[2024-01-25 19:36:20,598] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:36:20,600] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:36:20,600] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4cae1c3-0b7e-4f50-8273-b4b62ba63f43/dqc_reference
[2024-01-25 19:36:21,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:36:21,765] [INFO] Task started: Prodigal
[2024-01-25 19:36:21,765] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c962996-45eb-4f33-920f-2ff1fc0f9f36/GCF_000425845.1_ASM42584v1_genomic.fna.gz | prodigal -d GCF_000425845.1_ASM42584v1_genomic.fna/cds.fna -a GCF_000425845.1_ASM42584v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:36:26,163] [INFO] Task succeeded: Prodigal
[2024-01-25 19:36:26,164] [INFO] Task started: HMMsearch
[2024-01-25 19:36:26,164] [INFO] Running command: hmmsearch --tblout GCF_000425845.1_ASM42584v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4cae1c3-0b7e-4f50-8273-b4b62ba63f43/dqc_reference/reference_markers.hmm GCF_000425845.1_ASM42584v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:36:26,380] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:36:26,381] [INFO] Found 6/6 markers.
[2024-01-25 19:36:26,405] [INFO] Query marker FASTA was written to GCF_000425845.1_ASM42584v1_genomic.fna/markers.fasta
[2024-01-25 19:36:26,405] [INFO] Task started: Blastn
[2024-01-25 19:36:26,405] [INFO] Running command: blastn -query GCF_000425845.1_ASM42584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4cae1c3-0b7e-4f50-8273-b4b62ba63f43/dqc_reference/reference_markers.fasta -out GCF_000425845.1_ASM42584v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:26,961] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:26,964] [INFO] Selected 13 target genomes.
[2024-01-25 19:36:26,964] [INFO] Target genome list was writen to GCF_000425845.1_ASM42584v1_genomic.fna/target_genomes.txt
[2024-01-25 19:36:26,968] [INFO] Task started: fastANI
[2024-01-25 19:36:26,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c962996-45eb-4f33-920f-2ff1fc0f9f36/GCF_000425845.1_ASM42584v1_genomic.fna.gz --refList GCF_000425845.1_ASM42584v1_genomic.fna/target_genomes.txt --output GCF_000425845.1_ASM42584v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:36:33,709] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:33,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4cae1c3-0b7e-4f50-8273-b4b62ba63f43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:36:33,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4cae1c3-0b7e-4f50-8273-b4b62ba63f43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:36:33,718] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:36:33,718] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:36:33,719] [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 psychrophilus	strain=DSM 19085	GCA_000425845.1	157228	157228	type	True	99.9999	766	767	95	conclusive
Jeotgalicoccus coquinae	strain=DSM 22419	GCA_014207425.1	709509	709509	type	True	86.8216	609	767	95	below_threshold
Jeotgalicoccus coquinae	strain=CCM 7682	GCA_014635225.1	709509	709509	type	True	86.6765	618	767	95	below_threshold
Jeotgalicoccus coquinae	strain=CIP 111751	GCA_903994065.1	709509	709509	type	True	86.6102	628	767	95	below_threshold
Jeotgalicoccus halotolerans	strain=DSM 17274	GCA_003387165.1	157227	157227	type	True	85.0919	596	767	95	below_threshold
Jeotgalicoccus saudimassiliensis	strain=13MG44_air	GCA_000756715.2	1461582	1461582	type	True	84.887	605	767	95	below_threshold
Jeotgalicoccus aerolatus	strain=CIP 111750	GCA_903994055.1	709510	709510	type	True	82.7974	518	767	95	below_threshold
Jeotgalicoccus aerolatus	strain=DSM 22420	GCA_017873755.1	709510	709510	type	True	82.6819	544	767	95	below_threshold
Jeotgalicoccus aerolatus	strain=CCM 7679	GCA_014635205.1	709510	709510	type	True	82.6733	543	767	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:36:33,722] [INFO] DFAST Taxonomy check result was written to GCF_000425845.1_ASM42584v1_genomic.fna/tc_result.tsv
[2024-01-25 19:36:33,722] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:36:33,722] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:36:33,722] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4cae1c3-0b7e-4f50-8273-b4b62ba63f43/dqc_reference/checkm_data
[2024-01-25 19:36:33,723] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:36:33,758] [INFO] Task started: CheckM
[2024-01-25 19:36:33,758] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000425845.1_ASM42584v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000425845.1_ASM42584v1_genomic.fna/checkm_input GCF_000425845.1_ASM42584v1_genomic.fna/checkm_result
[2024-01-25 19:36:52,813] [INFO] Task succeeded: CheckM
[2024-01-25 19:36:52,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:36:52,865] [INFO] ===== Completeness check finished =====
[2024-01-25 19:36:52,865] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:36:52,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000425845.1_ASM42584v1_genomic.fna/markers.fasta)
[2024-01-25 19:36:52,865] [INFO] Task started: Blastn
[2024-01-25 19:36:52,865] [INFO] Running command: blastn -query GCF_000425845.1_ASM42584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4cae1c3-0b7e-4f50-8273-b4b62ba63f43/dqc_reference/reference_markers_gtdb.fasta -out GCF_000425845.1_ASM42584v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:53,632] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:53,635] [INFO] Selected 8 target genomes.
[2024-01-25 19:36:53,635] [INFO] Target genome list was writen to GCF_000425845.1_ASM42584v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:36:53,659] [INFO] Task started: fastANI
[2024-01-25 19:36:53,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c962996-45eb-4f33-920f-2ff1fc0f9f36/GCF_000425845.1_ASM42584v1_genomic.fna.gz --refList GCF_000425845.1_ASM42584v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000425845.1_ASM42584v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:36:58,159] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:58,164] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:36:58,165] [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_000425845.1	s__Jeotgalicoccus psychrophilus	99.9999	766	767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	97.52	97.52	0.90	0.90	2	conclusive
GCA_003513765.1	s__Jeotgalicoccus sp003513765	92.8895	625	767	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	86.8216	609	767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003387165.1	s__Jeotgalicoccus halotolerans	85.0919	596	767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	96.2898	N/A	N/A	N/A	N/A	1	-
GCF_000756715.1	s__Jeotgalicoccus saudimassiliensis	84.9042	604	767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004570955.1	s__Jeotgalicoccus nanhaiensis	84.8307	613	767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	96.2898	99.28	98.57	0.98	0.96	3	-
GCA_014635205.1	s__Jeotgalicoccus aerolatus	82.6584	544	767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	99.67	99.03	0.98	0.93	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:36:58,166] [INFO] GTDB search result was written to GCF_000425845.1_ASM42584v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:36:58,168] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:36:58,170] [INFO] DFAST_QC result json was written to GCF_000425845.1_ASM42584v1_genomic.fna/dqc_result.json
[2024-01-25 19:36:58,170] [INFO] DFAST_QC completed!
[2024-01-25 19:36:58,171] [INFO] Total running time: 0h0m38s