [INFO] DFAST Taxonomy check result was written to GCF_003807585.1_ASM380758v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:30,045] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:30,045] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:30,045] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7eb8820-3aa6-48a5-b137-b90298c9f78d/dqc_reference/checkm_data
[2024-01-25 17:40:30,046] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:30,108] [INFO] Task started: CheckM
[2024-01-25 17:40:30,109] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003807585.1_ASM380758v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003807585.1_ASM380758v1_genomic.fna/checkm_input GCF_003807585.1_ASM380758v1_genomic.fna/checkm_result
[2024-01-25 17:41:57,696] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:57,698] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:57,730] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:57,730] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:57,731] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003807585.1_ASM380758v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:57,731] [INFO] Task started: Blastn
[2024-01-25 17:41:57,731] [INFO] Running command: blastn -query GCF_003807585.1_ASM380758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7eb8820-3aa6-48a5-b137-b90298c9f78d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003807585.1_ASM380758v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:58,605] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:58,608] [INFO] Selected 10 target genomes.
[2024-01-25 17:41:58,608] [INFO] Target genome list was writen to GCF_003807585.1_ASM380758v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:58,621] [INFO] Task started: fastANI
[2024-01-25 17:41:58,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg69b6cf55-905c-4d10-a50e-ec350d6be872/GCF_003807585.1_ASM380758v1_genomic.fna.gz --refList GCF_003807585.1_ASM380758v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003807585.1_ASM380758v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:42:12,855] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:12,863] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:42:12,863] [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_003807585.1	s__Chitinophaga barathri	100.0	2268	2270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_017742215.1	s__Chitinophaga sp017742215	84.566	1516	2270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003813775.1	s__Chitinophaga lutea	80.0901	939	2270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003568665.1	s__Chitinophaga alhagiae	79.7924	874	2270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007992715.1	s__Chitinophaga cymbidii	79.7778	840	2270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086345.1	s__Chitinophaga sp008086345	79.1722	772	2270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003958645.1	s__Chitinophaga rhizosphaerae	79.1416	762	2270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017849435.1	s__Chitinophaga niabensis_A	79.0876	667	2270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902167325.1	s__Chitinophaga pinensis_A	78.8969	653	2270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	99.49	99.49	0.97	0.97	3	-
GCF_003149455.1	s__Chitinophaga deserti	78.8656	691	2270	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 17:42:12,865] [INFO] GTDB search result was written to GCF_003807585.1_ASM380758v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:42:12,865] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:42:12,868] [INFO] DFAST_QC result json was written to GCF_003807585.1_ASM380758v1_genomic.fna/dqc_result.json
[2024-01-25 17:42:12,868] [INFO] DFAST_QC completed!
[2024-01-25 17:42:12,868] [INFO] Total running time: 0h2m37s