[2023-06-05 18:50:30,439] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:50:30,448] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:50:30,448] [INFO] DQC Reference Directory: /var/lib/cwl/stg053f62f1-b156-4390-b13a-c0c5bdbd48a3/dqc_reference
[2023-06-05 18:50:31,745] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:50:31,746] [INFO] Task started: Prodigal
[2023-06-05 18:50:31,746] [INFO] Running command: gunzip -c /var/lib/cwl/stg9bd4fe0f-effc-4708-a29c-35cc30205357/GCA_001508175.1_ASM150817v1_genomic.fna.gz | prodigal -d GCA_001508175.1_ASM150817v1_genomic.fna/cds.fna -a GCA_001508175.1_ASM150817v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:50:34,938] [INFO] Task succeeded: Prodigal
[2023-06-05 18:50:34,939] [INFO] Task started: HMMsearch
[2023-06-05 18:50:34,939] [INFO] Running command: hmmsearch --tblout GCA_001508175.1_ASM150817v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg053f62f1-b156-4390-b13a-c0c5bdbd48a3/dqc_reference/reference_markers.hmm GCA_001508175.1_ASM150817v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:50:35,268] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:50:35,269] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg9bd4fe0f-effc-4708-a29c-35cc30205357/GCA_001508175.1_ASM150817v1_genomic.fna.gz]
[2023-06-05 18:50:35,296] [INFO] Query marker FASTA was written to GCA_001508175.1_ASM150817v1_genomic.fna/markers.fasta
[2023-06-05 18:50:35,297] [INFO] Task started: Blastn
[2023-06-05 18:50:35,297] [INFO] Running command: blastn -query GCA_001508175.1_ASM150817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg053f62f1-b156-4390-b13a-c0c5bdbd48a3/dqc_reference/reference_markers.fasta -out GCA_001508175.1_ASM150817v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:50:37,505] [INFO] Task succeeded: Blastn
[2023-06-05 18:50:37,520] [INFO] Selected 5 target genomes.
[2023-06-05 18:50:37,520] [INFO] Target genome list was writen to GCA_001508175.1_ASM150817v1_genomic.fna/target_genomes.txt
[2023-06-05 18:50:37,523] [INFO] Task started: fastANI
[2023-06-05 18:50:37,523] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bd4fe0f-effc-4708-a29c-35cc30205357/GCA_001508175.1_ASM150817v1_genomic.fna.gz --refList GCA_001508175.1_ASM150817v1_genomic.fna/target_genomes.txt --output GCA_001508175.1_ASM150817v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:50:43,829] [INFO] Task succeeded: fastANI
[2023-06-05 18:50:43,830] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg053f62f1-b156-4390-b13a-c0c5bdbd48a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:50:43,830] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg053f62f1-b156-4390-b13a-c0c5bdbd48a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:50:43,835] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2023-06-05 18:50:43,835] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 18:50:43,835] [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 sibiricus	strain=MM 739	GCA_000022545.1	172049	172049	type	True	98.5366	413	439	95	conclusive
Thermococcus aggregans	strain=TY	GCA_024022995.1	110163	110163	type	True	80.897	225	439	95	below_threshold
Thermococcus alcaliphilus	strain=AEDII12	GCA_024054535.1	139207	139207	type	True	78.2746	187	439	95	below_threshold
Thermococcus litoralis	strain=DSM 5473	GCA_000246985.3	2265	2265	type	True	78.2732	187	439	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:50:43,838] [INFO] DFAST Taxonomy check result was written to GCA_001508175.1_ASM150817v1_genomic.fna/tc_result.tsv
[2023-06-05 18:50:43,838] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:50:43,839] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:50:43,839] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg053f62f1-b156-4390-b13a-c0c5bdbd48a3/dqc_reference/checkm_data
[2023-06-05 18:50:43,840] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:50:43,859] [INFO] Task started: CheckM
[2023-06-05 18:50:43,859] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001508175.1_ASM150817v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001508175.1_ASM150817v1_genomic.fna/checkm_input GCA_001508175.1_ASM150817v1_genomic.fna/checkm_result
[2023-06-05 18:51:24,954] [INFO] Task succeeded: CheckM
[2023-06-05 18:51:24,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:51:25,075] [INFO] ===== Completeness check finished =====
[2023-06-05 18:51:25,076] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:51:25,076] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001508175.1_ASM150817v1_genomic.fna/markers.fasta)
[2023-06-05 18:51:25,076] [INFO] Task started: Blastn
[2023-06-05 18:51:25,077] [INFO] Running command: blastn -query GCA_001508175.1_ASM150817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg053f62f1-b156-4390-b13a-c0c5bdbd48a3/dqc_reference/reference_markers_gtdb.fasta -out GCA_001508175.1_ASM150817v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:51:25,845] [INFO] Task succeeded: Blastn
[2023-06-05 18:51:25,850] [INFO] Selected 6 target genomes.
[2023-06-05 18:51:25,851] [INFO] Target genome list was writen to GCA_001508175.1_ASM150817v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:51:25,862] [INFO] Task started: fastANI
[2023-06-05 18:51:25,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bd4fe0f-effc-4708-a29c-35cc30205357/GCA_001508175.1_ASM150817v1_genomic.fna.gz --refList GCA_001508175.1_ASM150817v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001508175.1_ASM150817v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:51:29,014] [INFO] Task succeeded: fastANI
[2023-06-05 18:51:29,023] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:51:29,023] [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_000022545.1	s__Thermococcus_A sibiricus	98.5366	413	439	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	conclusive
GCA_003663535.1	s__Thermococcus_A sp003663535	91.7461	231	439	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003663525.1	s__Thermococcus_A sp003663525	91.7379	263	439	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_000246985.2	s__Thermococcus_A litoralis	78.2732	187	439	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_001484685.1	s__Thermococcus_A sp001484685	78.1126	167	439	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_017656495.1	s__Thermococcus_B sp017656495	77.8979	77	439	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	-
--------------------------------------------------------------------------------
[2023-06-05 18:51:29,026] [INFO] GTDB search result was written to GCA_001508175.1_ASM150817v1_genomic.fna/result_gtdb.tsv
[2023-06-05 18:51:29,026] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:51:29,029] [INFO] DFAST_QC result json was written to GCA_001508175.1_ASM150817v1_genomic.fna/dqc_result.json
[2023-06-05 18:51:29,030] [INFO] DFAST_QC completed!
[2023-06-05 18:51:29,030] [INFO] Total running time: 0h0m59s