[2024-01-25 17:41:35,762] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:41:35,763] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:41:35,763] [INFO] DQC Reference Directory: /var/lib/cwl/stg9aa8541a-ae88-4e30-a5c3-99c0c20d743f/dqc_reference
[2024-01-25 17:41:36,937] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:41:36,941] [INFO] Task started: Prodigal
[2024-01-25 17:41:36,941] [INFO] Running command: gunzip -c /var/lib/cwl/stga4f66b83-d347-466b-a6e1-27aca0ff8fbb/GCF_021190955.1_ASM2119095v1_genomic.fna.gz | prodigal -d GCF_021190955.1_ASM2119095v1_genomic.fna/cds.fna -a GCF_021190955.1_ASM2119095v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:42:15,343] [INFO] Task succeeded: Prodigal
[2024-01-25 17:42:15,344] [INFO] Task started: HMMsearch
[2024-01-25 17:42:15,344] [INFO] Running command: hmmsearch --tblout GCF_021190955.1_ASM2119095v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9aa8541a-ae88-4e30-a5c3-99c0c20d743f/dqc_reference/reference_markers.hmm GCF_021190955.1_ASM2119095v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:42:15,655] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:42:15,656] [INFO] Found 6/6 markers.
[2024-01-25 17:42:15,714] [INFO] Query marker FASTA was written to GCF_021190955.1_ASM2119095v1_genomic.fna/markers.fasta
[2024-01-25 17:42:15,714] [INFO] Task started: Blastn
[2024-01-25 17:42:15,714] [INFO] Running command: blastn -query GCF_021190955.1_ASM2119095v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9aa8541a-ae88-4e30-a5c3-99c0c20d743f/dqc_reference/reference_markers.fasta -out GCF_021190955.1_ASM2119095v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:16,257] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:16,259] [INFO] Selected 14 target genomes.
[2024-01-25 17:42:16,260] [INFO] Target genome list was writen to GCF_021190955.1_ASM2119095v1_genomic.fna/target_genomes.txt
[2024-01-25 17:42:16,279] [INFO] Task started: fastANI
[2024-01-25 17:42:16,280] [INFO] Running command: fastANI --query /var/lib/cwl/stga4f66b83-d347-466b-a6e1-27aca0ff8fbb/GCF_021190955.1_ASM2119095v1_genomic.fna.gz --refList GCF_021190955.1_ASM2119095v1_genomic.fna/target_genomes.txt --output GCF_021190955.1_ASM2119095v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:42:33,756] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:33,757] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9aa8541a-ae88-4e30-a5c3-99c0c20d743f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:42:33,757] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9aa8541a-ae88-4e30-a5c3-99c0c20d743f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:42:33,763] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:42:33,763] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:42:33,763] [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
Dawidia cretensis	strain=PWU5	GCA_018598175.1	2782350	2782350	type	True	91.2266	2029	2642	95	below_threshold
Dawidia soli	strain=PWU37	GCA_018598185.1	2782352	2782352	type	True	84.0504	1786	2642	95	below_threshold
Chryseolinea soli	strain=KIS68-18	GCA_003589925.1	2321403	2321403	type	True	77.2343	296	2642	95	below_threshold
Chryseolinea serpens	strain=DSM 24574	GCA_900129725.1	947013	947013	type	True	77.0414	295	2642	95	below_threshold
Chryseosolibacter histidini	strain=PWU4	GCA_018598225.1	2782349	2782349	type	True	76.7626	237	2642	95	below_threshold
Ohtaekwangia koreensis	strain=DSM 25262	GCA_900167975.1	688867	688867	type	True	76.7482	201	2642	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:42:33,764] [INFO] DFAST Taxonomy check result was written to GCF_021190955.1_ASM2119095v1_genomic.fna/tc_result.tsv
[2024-01-25 17:42:33,765] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:42:33,765] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:42:33,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9aa8541a-ae88-4e30-a5c3-99c0c20d743f/dqc_reference/checkm_data
[2024-01-25 17:42:33,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:42:33,839] [INFO] Task started: CheckM
[2024-01-25 17:42:33,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021190955.1_ASM2119095v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021190955.1_ASM2119095v1_genomic.fna/checkm_input GCF_021190955.1_ASM2119095v1_genomic.fna/checkm_result
[2024-01-25 17:44:16,400] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:16,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:16,439] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:16,439] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:16,440] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021190955.1_ASM2119095v1_genomic.fna/markers.fasta)
[2024-01-25 17:44:16,440] [INFO] Task started: Blastn
[2024-01-25 17:44:16,440] [INFO] Running command: blastn -query GCF_021190955.1_ASM2119095v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9aa8541a-ae88-4e30-a5c3-99c0c20d743f/dqc_reference/reference_markers_gtdb.fasta -out GCF_021190955.1_ASM2119095v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:17,349] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:17,352] [INFO] Selected 16 target genomes.
[2024-01-25 17:44:17,352] [INFO] Target genome list was writen to GCF_021190955.1_ASM2119095v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:44:17,376] [INFO] Task started: fastANI
[2024-01-25 17:44:17,376] [INFO] Running command: fastANI --query /var/lib/cwl/stga4f66b83-d347-466b-a6e1-27aca0ff8fbb/GCF_021190955.1_ASM2119095v1_genomic.fna.gz --refList GCF_021190955.1_ASM2119095v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021190955.1_ASM2119095v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:44:34,625] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:34,633] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:44:34,633] [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
GCA_018598175.1	s__Ohtaekwangia sp018598175	91.24	2027	2642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018598185.1	s__Ohtaekwangia sp018598185	84.0362	1788	2642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003589925.1	s__Chryseolinea soli	77.2343	296	2642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Chryseolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168205.1	s__Ohtaekwangia sp902168205	77.1766	237	2642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129725.1	s__Chryseolinea serpens	77.0414	295	2642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Chryseolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735595.1	s__Chryseolinea sp016735595	76.9817	321	2642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Chryseolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168185.1	s__Ohtaekwangia sp902168185	76.8653	212	2642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018598225.1	s__PWU20 sp018598225	76.7624	236	2642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__PWU20	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167975.1	s__Ohtaekwangia koreensis	76.7482	201	2642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002432545.1	s__Ohtaekwangia sp002432545	76.4963	198	2642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786585.1	s__UBA2336 sp016786585	76.3684	63	2642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA2336	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015180985.1	s__UBA2336 sp015180985	76.1539	54	2642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA2336	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787605.1	s__ELB16-189 sp016787605	75.6888	69	2642	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:44:34,635] [INFO] GTDB search result was written to GCF_021190955.1_ASM2119095v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:44:34,635] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:44:34,638] [INFO] DFAST_QC result json was written to GCF_021190955.1_ASM2119095v1_genomic.fna/dqc_result.json
[2024-01-25 17:44:34,638] [INFO] DFAST_QC completed!
[2024-01-25 17:44:34,638] [INFO] Total running time: 0h2m59s