[2024-01-24 13:57:40,940] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:40,942] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:40,942] [INFO] DQC Reference Directory: /var/lib/cwl/stg35d0818f-71b9-454e-bb8c-ad958276c319/dqc_reference
[2024-01-24 13:57:42,269] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:42,270] [INFO] Task started: Prodigal
[2024-01-24 13:57:42,271] [INFO] Running command: gunzip -c /var/lib/cwl/stg2aa0a9f9-0586-43ae-a0d1-465f7977b728/GCF_002077945.1_ASM207794v1_genomic.fna.gz | prodigal -d GCF_002077945.1_ASM207794v1_genomic.fna/cds.fna -a GCF_002077945.1_ASM207794v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:34,264] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:34,265] [INFO] Task started: HMMsearch
[2024-01-24 13:58:34,265] [INFO] Running command: hmmsearch --tblout GCF_002077945.1_ASM207794v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35d0818f-71b9-454e-bb8c-ad958276c319/dqc_reference/reference_markers.hmm GCF_002077945.1_ASM207794v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:34,676] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:34,678] [INFO] Found 6/6 markers.
[2024-01-24 13:58:34,762] [INFO] Query marker FASTA was written to GCF_002077945.1_ASM207794v1_genomic.fna/markers.fasta
[2024-01-24 13:58:34,762] [INFO] Task started: Blastn
[2024-01-24 13:58:34,762] [INFO] Running command: blastn -query GCF_002077945.1_ASM207794v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35d0818f-71b9-454e-bb8c-ad958276c319/dqc_reference/reference_markers.fasta -out GCF_002077945.1_ASM207794v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:35,362] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:35,366] [INFO] Selected 13 target genomes.
[2024-01-24 13:58:35,367] [INFO] Target genome list was writen to GCF_002077945.1_ASM207794v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:35,387] [INFO] Task started: fastANI
[2024-01-24 13:58:35,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg2aa0a9f9-0586-43ae-a0d1-465f7977b728/GCF_002077945.1_ASM207794v1_genomic.fna.gz --refList GCF_002077945.1_ASM207794v1_genomic.fna/target_genomes.txt --output GCF_002077945.1_ASM207794v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:54,866] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:54,867] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35d0818f-71b9-454e-bb8c-ad958276c319/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:54,867] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35d0818f-71b9-454e-bb8c-ad958276c319/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:54,884] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:54,884] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:54,885] [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
Niastella vici	strain=DJ57	GCA_002077945.1	1703345	1703345	type	True	100.0	3296	3300	95	conclusive
Niastella caeni	strain=HX-16-21	GCA_004834005.1	2569763	2569763	type	True	82.1369	1672	3300	95	below_threshold
Niastella populi	strain=CCTCC AB 208238	GCA_002078015.1	550983	550983	type	True	81.3406	1530	3300	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_002077935.1	354355	354355	type	True	81.1091	1388	3300	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	81.0604	1403	3300	95	below_threshold
Niastella koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	81.0069	1597	3300	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	80.9968	1601	3300	95	below_threshold
Niastella soli	strain=MAH-29	GCA_017742245.1	2821487	2821487	type	True	80.9224	1458	3300	95	below_threshold
Pinibacter aurantiacus	strain=MAH-26	GCA_019130065.1	2851599	2851599	type	True	76.1916	110	3300	95	below_threshold
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	75.9039	100	3300	95	below_threshold
Filimonas effusa	strain=TTM-71	GCA_004118675.1	2508721	2508721	type	True	75.8913	106	3300	95	below_threshold
Niabella pedocola	strain=JCM 31011	GCA_021044425.1	1752077	1752077	type	True	75.8037	96	3300	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:54,886] [INFO] DFAST Taxonomy check result was written to GCF_002077945.1_ASM207794v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:54,887] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:54,887] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:54,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35d0818f-71b9-454e-bb8c-ad958276c319/dqc_reference/checkm_data
[2024-01-24 13:58:54,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:54,974] [INFO] Task started: CheckM
[2024-01-24 13:58:54,975] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002077945.1_ASM207794v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002077945.1_ASM207794v1_genomic.fna/checkm_input GCF_002077945.1_ASM207794v1_genomic.fna/checkm_result
[2024-01-24 14:01:00,611] [INFO] Task succeeded: CheckM
[2024-01-24 14:01:00,612] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:01:00,633] [INFO] ===== Completeness check finished =====
[2024-01-24 14:01:00,634] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:01:00,634] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002077945.1_ASM207794v1_genomic.fna/markers.fasta)
[2024-01-24 14:01:00,634] [INFO] Task started: Blastn
[2024-01-24 14:01:00,635] [INFO] Running command: blastn -query GCF_002077945.1_ASM207794v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35d0818f-71b9-454e-bb8c-ad958276c319/dqc_reference/reference_markers_gtdb.fasta -out GCF_002077945.1_ASM207794v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:01:01,446] [INFO] Task succeeded: Blastn
[2024-01-24 14:01:01,451] [INFO] Selected 9 target genomes.
[2024-01-24 14:01:01,451] [INFO] Target genome list was writen to GCF_002077945.1_ASM207794v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:01:01,463] [INFO] Task started: fastANI
[2024-01-24 14:01:01,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg2aa0a9f9-0586-43ae-a0d1-465f7977b728/GCF_002077945.1_ASM207794v1_genomic.fna.gz --refList GCF_002077945.1_ASM207794v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002077945.1_ASM207794v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:01:19,010] [INFO] Task succeeded: fastANI
[2024-01-24 14:01:19,018] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:01:19,019] [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_002077945.1	s__Niastella vici	100.0	3296	3300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004834005.1	s__Niastella caeni	82.1531	1667	3300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341975.1	s__Niastella sp004341975	81.4097	1692	3300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002078015.1	s__Niastella populi	81.3449	1529	3300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924755.1	s__Niastella sp016924755	81.2436	1376	3300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356035.1	s__Niastella sp017356035	81.2309	1353	3300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110245.1	s__Niastella yeongjuensis	81.0697	1401	3300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000246855.1	s__Niastella koreensis	81.0031	1597	3300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017742245.1	s__Niastella sp017742245	80.9154	1460	3300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:01:19,020] [INFO] GTDB search result was written to GCF_002077945.1_ASM207794v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:01:19,021] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:01:19,024] [INFO] DFAST_QC result json was written to GCF_002077945.1_ASM207794v1_genomic.fna/dqc_result.json
[2024-01-24 14:01:19,025] [INFO] DFAST_QC completed!
[2024-01-24 14:01:19,025] [INFO] Total running time: 0h3m38s