[2024-01-24 10:47:40,960] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,966] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,967] [INFO] DQC Reference Directory: /var/lib/cwl/stgae4deb41-0397-4502-abdc-92809c046dd5/dqc_reference
[2024-01-24 10:47:44,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,789] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,789] [INFO] Running command: gunzip -c /var/lib/cwl/stg96dd126e-1eb4-4a07-8831-099b05faf4d0/GCF_014207425.1_ASM1420742v1_genomic.fna.gz | prodigal -d GCF_014207425.1_ASM1420742v1_genomic.fna/cds.fna -a GCF_014207425.1_ASM1420742v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:49,576] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:49,576] [INFO] Task started: HMMsearch
[2024-01-24 10:47:49,576] [INFO] Running command: hmmsearch --tblout GCF_014207425.1_ASM1420742v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae4deb41-0397-4502-abdc-92809c046dd5/dqc_reference/reference_markers.hmm GCF_014207425.1_ASM1420742v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:49,835] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:49,836] [INFO] Found 6/6 markers.
[2024-01-24 10:47:49,861] [INFO] Query marker FASTA was written to GCF_014207425.1_ASM1420742v1_genomic.fna/markers.fasta
[2024-01-24 10:47:49,861] [INFO] Task started: Blastn
[2024-01-24 10:47:49,861] [INFO] Running command: blastn -query GCF_014207425.1_ASM1420742v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae4deb41-0397-4502-abdc-92809c046dd5/dqc_reference/reference_markers.fasta -out GCF_014207425.1_ASM1420742v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:50,831] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:50,837] [INFO] Selected 11 target genomes.
[2024-01-24 10:47:50,837] [INFO] Target genome list was writen to GCF_014207425.1_ASM1420742v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:50,867] [INFO] Task started: fastANI
[2024-01-24 10:47:50,867] [INFO] Running command: fastANI --query /var/lib/cwl/stg96dd126e-1eb4-4a07-8831-099b05faf4d0/GCF_014207425.1_ASM1420742v1_genomic.fna.gz --refList GCF_014207425.1_ASM1420742v1_genomic.fna/target_genomes.txt --output GCF_014207425.1_ASM1420742v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:58,527] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:58,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae4deb41-0397-4502-abdc-92809c046dd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:58,527] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae4deb41-0397-4502-abdc-92809c046dd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:58,534] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:47:58,534] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:58,534] [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 coquinae	strain=DSM 22419	GCA_014207425.1	709509	709509	type	True	100.0	732	733	95	conclusive
Jeotgalicoccus coquinae	strain=CCM 7682	GCA_014635225.1	709509	709509	type	True	99.9986	732	733	95	conclusive
Jeotgalicoccus coquinae	strain=CIP 111751	GCA_903994065.1	709509	709509	type	True	99.9943	730	733	95	conclusive
Jeotgalicoccus saudimassiliensis	strain=13MG44_air	GCA_000756715.2	1461582	1461582	type	True	87.9331	638	733	95	below_threshold
Jeotgalicoccus psychrophilus	strain=DSM 19085	GCA_000425845.1	157228	157228	type	True	86.601	623	733	95	below_threshold
Jeotgalicoccus halotolerans	strain=DSM 17274	GCA_003387165.1	157227	157227	type	True	84.4168	575	733	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:58,536] [INFO] DFAST Taxonomy check result was written to GCF_014207425.1_ASM1420742v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:58,536] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:58,537] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:58,537] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae4deb41-0397-4502-abdc-92809c046dd5/dqc_reference/checkm_data
[2024-01-24 10:47:58,538] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:58,565] [INFO] Task started: CheckM
[2024-01-24 10:47:58,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014207425.1_ASM1420742v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014207425.1_ASM1420742v1_genomic.fna/checkm_input GCF_014207425.1_ASM1420742v1_genomic.fna/checkm_result
[2024-01-24 10:48:20,262] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:20,263] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:20,280] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:20,280] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:20,281] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014207425.1_ASM1420742v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:20,281] [INFO] Task started: Blastn
[2024-01-24 10:48:20,281] [INFO] Running command: blastn -query GCF_014207425.1_ASM1420742v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae4deb41-0397-4502-abdc-92809c046dd5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014207425.1_ASM1420742v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:21,092] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:21,095] [INFO] Selected 8 target genomes.
[2024-01-24 10:48:21,096] [INFO] Target genome list was writen to GCF_014207425.1_ASM1420742v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:21,103] [INFO] Task started: fastANI
[2024-01-24 10:48:21,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg96dd126e-1eb4-4a07-8831-099b05faf4d0/GCF_014207425.1_ASM1420742v1_genomic.fna.gz --refList GCF_014207425.1_ASM1420742v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014207425.1_ASM1420742v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:25,620] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:25,632] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:25,632] [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_014207425.1	s__Jeotgalicoccus coquinae	100.0	732	733	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_000756715.1	s__Jeotgalicoccus saudimassiliensis	87.95	637	733	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003513765.1	s__Jeotgalicoccus sp003513765	87.4283	614	733	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425845.1	s__Jeotgalicoccus psychrophilus	86.6205	622	733	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	97.52	97.52	0.90	0.90	2	-
GCA_004570955.1	s__Jeotgalicoccus nanhaiensis	84.5279	605	733	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	96.2898	99.28	98.57	0.98	0.96	3	-
GCF_003387165.1	s__Jeotgalicoccus halotolerans	84.4168	575	733	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	96.2898	N/A	N/A	N/A	N/A	1	-
GCA_014635205.1	s__Jeotgalicoccus aerolatus	82.1988	522	733	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	99.67	99.03	0.98	0.93	4	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:25,634] [INFO] GTDB search result was written to GCF_014207425.1_ASM1420742v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:25,634] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:25,637] [INFO] DFAST_QC result json was written to GCF_014207425.1_ASM1420742v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:25,637] [INFO] DFAST_QC completed!
[2024-01-24 10:48:25,637] [INFO] Total running time: 0h0m45s