[2024-01-24 13:45:41,539] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:41,544] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:41,544] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6343a4e-3878-449f-a2c0-31e05a415d76/dqc_reference
[2024-01-24 13:45:42,770] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:42,771] [INFO] Task started: Prodigal
[2024-01-24 13:45:42,772] [INFO] Running command: gunzip -c /var/lib/cwl/stge12d63de-a04a-4dbe-9dc5-9bb0dcf45665/GCF_014635205.1_ASM1463520v1_genomic.fna.gz | prodigal -d GCF_014635205.1_ASM1463520v1_genomic.fna/cds.fna -a GCF_014635205.1_ASM1463520v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:47,236] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:47,236] [INFO] Task started: HMMsearch
[2024-01-24 13:45:47,237] [INFO] Running command: hmmsearch --tblout GCF_014635205.1_ASM1463520v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6343a4e-3878-449f-a2c0-31e05a415d76/dqc_reference/reference_markers.hmm GCF_014635205.1_ASM1463520v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:47,461] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:47,463] [INFO] Found 6/6 markers.
[2024-01-24 13:45:47,485] [INFO] Query marker FASTA was written to GCF_014635205.1_ASM1463520v1_genomic.fna/markers.fasta
[2024-01-24 13:45:47,485] [INFO] Task started: Blastn
[2024-01-24 13:45:47,486] [INFO] Running command: blastn -query GCF_014635205.1_ASM1463520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6343a4e-3878-449f-a2c0-31e05a415d76/dqc_reference/reference_markers.fasta -out GCF_014635205.1_ASM1463520v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:48,071] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:48,075] [INFO] Selected 12 target genomes.
[2024-01-24 13:45:48,076] [INFO] Target genome list was writen to GCF_014635205.1_ASM1463520v1_genomic.fna/target_genomes.txt
[2024-01-24 13:45:48,130] [INFO] Task started: fastANI
[2024-01-24 13:45:48,131] [INFO] Running command: fastANI --query /var/lib/cwl/stge12d63de-a04a-4dbe-9dc5-9bb0dcf45665/GCF_014635205.1_ASM1463520v1_genomic.fna.gz --refList GCF_014635205.1_ASM1463520v1_genomic.fna/target_genomes.txt --output GCF_014635205.1_ASM1463520v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:45:53,698] [INFO] Task succeeded: fastANI
[2024-01-24 13:45:53,699] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6343a4e-3878-449f-a2c0-31e05a415d76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:45:53,699] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6343a4e-3878-449f-a2c0-31e05a415d76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:45:53,711] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:45:53,712] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:45:53,712] [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 aerolatus	strain=CCM 7679	GCA_014635205.1	709510	709510	type	True	100.0	696	697	95	conclusive
Jeotgalicoccus aerolatus	strain=CIP 111750	GCA_903994055.1	709510	709510	type	True	99.9908	696	697	95	conclusive
Jeotgalicoccus aerolatus	strain=DSM 22420	GCA_017873755.1	709510	709510	type	True	99.9814	694	697	95	conclusive
Jeotgalicoccus halotolerans	strain=DSM 17274	GCA_003387165.1	157227	157227	type	True	83.156	513	697	95	below_threshold
Jeotgalicoccus psychrophilus	strain=DSM 19085	GCA_000425845.1	157228	157228	type	True	82.7351	532	697	95	below_threshold
Jeotgalicoccus coquinae	strain=CIP 111751	GCA_903994065.1	709509	709509	type	True	82.1732	525	697	95	below_threshold
Jeotgalicoccus saudimassiliensis	strain=13MG44_air	GCA_000756715.2	1461582	1461582	type	True	81.9799	506	697	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:45:53,714] [INFO] DFAST Taxonomy check result was written to GCF_014635205.1_ASM1463520v1_genomic.fna/tc_result.tsv
[2024-01-24 13:45:53,715] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:45:53,715] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:45:53,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6343a4e-3878-449f-a2c0-31e05a415d76/dqc_reference/checkm_data
[2024-01-24 13:45:53,718] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:45:53,747] [INFO] Task started: CheckM
[2024-01-24 13:45:53,747] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635205.1_ASM1463520v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635205.1_ASM1463520v1_genomic.fna/checkm_input GCF_014635205.1_ASM1463520v1_genomic.fna/checkm_result
[2024-01-24 13:46:15,183] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:15,184] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:15,203] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:15,203] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:15,203] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635205.1_ASM1463520v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:15,204] [INFO] Task started: Blastn
[2024-01-24 13:46:15,204] [INFO] Running command: blastn -query GCF_014635205.1_ASM1463520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6343a4e-3878-449f-a2c0-31e05a415d76/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635205.1_ASM1463520v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:16,270] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:16,273] [INFO] Selected 7 target genomes.
[2024-01-24 13:46:16,273] [INFO] Target genome list was writen to GCF_014635205.1_ASM1463520v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:16,285] [INFO] Task started: fastANI
[2024-01-24 13:46:16,285] [INFO] Running command: fastANI --query /var/lib/cwl/stge12d63de-a04a-4dbe-9dc5-9bb0dcf45665/GCF_014635205.1_ASM1463520v1_genomic.fna.gz --refList GCF_014635205.1_ASM1463520v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635205.1_ASM1463520v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:46:20,054] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:20,061] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:46:20,062] [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_014635205.1	s__Jeotgalicoccus aerolatus	100.0	696	697	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	99.67	99.03	0.98	0.93	4	conclusive
GCF_003387165.1	s__Jeotgalicoccus halotolerans	83.156	513	697	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	96.2898	N/A	N/A	N/A	N/A	1	-
GCA_004570955.1	s__Jeotgalicoccus nanhaiensis	82.7799	537	697	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	96.2898	99.28	98.57	0.98	0.96	3	-
GCF_000425845.1	s__Jeotgalicoccus psychrophilus	82.7351	532	697	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	97.52	97.52	0.90	0.90	2	-
GCA_003513765.1	s__Jeotgalicoccus sp003513765	82.4345	508	697	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207425.1	s__Jeotgalicoccus coquinae	82.1887	520	697	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000756715.1	s__Jeotgalicoccus saudimassiliensis	81.9799	506	697	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:46:20,064] [INFO] GTDB search result was written to GCF_014635205.1_ASM1463520v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:46:20,064] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:46:20,067] [INFO] DFAST_QC result json was written to GCF_014635205.1_ASM1463520v1_genomic.fna/dqc_result.json
[2024-01-24 13:46:20,067] [INFO] DFAST_QC completed!
[2024-01-24 13:46:20,068] [INFO] Total running time: 0h0m39s