[2024-01-24 13:41:20,680] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:20,685] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:20,686] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ec0dcf4-f502-417a-8d62-ec5076514db1/dqc_reference
[2024-01-24 13:41:22,132] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:22,133] [INFO] Task started: Prodigal
[2024-01-24 13:41:22,133] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2d5ca03-e53a-4a0f-b3f2-f1700c11d9f3/GCF_001661595.2_ASM166159v2_genomic.fna.gz | prodigal -d GCF_001661595.2_ASM166159v2_genomic.fna/cds.fna -a GCF_001661595.2_ASM166159v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:36,087] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:36,087] [INFO] Task started: HMMsearch
[2024-01-24 13:41:36,087] [INFO] Running command: hmmsearch --tblout GCF_001661595.2_ASM166159v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ec0dcf4-f502-417a-8d62-ec5076514db1/dqc_reference/reference_markers.hmm GCF_001661595.2_ASM166159v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:36,427] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:36,429] [INFO] Found 6/6 markers.
[2024-01-24 13:41:36,478] [INFO] Query marker FASTA was written to GCF_001661595.2_ASM166159v2_genomic.fna/markers.fasta
[2024-01-24 13:41:36,479] [INFO] Task started: Blastn
[2024-01-24 13:41:36,479] [INFO] Running command: blastn -query GCF_001661595.2_ASM166159v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ec0dcf4-f502-417a-8d62-ec5076514db1/dqc_reference/reference_markers.fasta -out GCF_001661595.2_ASM166159v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:37,122] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:37,125] [INFO] Selected 20 target genomes.
[2024-01-24 13:41:37,126] [INFO] Target genome list was writen to GCF_001661595.2_ASM166159v2_genomic.fna/target_genomes.txt
[2024-01-24 13:41:37,133] [INFO] Task started: fastANI
[2024-01-24 13:41:37,134] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2d5ca03-e53a-4a0f-b3f2-f1700c11d9f3/GCF_001661595.2_ASM166159v2_genomic.fna.gz --refList GCF_001661595.2_ASM166159v2_genomic.fna/target_genomes.txt --output GCF_001661595.2_ASM166159v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:49,256] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:49,256] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ec0dcf4-f502-417a-8d62-ec5076514db1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:49,256] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ec0dcf4-f502-417a-8d62-ec5076514db1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:49,261] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:49,262] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:49,262] [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
Crocinitomix algicola	strain=0182	GCA_001661595.2	1740263	1740263	type	True	100.0	1221	1222	95	conclusive
Crocinitomix catalasitica	strain=ATCC 23190	GCA_000621625.1	184607	184607	type	True	76.7542	178	1222	95	below_threshold
Putridiphycobacter roseus	strain=SM1701	GCA_003234935.1	2219161	2219161	type	True	75.8986	86	1222	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:49,264] [INFO] DFAST Taxonomy check result was written to GCF_001661595.2_ASM166159v2_genomic.fna/tc_result.tsv
[2024-01-24 13:41:49,265] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:49,265] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:49,265] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ec0dcf4-f502-417a-8d62-ec5076514db1/dqc_reference/checkm_data
[2024-01-24 13:41:49,267] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:49,304] [INFO] Task started: CheckM
[2024-01-24 13:41:49,305] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001661595.2_ASM166159v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001661595.2_ASM166159v2_genomic.fna/checkm_input GCF_001661595.2_ASM166159v2_genomic.fna/checkm_result
[2024-01-24 13:42:32,480] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:32,481] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:32,502] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:32,502] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:32,502] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001661595.2_ASM166159v2_genomic.fna/markers.fasta)
[2024-01-24 13:42:32,503] [INFO] Task started: Blastn
[2024-01-24 13:42:32,503] [INFO] Running command: blastn -query GCF_001661595.2_ASM166159v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ec0dcf4-f502-417a-8d62-ec5076514db1/dqc_reference/reference_markers_gtdb.fasta -out GCF_001661595.2_ASM166159v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:33,276] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:33,281] [INFO] Selected 21 target genomes.
[2024-01-24 13:42:33,281] [INFO] Target genome list was writen to GCF_001661595.2_ASM166159v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:33,299] [INFO] Task started: fastANI
[2024-01-24 13:42:33,299] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2d5ca03-e53a-4a0f-b3f2-f1700c11d9f3/GCF_001661595.2_ASM166159v2_genomic.fna.gz --refList GCF_001661595.2_ASM166159v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001661595.2_ASM166159v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:44,652] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:44,662] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:44,662] [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_001661595.2	s__Crocinitomix algicola	100.0	1221	1222	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905478225.1	s__Crocinitomix sp905478225	77.1847	177	1222	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013138735.1	s__Crocinitomix sp013138735	76.917	205	1222	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621625.1	s__Crocinitomix catalasitica	76.7419	179	1222	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003234935.1	s__Putridiphycobacter roseus	75.8986	86	1222	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Putridiphycobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:44,664] [INFO] GTDB search result was written to GCF_001661595.2_ASM166159v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:44,665] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:44,668] [INFO] DFAST_QC result json was written to GCF_001661595.2_ASM166159v2_genomic.fna/dqc_result.json
[2024-01-24 13:42:44,668] [INFO] DFAST_QC completed!
[2024-01-24 13:42:44,668] [INFO] Total running time: 0h1m24s