[2023-06-29 13:07:25,117] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:07:25,119] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:07:25,119] [INFO] DQC Reference Directory: /var/lib/cwl/stg25ad01fb-548e-49f9-9f36-f989d030a629/dqc_reference
[2023-06-29 13:07:26,407] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:07:26,408] [INFO] Task started: Prodigal
[2023-06-29 13:07:26,408] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf016f85-c3df-4ab3-80c7-e0af634c7d07/GCA_023439005.1_ASM2343900v1_genomic.fna.gz | prodigal -d GCA_023439005.1_ASM2343900v1_genomic.fna/cds.fna -a GCA_023439005.1_ASM2343900v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:07:28,633] [INFO] Task succeeded: Prodigal
[2023-06-29 13:07:28,633] [INFO] Task started: HMMsearch
[2023-06-29 13:07:28,633] [INFO] Running command: hmmsearch --tblout GCA_023439005.1_ASM2343900v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25ad01fb-548e-49f9-9f36-f989d030a629/dqc_reference/reference_markers.hmm GCA_023439005.1_ASM2343900v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:07:28,816] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:07:28,817] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgdf016f85-c3df-4ab3-80c7-e0af634c7d07/GCA_023439005.1_ASM2343900v1_genomic.fna.gz]
[2023-06-29 13:07:28,835] [INFO] Query marker FASTA was written to GCA_023439005.1_ASM2343900v1_genomic.fna/markers.fasta
[2023-06-29 13:07:28,835] [INFO] Task started: Blastn
[2023-06-29 13:07:28,836] [INFO] Running command: blastn -query GCA_023439005.1_ASM2343900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25ad01fb-548e-49f9-9f36-f989d030a629/dqc_reference/reference_markers.fasta -out GCA_023439005.1_ASM2343900v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:07:29,438] [INFO] Task succeeded: Blastn
[2023-06-29 13:07:29,442] [INFO] Selected 7 target genomes.
[2023-06-29 13:07:29,443] [INFO] Target genome list was writen to GCA_023439005.1_ASM2343900v1_genomic.fna/target_genomes.txt
[2023-06-29 13:07:29,445] [INFO] Task started: fastANI
[2023-06-29 13:07:29,446] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf016f85-c3df-4ab3-80c7-e0af634c7d07/GCA_023439005.1_ASM2343900v1_genomic.fna.gz --refList GCA_023439005.1_ASM2343900v1_genomic.fna/target_genomes.txt --output GCA_023439005.1_ASM2343900v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:07:33,554] [INFO] Task succeeded: fastANI
[2023-06-29 13:07:33,554] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25ad01fb-548e-49f9-9f36-f989d030a629/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:07:33,555] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25ad01fb-548e-49f9-9f36-f989d030a629/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:07:33,556] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:07:33,557] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 13:07:33,557] [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
--------------------------------------------------------------------------------
[2023-06-29 13:07:33,558] [INFO] DFAST Taxonomy check result was written to GCA_023439005.1_ASM2343900v1_genomic.fna/tc_result.tsv
[2023-06-29 13:07:33,559] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:07:33,559] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:07:33,559] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25ad01fb-548e-49f9-9f36-f989d030a629/dqc_reference/checkm_data
[2023-06-29 13:07:33,562] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:07:33,580] [INFO] Task started: CheckM
[2023-06-29 13:07:33,580] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023439005.1_ASM2343900v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023439005.1_ASM2343900v1_genomic.fna/checkm_input GCA_023439005.1_ASM2343900v1_genomic.fna/checkm_result
[2023-06-29 13:07:48,636] [INFO] Task succeeded: CheckM
[2023-06-29 13:07:48,637] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.36%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 13:07:48,656] [INFO] ===== Completeness check finished =====
[2023-06-29 13:07:48,657] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:07:48,657] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023439005.1_ASM2343900v1_genomic.fna/markers.fasta)
[2023-06-29 13:07:48,658] [INFO] Task started: Blastn
[2023-06-29 13:07:48,658] [INFO] Running command: blastn -query GCA_023439005.1_ASM2343900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25ad01fb-548e-49f9-9f36-f989d030a629/dqc_reference/reference_markers_gtdb.fasta -out GCA_023439005.1_ASM2343900v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:07:49,396] [INFO] Task succeeded: Blastn
[2023-06-29 13:07:49,407] [INFO] Selected 6 target genomes.
[2023-06-29 13:07:49,407] [INFO] Target genome list was writen to GCA_023439005.1_ASM2343900v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:07:49,412] [INFO] Task started: fastANI
[2023-06-29 13:07:49,412] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf016f85-c3df-4ab3-80c7-e0af634c7d07/GCA_023439005.1_ASM2343900v1_genomic.fna.gz --refList GCA_023439005.1_ASM2343900v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023439005.1_ASM2343900v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:07:51,554] [INFO] Task succeeded: fastANI
[2023-06-29 13:07:51,561] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 13:07:51,561] [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
GCA_900769355.1	s__Stercorousia sp900769355	97.7688	223	262	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900767135.1	s__Stercorousia sp900767135	91.2738	209	262	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900769645.1	s__Stercorousia sp900769645	91.1563	229	262	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556295.1	s__Stercorousia sp900556295	82.6765	137	262	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	97.71	97.55	0.83	0.77	3	-
GCA_001765415.1	s__Stercorousia sp001765415	80.428	179	262	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	98.74	98.70	0.94	0.93	5	-
GCA_910588555.1	s__Stercorousia sp910588555	77.5402	107	262	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 13:07:51,569] [INFO] GTDB search result was written to GCA_023439005.1_ASM2343900v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:07:51,570] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:07:51,574] [INFO] DFAST_QC result json was written to GCA_023439005.1_ASM2343900v1_genomic.fna/dqc_result.json
[2023-06-29 13:07:51,574] [INFO] DFAST_QC completed!
[2023-06-29 13:07:51,575] [INFO] Total running time: 0h0m26s