[2024-01-25 18:08:20,435] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:08:20,436] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:08:20,436] [INFO] DQC Reference Directory: /var/lib/cwl/stg71dd7d5a-76b7-463d-9d5e-c633b006e4c6/dqc_reference
[2024-01-25 18:08:21,549] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:08:21,550] [INFO] Task started: Prodigal
[2024-01-25 18:08:21,550] [INFO] Running command: gunzip -c /var/lib/cwl/stgb415a703-4af5-4e7e-b0c8-010ba3ce0a27/GCF_003614855.1_ASM361485v1_genomic.fna.gz | prodigal -d GCF_003614855.1_ASM361485v1_genomic.fna/cds.fna -a GCF_003614855.1_ASM361485v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:53,495] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:53,495] [INFO] Task started: HMMsearch
[2024-01-25 18:08:53,495] [INFO] Running command: hmmsearch --tblout GCF_003614855.1_ASM361485v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71dd7d5a-76b7-463d-9d5e-c633b006e4c6/dqc_reference/reference_markers.hmm GCF_003614855.1_ASM361485v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:53,785] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:53,786] [INFO] Found 6/6 markers.
[2024-01-25 18:08:53,836] [INFO] Query marker FASTA was written to GCF_003614855.1_ASM361485v1_genomic.fna/markers.fasta
[2024-01-25 18:08:53,837] [INFO] Task started: Blastn
[2024-01-25 18:08:53,837] [INFO] Running command: blastn -query GCF_003614855.1_ASM361485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71dd7d5a-76b7-463d-9d5e-c633b006e4c6/dqc_reference/reference_markers.fasta -out GCF_003614855.1_ASM361485v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:54,400] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:54,402] [INFO] Selected 15 target genomes.
[2024-01-25 18:08:54,403] [INFO] Target genome list was writen to GCF_003614855.1_ASM361485v1_genomic.fna/target_genomes.txt
[2024-01-25 18:08:54,414] [INFO] Task started: fastANI
[2024-01-25 18:08:54,414] [INFO] Running command: fastANI --query /var/lib/cwl/stgb415a703-4af5-4e7e-b0c8-010ba3ce0a27/GCF_003614855.1_ASM361485v1_genomic.fna.gz --refList GCF_003614855.1_ASM361485v1_genomic.fna/target_genomes.txt --output GCF_003614855.1_ASM361485v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:09:11,638] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:11,638] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71dd7d5a-76b7-463d-9d5e-c633b006e4c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:09:11,638] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71dd7d5a-76b7-463d-9d5e-c633b006e4c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:09:11,647] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:09:11,647] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:09:11,647] [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_003614855.1	1647451	1647451	type	True	100.0	2283	2294	95	conclusive
Chitinophaga barathri	strain=YLT18	GCA_003807585.1	1647451	1647451	type	True	99.9994	2267	2294	95	conclusive
Chitinophaga chungangae	strain=MAH-28	GCA_017742215.1	2821488	2821488	type	True	84.5488	1525	2294	95	below_threshold
Chitinophaga lutea	strain=ZY74	GCA_003813775.1	2488634	2488634	type	True	80.0636	940	2294	95	below_threshold
Chitinophaga alhagiae	strain=T22	GCA_003177275.1	2203219	2203219	suspected-type	True	79.9538	463	2294	95	below_threshold
Chitinophaga alhagiae	strain=T22	GCA_003568665.1	2203219	2203219	suspected-type	True	79.7153	891	2294	95	below_threshold
Chitinophaga rhizosphaerae	strain=T16R-86	GCA_003958645.1	1864947	1864947	type	True	79.1483	751	2294	95	below_threshold
Chitinophaga deserti	strain=XJ-2	GCA_003149455.1	2164099	2164099	type	True	78.834	679	2294	95	below_threshold
Chitinophaga fulva	strain=G-6-1-13	GCA_012927205.1	2728842	2728842	type	True	77.1888	330	2294	95	below_threshold
Chitinophaga filiformis	strain=DSM 527	GCA_900102545.1	104663	104663	type	True	76.8717	241	2294	95	below_threshold
Chitinophaga rhizophila	strain=B61	GCA_019492185.1	2866212	2866212	type	True	76.7632	141	2294	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:09:11,648] [INFO] DFAST Taxonomy check result was written to GCF_003614855.1_ASM361485v1_genomic.fna/tc_result.tsv
[2024-01-25 18:09:11,649] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:09:11,649] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:09:11,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71dd7d5a-76b7-463d-9d5e-c633b006e4c6/dqc_reference/checkm_data
[2024-01-25 18:09:11,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:09:11,714] [INFO] Task started: CheckM
[2024-01-25 18:09:11,714] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003614855.1_ASM361485v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003614855.1_ASM361485v1_genomic.fna/checkm_input GCF_003614855.1_ASM361485v1_genomic.fna/checkm_result
[2024-01-25 18:10:33,799] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:33,800] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:33,816] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:33,816] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:33,817] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003614855.1_ASM361485v1_genomic.fna/markers.fasta)
[2024-01-25 18:10:33,817] [INFO] Task started: Blastn
[2024-01-25 18:10:33,817] [INFO] Running command: blastn -query GCF_003614855.1_ASM361485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71dd7d5a-76b7-463d-9d5e-c633b006e4c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003614855.1_ASM361485v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:34,647] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:34,650] [INFO] Selected 10 target genomes.
[2024-01-25 18:10:34,650] [INFO] Target genome list was writen to GCF_003614855.1_ASM361485v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:34,658] [INFO] Task started: fastANI
[2024-01-25 18:10:34,658] [INFO] Running command: fastANI --query /var/lib/cwl/stgb415a703-4af5-4e7e-b0c8-010ba3ce0a27/GCF_003614855.1_ASM361485v1_genomic.fna.gz --refList GCF_003614855.1_ASM361485v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003614855.1_ASM361485v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:48,353] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:48,361] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:10:48,361] [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	99.9994	2266	2294	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	84.5488	1525	2294	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	80.0517	942	2294	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992715.1	s__Chitinophaga cymbidii	79.8044	835	2294	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	79.7134	893	2294	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008086345.1	s__Chitinophaga sp008086345	79.2594	757	2294	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	79.1444	751	2294	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	79.0581	673	2294	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149455.1	s__Chitinophaga deserti	78.847	677	2294	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	78.8232	661	2294	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	99.49	99.49	0.97	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:48,363] [INFO] GTDB search result was written to GCF_003614855.1_ASM361485v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:48,363] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:48,367] [INFO] DFAST_QC result json was written to GCF_003614855.1_ASM361485v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:48,367] [INFO] DFAST_QC completed!
[2024-01-25 18:10:48,367] [INFO] Total running time: 0h2m28s