[2023-06-27 06:16:02,582] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:16:02,624] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:16:02,624] [INFO] DQC Reference Directory: /var/lib/cwl/stg9362b03e-b545-4436-bce5-7201aab718be/dqc_reference
[2023-06-27 06:16:05,564] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:16:05,565] [INFO] Task started: Prodigal
[2023-06-27 06:16:05,565] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5aa0a68-7bd8-408e-887f-bf7c37431c9f/GCA_026129495.1_ASM2612949v1_genomic.fna.gz | prodigal -d GCA_026129495.1_ASM2612949v1_genomic.fna/cds.fna -a GCA_026129495.1_ASM2612949v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:16:31,214] [INFO] Task succeeded: Prodigal
[2023-06-27 06:16:31,215] [INFO] Task started: HMMsearch
[2023-06-27 06:16:31,215] [INFO] Running command: hmmsearch --tblout GCA_026129495.1_ASM2612949v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9362b03e-b545-4436-bce5-7201aab718be/dqc_reference/reference_markers.hmm GCA_026129495.1_ASM2612949v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:16:31,429] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:16:31,431] [INFO] Found 6/6 markers.
[2023-06-27 06:16:31,463] [INFO] Query marker FASTA was written to GCA_026129495.1_ASM2612949v1_genomic.fna/markers.fasta
[2023-06-27 06:16:31,464] [INFO] Task started: Blastn
[2023-06-27 06:16:31,464] [INFO] Running command: blastn -query GCA_026129495.1_ASM2612949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9362b03e-b545-4436-bce5-7201aab718be/dqc_reference/reference_markers.fasta -out GCA_026129495.1_ASM2612949v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:16:32,075] [INFO] Task succeeded: Blastn
[2023-06-27 06:16:32,078] [INFO] Selected 28 target genomes.
[2023-06-27 06:16:32,079] [INFO] Target genome list was writen to GCA_026129495.1_ASM2612949v1_genomic.fna/target_genomes.txt
[2023-06-27 06:16:32,084] [INFO] Task started: fastANI
[2023-06-27 06:16:32,084] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5aa0a68-7bd8-408e-887f-bf7c37431c9f/GCA_026129495.1_ASM2612949v1_genomic.fna.gz --refList GCA_026129495.1_ASM2612949v1_genomic.fna/target_genomes.txt --output GCA_026129495.1_ASM2612949v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:16:52,954] [INFO] Task succeeded: fastANI
[2023-06-27 06:16:52,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9362b03e-b545-4436-bce5-7201aab718be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:16:52,955] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9362b03e-b545-4436-bce5-7201aab718be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:16:52,959] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 06:16:52,959] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 06:16:52,960] [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
Chryseolinea serpens	strain=DSM 24574	GCA_900129725.1	947013	947013	type	True	75.6606	68	1185	95	below_threshold
Chryseolinea soli	strain=KIS68-18	GCA_003589925.1	2321403	2321403	type	True	75.3966	73	1185	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 06:16:52,961] [INFO] DFAST Taxonomy check result was written to GCA_026129495.1_ASM2612949v1_genomic.fna/tc_result.tsv
[2023-06-27 06:16:52,962] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:16:52,962] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:16:52,962] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9362b03e-b545-4436-bce5-7201aab718be/dqc_reference/checkm_data
[2023-06-27 06:16:52,963] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:16:53,003] [INFO] Task started: CheckM
[2023-06-27 06:16:53,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026129495.1_ASM2612949v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026129495.1_ASM2612949v1_genomic.fna/checkm_input GCA_026129495.1_ASM2612949v1_genomic.fna/checkm_result
[2023-06-27 06:17:59,482] [INFO] Task succeeded: CheckM
[2023-06-27 06:17:59,483] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 06:17:59,495] [INFO] ===== Completeness check finished =====
[2023-06-27 06:17:59,496] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:17:59,496] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026129495.1_ASM2612949v1_genomic.fna/markers.fasta)
[2023-06-27 06:17:59,496] [INFO] Task started: Blastn
[2023-06-27 06:17:59,496] [INFO] Running command: blastn -query GCA_026129495.1_ASM2612949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9362b03e-b545-4436-bce5-7201aab718be/dqc_reference/reference_markers_gtdb.fasta -out GCA_026129495.1_ASM2612949v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:18:00,245] [INFO] Task succeeded: Blastn
[2023-06-27 06:18:00,381] [INFO] Selected 30 target genomes.
[2023-06-27 06:18:00,381] [INFO] Target genome list was writen to GCA_026129495.1_ASM2612949v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:18:00,397] [INFO] Task started: fastANI
[2023-06-27 06:18:00,397] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5aa0a68-7bd8-408e-887f-bf7c37431c9f/GCA_026129495.1_ASM2612949v1_genomic.fna.gz --refList GCA_026129495.1_ASM2612949v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026129495.1_ASM2612949v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:18:20,762] [INFO] Task succeeded: fastANI
[2023-06-27 06:18:20,768] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 06:18:20,768] [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_002344795.1	s__ELB16-189 sp002344795	77.9705	298	1185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002345965.1	s__ELB16-189 sp002345965	76.972	224	1185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	99.88	99.88	0.94	0.94	2	-
GCF_900129725.1	s__Chryseolinea serpens	75.6606	68	1185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Chryseolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787605.1	s__ELB16-189 sp016787605	75.632	61	1185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003589925.1	s__Chryseolinea soli	75.3966	73	1185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Chryseolinea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 06:18:20,770] [INFO] GTDB search result was written to GCA_026129495.1_ASM2612949v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:18:20,770] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:18:20,773] [INFO] DFAST_QC result json was written to GCA_026129495.1_ASM2612949v1_genomic.fna/dqc_result.json
[2023-06-27 06:18:20,773] [INFO] DFAST_QC completed!
[2023-06-27 06:18:20,773] [INFO] Total running time: 0h2m18s