[2024-01-24 13:49:00,142] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:00,144] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:00,145] [INFO] DQC Reference Directory: /var/lib/cwl/stg090d6bc5-395e-4f88-a5c1-bc0bfb22e650/dqc_reference
[2024-01-24 13:49:01,466] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,467] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,467] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd384439-0c97-4fbc-972f-184f046e497f/GCF_024022995.1_ASM2402299v1_genomic.fna.gz | prodigal -d GCF_024022995.1_ASM2402299v1_genomic.fna/cds.fna -a GCF_024022995.1_ASM2402299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:05,788] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:05,789] [INFO] Task started: HMMsearch
[2024-01-24 13:49:05,789] [INFO] Running command: hmmsearch --tblout GCF_024022995.1_ASM2402299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg090d6bc5-395e-4f88-a5c1-bc0bfb22e650/dqc_reference/reference_markers.hmm GCF_024022995.1_ASM2402299v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:05,993] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:05,994] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgcd384439-0c97-4fbc-972f-184f046e497f/GCF_024022995.1_ASM2402299v1_genomic.fna.gz]
[2024-01-24 13:49:06,013] [INFO] Query marker FASTA was written to GCF_024022995.1_ASM2402299v1_genomic.fna/markers.fasta
[2024-01-24 13:49:06,014] [INFO] Task started: Blastn
[2024-01-24 13:49:06,014] [INFO] Running command: blastn -query GCF_024022995.1_ASM2402299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg090d6bc5-395e-4f88-a5c1-bc0bfb22e650/dqc_reference/reference_markers.fasta -out GCF_024022995.1_ASM2402299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:06,504] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:06,507] [INFO] Selected 7 target genomes.
[2024-01-24 13:49:06,508] [INFO] Target genome list was writen to GCF_024022995.1_ASM2402299v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:06,556] [INFO] Task started: fastANI
[2024-01-24 13:49:06,556] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd384439-0c97-4fbc-972f-184f046e497f/GCF_024022995.1_ASM2402299v1_genomic.fna.gz --refList GCF_024022995.1_ASM2402299v1_genomic.fna/target_genomes.txt --output GCF_024022995.1_ASM2402299v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:09,411] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:09,412] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg090d6bc5-395e-4f88-a5c1-bc0bfb22e650/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:09,412] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg090d6bc5-395e-4f88-a5c1-bc0bfb22e650/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:09,419] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:09,420] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:09,420] [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
Thermococcus aggregans	strain=TY	GCA_024022995.1	110163	110163	type	True	100.0	629	629	95	conclusive
Thermococcus alcaliphilus	strain=AEDII12	GCA_024054535.1	139207	139207	type	True	81.4599	394	629	95	below_threshold
Thermococcus litoralis	strain=DSM 5473	GCA_000246985.3	2265	2265	type	True	81.0908	426	629	95	below_threshold
Thermococcus sibiricus	strain=MM 739	GCA_000022545.1	172049	172049	type	True	80.899	298	629	95	below_threshold
Thermococcus bergensis	strain=T7324	GCA_020386975.1	2689387	2689387	type	True	80.5223	391	629	95	below_threshold
Thermococcus paralvinellae	strain=ES1	GCA_000517445.1	582419	582419	type	True	77.5475	125	629	95	below_threshold
Thermococcus peptonophilus	strain=OG-1	GCA_001592435.1	53952	53952	type	True	77.3665	60	629	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:09,421] [INFO] DFAST Taxonomy check result was written to GCF_024022995.1_ASM2402299v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:09,422] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:09,422] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:09,422] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg090d6bc5-395e-4f88-a5c1-bc0bfb22e650/dqc_reference/checkm_data
[2024-01-24 13:49:09,423] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:09,449] [INFO] Task started: CheckM
[2024-01-24 13:49:09,449] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024022995.1_ASM2402299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024022995.1_ASM2402299v1_genomic.fna/checkm_input GCF_024022995.1_ASM2402299v1_genomic.fna/checkm_result
[2024-01-24 13:49:29,510] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:29,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:29,530] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:29,531] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:29,531] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024022995.1_ASM2402299v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:29,532] [INFO] Task started: Blastn
[2024-01-24 13:49:29,532] [INFO] Running command: blastn -query GCF_024022995.1_ASM2402299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg090d6bc5-395e-4f88-a5c1-bc0bfb22e650/dqc_reference/reference_markers_gtdb.fasta -out GCF_024022995.1_ASM2402299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:30,063] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:30,067] [INFO] Selected 8 target genomes.
[2024-01-24 13:49:30,067] [INFO] Target genome list was writen to GCF_024022995.1_ASM2402299v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:30,126] [INFO] Task started: fastANI
[2024-01-24 13:49:30,127] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd384439-0c97-4fbc-972f-184f046e497f/GCF_024022995.1_ASM2402299v1_genomic.fna.gz --refList GCF_024022995.1_ASM2402299v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024022995.1_ASM2402299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:33,541] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:33,552] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:49:33,553] [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_000246985.2	s__Thermococcus_A litoralis	81.0908	426	629	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A	95.0	96.93	96.93	0.89	0.89	2	-
GCF_000022545.1	s__Thermococcus_A sibiricus	80.899	298	629	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A	95.0	98.36	98.17	0.89	0.84	5	-
GCF_001484685.1	s__Thermococcus_A sp001484685	80.7812	373	629	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A	95.0	98.39	98.39	0.89	0.89	2	-
GCA_003663525.1	s__Thermococcus_A sp003663525	80.5729	198	629	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A	95.0	98.62	98.62	0.75	0.75	2	-
GCF_000430485.1	s__Thermococcus_A sp000430485	80.5384	392	629	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A	95.0	96.03	95.46	0.86	0.83	4	-
GCF_000517445.1	s__Thermococcus_B paralvinellae	77.5046	125	629	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017656495.1	s__Thermococcus_B sp017656495	77.4293	112	629	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592435.1	s__Thermococcus peptonophilus	77.3207	61	629	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	99.53	99.53	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:33,554] [INFO] GTDB search result was written to GCF_024022995.1_ASM2402299v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:33,555] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:33,558] [INFO] DFAST_QC result json was written to GCF_024022995.1_ASM2402299v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:33,558] [INFO] DFAST_QC completed!
[2024-01-24 13:49:33,559] [INFO] Total running time: 0h0m33s