[2024-01-24 15:18:18,433] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:18,435] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:18,435] [INFO] DQC Reference Directory: /var/lib/cwl/stgc95bd849-2e43-4b63-997a-f355c6c07ca7/dqc_reference
[2024-01-24 15:18:19,725] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:19,726] [INFO] Task started: Prodigal
[2024-01-24 15:18:19,726] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0735cd7-2b03-4827-a78a-8e2f31b1f579/GCF_017873645.1_ASM1787364v1_genomic.fna.gz | prodigal -d GCF_017873645.1_ASM1787364v1_genomic.fna/cds.fna -a GCF_017873645.1_ASM1787364v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:22,937] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:22,938] [INFO] Task started: HMMsearch
[2024-01-24 15:18:22,938] [INFO] Running command: hmmsearch --tblout GCF_017873645.1_ASM1787364v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc95bd849-2e43-4b63-997a-f355c6c07ca7/dqc_reference/reference_markers.hmm GCF_017873645.1_ASM1787364v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:23,216] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:23,218] [INFO] Found 6/6 markers.
[2024-01-24 15:18:23,240] [INFO] Query marker FASTA was written to GCF_017873645.1_ASM1787364v1_genomic.fna/markers.fasta
[2024-01-24 15:18:23,240] [INFO] Task started: Blastn
[2024-01-24 15:18:23,240] [INFO] Running command: blastn -query GCF_017873645.1_ASM1787364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc95bd849-2e43-4b63-997a-f355c6c07ca7/dqc_reference/reference_markers.fasta -out GCF_017873645.1_ASM1787364v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:23,857] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:23,860] [INFO] Selected 15 target genomes.
[2024-01-24 15:18:23,860] [INFO] Target genome list was writen to GCF_017873645.1_ASM1787364v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:23,866] [INFO] Task started: fastANI
[2024-01-24 15:18:23,866] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0735cd7-2b03-4827-a78a-8e2f31b1f579/GCF_017873645.1_ASM1787364v1_genomic.fna.gz --refList GCF_017873645.1_ASM1787364v1_genomic.fna/target_genomes.txt --output GCF_017873645.1_ASM1787364v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:31,493] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:31,494] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc95bd849-2e43-4b63-997a-f355c6c07ca7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:31,494] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc95bd849-2e43-4b63-997a-f355c6c07ca7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:31,507] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:18:31,507] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:31,507] [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
Jeotgalicoccus pinnipedialis	strain=DSM 17030	GCA_017873645.1	110845	110845	type	True	100.0	514	514	95	conclusive
Jeotgalicoccus pinnipedialis	strain=CIP 107946	GCA_903994035.1	110845	110845	type	True	99.9873	505	514	95	conclusive
Jeotgalicoccus schoeneichii	strain=CIP 111030	GCA_903994025.1	1812261	1812261	type	True	83.8396	412	514	95	below_threshold
Jeotgalicoccus schoeneichii	strain=CCM 8667	GCA_014635565.1	1812261	1812261	type	True	83.8391	417	514	95	below_threshold
Jeotgalicoccus psychrophilus	strain=DSM 19085	GCA_000425845.1	157228	157228	type	True	77.204	55	514	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:31,509] [INFO] DFAST Taxonomy check result was written to GCF_017873645.1_ASM1787364v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:31,510] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:31,510] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:31,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc95bd849-2e43-4b63-997a-f355c6c07ca7/dqc_reference/checkm_data
[2024-01-24 15:18:31,512] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:31,530] [INFO] Task started: CheckM
[2024-01-24 15:18:31,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873645.1_ASM1787364v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873645.1_ASM1787364v1_genomic.fna/checkm_input GCF_017873645.1_ASM1787364v1_genomic.fna/checkm_result
[2024-01-24 15:18:49,570] [INFO] Task succeeded: CheckM
[2024-01-24 15:18:49,572] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:18:49,593] [INFO] ===== Completeness check finished =====
[2024-01-24 15:18:49,593] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:18:49,594] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873645.1_ASM1787364v1_genomic.fna/markers.fasta)
[2024-01-24 15:18:49,594] [INFO] Task started: Blastn
[2024-01-24 15:18:49,594] [INFO] Running command: blastn -query GCF_017873645.1_ASM1787364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc95bd849-2e43-4b63-997a-f355c6c07ca7/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873645.1_ASM1787364v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:50,354] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:50,357] [INFO] Selected 21 target genomes.
[2024-01-24 15:18:50,357] [INFO] Target genome list was writen to GCF_017873645.1_ASM1787364v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:18:50,378] [INFO] Task started: fastANI
[2024-01-24 15:18:50,379] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0735cd7-2b03-4827-a78a-8e2f31b1f579/GCF_017873645.1_ASM1787364v1_genomic.fna.gz --refList GCF_017873645.1_ASM1787364v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873645.1_ASM1787364v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:00,589] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:00,599] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:00,599] [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_903994035.1	s__Jeotgalicoccus_A pinnipedialis	99.9873	505	514	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus_A	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_014635565.1	s__Jeotgalicoccus_A schoeneichii	83.8391	417	514	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus_A	95.0	99.97	99.97	0.99	0.99	2	-
GCA_019119225.1	s__Nosocomiicoccus stercorigallinarum	77.6479	100	514	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Nosocomiicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425845.1	s__Jeotgalicoccus psychrophilus	77.2256	56	514	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	97.52	97.52	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:00,601] [INFO] GTDB search result was written to GCF_017873645.1_ASM1787364v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:00,602] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:00,605] [INFO] DFAST_QC result json was written to GCF_017873645.1_ASM1787364v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:00,605] [INFO] DFAST_QC completed!
[2024-01-24 15:19:00,606] [INFO] Total running time: 0h0m42s