[2024-01-24 13:18:40,802] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:40,804] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:40,804] [INFO] DQC Reference Directory: /var/lib/cwl/stg61f162d8-d340-40f7-84ea-2fae6573821d/dqc_reference
[2024-01-24 13:18:42,033] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:42,034] [INFO] Task started: Prodigal
[2024-01-24 13:18:42,034] [INFO] Running command: gunzip -c /var/lib/cwl/stgc28b36f0-4fce-4b30-a054-4c2eb400f7d2/GCF_014192515.1_ASM1419251v1_genomic.fna.gz | prodigal -d GCF_014192515.1_ASM1419251v1_genomic.fna/cds.fna -a GCF_014192515.1_ASM1419251v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:58,575] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:58,576] [INFO] Task started: HMMsearch
[2024-01-24 13:18:58,576] [INFO] Running command: hmmsearch --tblout GCF_014192515.1_ASM1419251v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61f162d8-d340-40f7-84ea-2fae6573821d/dqc_reference/reference_markers.hmm GCF_014192515.1_ASM1419251v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:58,831] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:58,833] [INFO] Found 6/6 markers.
[2024-01-24 13:18:58,865] [INFO] Query marker FASTA was written to GCF_014192515.1_ASM1419251v1_genomic.fna/markers.fasta
[2024-01-24 13:18:58,866] [INFO] Task started: Blastn
[2024-01-24 13:18:58,866] [INFO] Running command: blastn -query GCF_014192515.1_ASM1419251v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61f162d8-d340-40f7-84ea-2fae6573821d/dqc_reference/reference_markers.fasta -out GCF_014192515.1_ASM1419251v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:59,452] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:59,456] [INFO] Selected 23 target genomes.
[2024-01-24 13:18:59,456] [INFO] Target genome list was writen to GCF_014192515.1_ASM1419251v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:59,533] [INFO] Task started: fastANI
[2024-01-24 13:18:59,533] [INFO] Running command: fastANI --query /var/lib/cwl/stgc28b36f0-4fce-4b30-a054-4c2eb400f7d2/GCF_014192515.1_ASM1419251v1_genomic.fna.gz --refList GCF_014192515.1_ASM1419251v1_genomic.fna/target_genomes.txt --output GCF_014192515.1_ASM1419251v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:13,980] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:13,981] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61f162d8-d340-40f7-84ea-2fae6573821d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:13,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61f162d8-d340-40f7-84ea-2fae6573821d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:13,985] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:13,985] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:13,985] [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
Microbacter margulisiae	strain=DSM 27471	GCA_014192515.1	1350067	1350067	type	True	100.0	1182	1186	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:19:13,987] [INFO] DFAST Taxonomy check result was written to GCF_014192515.1_ASM1419251v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:13,987] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:13,988] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:13,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61f162d8-d340-40f7-84ea-2fae6573821d/dqc_reference/checkm_data
[2024-01-24 13:19:13,989] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:14,025] [INFO] Task started: CheckM
[2024-01-24 13:19:14,026] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014192515.1_ASM1419251v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014192515.1_ASM1419251v1_genomic.fna/checkm_input GCF_014192515.1_ASM1419251v1_genomic.fna/checkm_result
[2024-01-24 13:20:04,576] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:04,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:04,610] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:04,611] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:04,612] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014192515.1_ASM1419251v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:04,612] [INFO] Task started: Blastn
[2024-01-24 13:20:04,612] [INFO] Running command: blastn -query GCF_014192515.1_ASM1419251v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61f162d8-d340-40f7-84ea-2fae6573821d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014192515.1_ASM1419251v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:05,436] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:05,440] [INFO] Selected 25 target genomes.
[2024-01-24 13:20:05,440] [INFO] Target genome list was writen to GCF_014192515.1_ASM1419251v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:05,762] [INFO] Task started: fastANI
[2024-01-24 13:20:05,762] [INFO] Running command: fastANI --query /var/lib/cwl/stgc28b36f0-4fce-4b30-a054-4c2eb400f7d2/GCF_014192515.1_ASM1419251v1_genomic.fna.gz --refList GCF_014192515.1_ASM1419251v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014192515.1_ASM1419251v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:19,365] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:19,373] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:19,373] [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_014192515.1	s__Microbacter margulisiae	100.0	1183	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Microbacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017860295.1	s__Microbacter sp017860295	76.4988	67	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Microbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009712605.1	s__Microbacter sp009712605	76.3467	57	1186	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__Microbacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:19,375] [INFO] GTDB search result was written to GCF_014192515.1_ASM1419251v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:19,375] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:19,377] [INFO] DFAST_QC result json was written to GCF_014192515.1_ASM1419251v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:19,377] [INFO] DFAST_QC completed!
[2024-01-24 13:20:19,377] [INFO] Total running time: 0h1m39s