[2024-01-24 12:46:35,298] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:35,301] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:35,301] [INFO] DQC Reference Directory: /var/lib/cwl/stg698a374d-0590-437a-8483-04f7656faa90/dqc_reference
[2024-01-24 12:46:36,463] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:36,464] [INFO] Task started: Prodigal
[2024-01-24 12:46:36,464] [INFO] Running command: gunzip -c /var/lib/cwl/stg29145bb8-c6a3-4d1a-9aff-3ad2f6082978/GCF_000018945.1_ASM1894v1_genomic.fna.gz | prodigal -d GCF_000018945.1_ASM1894v1_genomic.fna/cds.fna -a GCF_000018945.1_ASM1894v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:46:41,490] [INFO] Task succeeded: Prodigal
[2024-01-24 12:46:41,490] [INFO] Task started: HMMsearch
[2024-01-24 12:46:41,490] [INFO] Running command: hmmsearch --tblout GCF_000018945.1_ASM1894v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg698a374d-0590-437a-8483-04f7656faa90/dqc_reference/reference_markers.hmm GCF_000018945.1_ASM1894v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:46:41,696] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:46:41,697] [INFO] Found 6/6 markers.
[2024-01-24 12:46:41,720] [INFO] Query marker FASTA was written to GCF_000018945.1_ASM1894v1_genomic.fna/markers.fasta
[2024-01-24 12:46:41,720] [INFO] Task started: Blastn
[2024-01-24 12:46:41,720] [INFO] Running command: blastn -query GCF_000018945.1_ASM1894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg698a374d-0590-437a-8483-04f7656faa90/dqc_reference/reference_markers.fasta -out GCF_000018945.1_ASM1894v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:42,265] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:42,268] [INFO] Selected 14 target genomes.
[2024-01-24 12:46:42,269] [INFO] Target genome list was writen to GCF_000018945.1_ASM1894v1_genomic.fna/target_genomes.txt
[2024-01-24 12:46:42,298] [INFO] Task started: fastANI
[2024-01-24 12:46:42,298] [INFO] Running command: fastANI --query /var/lib/cwl/stg29145bb8-c6a3-4d1a-9aff-3ad2f6082978/GCF_000018945.1_ASM1894v1_genomic.fna.gz --refList GCF_000018945.1_ASM1894v1_genomic.fna/target_genomes.txt --output GCF_000018945.1_ASM1894v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:46:49,272] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:49,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg698a374d-0590-437a-8483-04f7656faa90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:46:49,273] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg698a374d-0590-437a-8483-04f7656faa90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:46:49,279] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:46:49,280] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:46:49,280] [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
Thermotoga neapolitana	strain=DSM 4359	GCA_000018945.1	2337	2337	type	True	100.0	628	628	95	conclusive
Thermotoga maritima	strain=MSB8	GCA_000390265.1	2336	2336	type	True	82.9171	398	628	95	below_threshold
Thermotoga maritima	strain=MSB8	GCA_000978555.1	2336	2336	type	True	82.9146	398	628	95	below_threshold
Thermotoga maritima	strain=MSB8	GCA_000230655.3	2336	2336	type	True	82.912	401	628	95	below_threshold
Thermotoga maritima	strain=MSB8	GCA_000008545.1	2336	2336	type	True	82.8421	397	628	95	below_threshold
Thermotoga petrophila	strain=RKU-1	GCA_000016785.1	93929	93929	type	True	81.8968	364	628	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:46:49,281] [INFO] DFAST Taxonomy check result was written to GCF_000018945.1_ASM1894v1_genomic.fna/tc_result.tsv
[2024-01-24 12:46:49,282] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:46:49,282] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:46:49,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg698a374d-0590-437a-8483-04f7656faa90/dqc_reference/checkm_data
[2024-01-24 12:46:49,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:46:49,302] [INFO] Task started: CheckM
[2024-01-24 12:46:49,303] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000018945.1_ASM1894v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000018945.1_ASM1894v1_genomic.fna/checkm_input GCF_000018945.1_ASM1894v1_genomic.fna/checkm_result
[2024-01-24 12:47:10,669] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:10,670] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:10,686] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:10,686] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:10,687] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000018945.1_ASM1894v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:10,687] [INFO] Task started: Blastn
[2024-01-24 12:47:10,687] [INFO] Running command: blastn -query GCF_000018945.1_ASM1894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg698a374d-0590-437a-8483-04f7656faa90/dqc_reference/reference_markers_gtdb.fasta -out GCF_000018945.1_ASM1894v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:11,449] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:11,452] [INFO] Selected 10 target genomes.
[2024-01-24 12:47:11,453] [INFO] Target genome list was writen to GCF_000018945.1_ASM1894v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:11,461] [INFO] Task started: fastANI
[2024-01-24 12:47:11,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg29145bb8-c6a3-4d1a-9aff-3ad2f6082978/GCF_000018945.1_ASM1894v1_genomic.fna.gz --refList GCF_000018945.1_ASM1894v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000018945.1_ASM1894v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:15,447] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:15,453] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:15,453] [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_000018945.1	s__Thermotoga neapolitana	100.0	628	628	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Thermotogaceae;g__Thermotoga	95.0	99.53	98.63	0.97	0.93	4	conclusive
GCF_002865985.1	s__Thermotoga sp002865985	90.4939	541	628	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Thermotogaceae;g__Thermotoga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000008545.1	s__Thermotoga maritima	82.8421	397	628	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Thermotogaceae;g__Thermotoga	95.1972	98.60	96.82	0.97	0.93	11	-
GCF_000016785.1	s__Thermotoga petrophila	81.8963	364	628	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Thermotogaceae;g__Thermotoga	95.1972	97.11	96.82	0.93	0.85	13	-
GCF_000784835.1	s__Thermotoga sp000784835	81.8227	372	628	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Thermotogaceae;g__Thermotoga	95.0	97.67	97.67	0.94	0.94	2	-
GCF_002866025.1	s__Thermotoga sp002866025	77.5055	168	628	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Thermotogaceae;g__Thermotoga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:15,455] [INFO] GTDB search result was written to GCF_000018945.1_ASM1894v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:15,456] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:15,459] [INFO] DFAST_QC result json was written to GCF_000018945.1_ASM1894v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:15,459] [INFO] DFAST_QC completed!
[2024-01-24 12:47:15,459] [INFO] Total running time: 0h0m40s