[2024-01-24 13:55:19,749] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:19,751] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:19,751] [INFO] DQC Reference Directory: /var/lib/cwl/stg276c43bd-98e3-435e-b92c-053da0c87b3f/dqc_reference
[2024-01-24 13:55:21,264] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:21,265] [INFO] Task started: Prodigal
[2024-01-24 13:55:21,265] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f7bc541-f4b5-49ea-9365-76744db62287/GCF_903994045.1_CIP111649_genomic.fna.gz | prodigal -d GCF_903994045.1_CIP111649_genomic.fna/cds.fna -a GCF_903994045.1_CIP111649_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:25,516] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:25,517] [INFO] Task started: HMMsearch
[2024-01-24 13:55:25,517] [INFO] Running command: hmmsearch --tblout GCF_903994045.1_CIP111649_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg276c43bd-98e3-435e-b92c-053da0c87b3f/dqc_reference/reference_markers.hmm GCF_903994045.1_CIP111649_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:25,791] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:25,793] [INFO] Found 6/6 markers.
[2024-01-24 13:55:25,820] [INFO] Query marker FASTA was written to GCF_903994045.1_CIP111649_genomic.fna/markers.fasta
[2024-01-24 13:55:25,820] [INFO] Task started: Blastn
[2024-01-24 13:55:25,821] [INFO] Running command: blastn -query GCF_903994045.1_CIP111649_genomic.fna/markers.fasta -db /var/lib/cwl/stg276c43bd-98e3-435e-b92c-053da0c87b3f/dqc_reference/reference_markers.fasta -out GCF_903994045.1_CIP111649_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:26,477] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:26,480] [INFO] Selected 12 target genomes.
[2024-01-24 13:55:26,480] [INFO] Target genome list was writen to GCF_903994045.1_CIP111649_genomic.fna/target_genomes.txt
[2024-01-24 13:55:26,486] [INFO] Task started: fastANI
[2024-01-24 13:55:26,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f7bc541-f4b5-49ea-9365-76744db62287/GCF_903994045.1_CIP111649_genomic.fna.gz --refList GCF_903994045.1_CIP111649_genomic.fna/target_genomes.txt --output GCF_903994045.1_CIP111649_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:31,848] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:31,849] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg276c43bd-98e3-435e-b92c-053da0c87b3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:31,849] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg276c43bd-98e3-435e-b92c-053da0c87b3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:31,857] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:31,857] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:31,857] [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 meleagridis	strain=CIP 111649	GCA_903994045.1	2759181	2759181	type	True	100.0	684	684	95	conclusive
Jeotgalicoccus marinus	strain=DSM 19772	GCA_000425825.1	516700	516700	type	True	80.1173	367	684	95	below_threshold
Jeotgalicoccus aerolatus	strain=CIP 111750	GCA_903994055.1	709510	709510	type	True	79.0628	224	684	95	below_threshold
Jeotgalicoccus aerolatus	strain=DSM 22420	GCA_017873755.1	709510	709510	type	True	78.9872	227	684	95	below_threshold
Jeotgalicoccus aerolatus	strain=CCM 7679	GCA_014635205.1	709510	709510	type	True	78.9328	233	684	95	below_threshold
Jeotgalicoccus psychrophilus	strain=DSM 19085	GCA_000425845.1	157228	157228	type	True	78.785	222	684	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:31,859] [INFO] DFAST Taxonomy check result was written to GCF_903994045.1_CIP111649_genomic.fna/tc_result.tsv
[2024-01-24 13:55:31,860] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:31,861] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:31,861] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg276c43bd-98e3-435e-b92c-053da0c87b3f/dqc_reference/checkm_data
[2024-01-24 13:55:31,863] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:31,887] [INFO] Task started: CheckM
[2024-01-24 13:55:31,887] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_903994045.1_CIP111649_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_903994045.1_CIP111649_genomic.fna/checkm_input GCF_903994045.1_CIP111649_genomic.fna/checkm_result
[2024-01-24 13:55:51,873] [INFO] Task succeeded: CheckM
[2024-01-24 13:55:51,875] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:55:51,894] [INFO] ===== Completeness check finished =====
[2024-01-24 13:55:51,895] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:55:51,895] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_903994045.1_CIP111649_genomic.fna/markers.fasta)
[2024-01-24 13:55:51,896] [INFO] Task started: Blastn
[2024-01-24 13:55:51,896] [INFO] Running command: blastn -query GCF_903994045.1_CIP111649_genomic.fna/markers.fasta -db /var/lib/cwl/stg276c43bd-98e3-435e-b92c-053da0c87b3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_903994045.1_CIP111649_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:52,751] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:52,755] [INFO] Selected 11 target genomes.
[2024-01-24 13:55:52,755] [INFO] Target genome list was writen to GCF_903994045.1_CIP111649_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:55:52,770] [INFO] Task started: fastANI
[2024-01-24 13:55:52,771] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f7bc541-f4b5-49ea-9365-76744db62287/GCF_903994045.1_CIP111649_genomic.fna.gz --refList GCF_903994045.1_CIP111649_genomic.fna/target_genomes_gtdb.txt --output GCF_903994045.1_CIP111649_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:55:57,386] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:57,396] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:55:57,397] [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_903994045.1	s__Jeotgalicoccus meleagridis	100.0	684	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	98.59	98.59	0.94	0.94	2	conclusive
GCF_000425825.1	s__Jeotgalicoccus marinus	80.0798	369	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	99.04	99.00	0.94	0.94	3	-
GCA_014635205.1	s__Jeotgalicoccus aerolatus	78.952	232	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	99.67	99.03	0.98	0.93	4	-
GCF_000425845.1	s__Jeotgalicoccus psychrophilus	78.7653	223	684	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	78.6808	194	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756715.1	s__Jeotgalicoccus saudimassiliensis	78.6571	203	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635565.1	s__Jeotgalicoccus_A schoeneichii	78.2721	78	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus_A	95.0	99.97	99.97	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:55:57,399] [INFO] GTDB search result was written to GCF_903994045.1_CIP111649_genomic.fna/result_gtdb.tsv
[2024-01-24 13:55:57,400] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:55:57,403] [INFO] DFAST_QC result json was written to GCF_903994045.1_CIP111649_genomic.fna/dqc_result.json
[2024-01-24 13:55:57,403] [INFO] DFAST_QC completed!
[2024-01-24 13:55:57,404] [INFO] Total running time: 0h0m38s