[2023-06-17 14:17:51,622] [INFO] DFAST_QC pipeline started.
[2023-06-17 14:17:51,627] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 14:17:51,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg15096e14-70fa-4a22-bcb0-998846e56b5f/dqc_reference
[2023-06-17 14:17:54,784] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 14:17:54,785] [INFO] Task started: Prodigal
[2023-06-17 14:17:54,786] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b8651ae-12cd-4c1f-b621-3b2063941fac/GCA_028278545.1_ASM2827854v1_genomic.fna.gz | prodigal -d GCA_028278545.1_ASM2827854v1_genomic.fna/cds.fna -a GCA_028278545.1_ASM2827854v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 14:18:05,871] [INFO] Task succeeded: Prodigal
[2023-06-17 14:18:05,871] [INFO] Task started: HMMsearch
[2023-06-17 14:18:05,871] [INFO] Running command: hmmsearch --tblout GCA_028278545.1_ASM2827854v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15096e14-70fa-4a22-bcb0-998846e56b5f/dqc_reference/reference_markers.hmm GCA_028278545.1_ASM2827854v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 14:18:06,203] [INFO] Task succeeded: HMMsearch
[2023-06-17 14:18:06,204] [INFO] Found 6/6 markers.
[2023-06-17 14:18:06,238] [INFO] Query marker FASTA was written to GCA_028278545.1_ASM2827854v1_genomic.fna/markers.fasta
[2023-06-17 14:18:06,239] [INFO] Task started: Blastn
[2023-06-17 14:18:06,239] [INFO] Running command: blastn -query GCA_028278545.1_ASM2827854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15096e14-70fa-4a22-bcb0-998846e56b5f/dqc_reference/reference_markers.fasta -out GCA_028278545.1_ASM2827854v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:18:06,893] [INFO] Task succeeded: Blastn
[2023-06-17 14:18:06,897] [INFO] Selected 26 target genomes.
[2023-06-17 14:18:06,898] [INFO] Target genome list was writen to GCA_028278545.1_ASM2827854v1_genomic.fna/target_genomes.txt
[2023-06-17 14:18:06,901] [INFO] Task started: fastANI
[2023-06-17 14:18:06,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b8651ae-12cd-4c1f-b621-3b2063941fac/GCA_028278545.1_ASM2827854v1_genomic.fna.gz --refList GCA_028278545.1_ASM2827854v1_genomic.fna/target_genomes.txt --output GCA_028278545.1_ASM2827854v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 14:18:23,544] [INFO] Task succeeded: fastANI
[2023-06-17 14:18:23,544] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15096e14-70fa-4a22-bcb0-998846e56b5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 14:18:23,544] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15096e14-70fa-4a22-bcb0-998846e56b5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 14:18:23,549] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 14:18:23,549] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 14:18:23,549] [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
--------------------------------------------------------------------------------
[2023-06-17 14:18:23,552] [INFO] DFAST Taxonomy check result was written to GCA_028278545.1_ASM2827854v1_genomic.fna/tc_result.tsv
[2023-06-17 14:18:23,552] [INFO] ===== Taxonomy check completed =====
[2023-06-17 14:18:23,552] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 14:18:23,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15096e14-70fa-4a22-bcb0-998846e56b5f/dqc_reference/checkm_data
[2023-06-17 14:18:23,556] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 14:18:23,599] [INFO] Task started: CheckM
[2023-06-17 14:18:23,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028278545.1_ASM2827854v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028278545.1_ASM2827854v1_genomic.fna/checkm_input GCA_028278545.1_ASM2827854v1_genomic.fna/checkm_result
[2023-06-17 14:19:00,274] [INFO] Task succeeded: CheckM
[2023-06-17 14:19:00,275] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 14:19:00,295] [INFO] ===== Completeness check finished =====
[2023-06-17 14:19:00,295] [INFO] ===== Start GTDB Search =====
[2023-06-17 14:19:00,296] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028278545.1_ASM2827854v1_genomic.fna/markers.fasta)
[2023-06-17 14:19:00,296] [INFO] Task started: Blastn
[2023-06-17 14:19:00,296] [INFO] Running command: blastn -query GCA_028278545.1_ASM2827854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15096e14-70fa-4a22-bcb0-998846e56b5f/dqc_reference/reference_markers_gtdb.fasta -out GCA_028278545.1_ASM2827854v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:19:01,145] [INFO] Task succeeded: Blastn
[2023-06-17 14:19:01,151] [INFO] Selected 24 target genomes.
[2023-06-17 14:19:01,151] [INFO] Target genome list was writen to GCA_028278545.1_ASM2827854v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 14:19:01,171] [INFO] Task started: fastANI
[2023-06-17 14:19:01,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b8651ae-12cd-4c1f-b621-3b2063941fac/GCA_028278545.1_ASM2827854v1_genomic.fna.gz --refList GCA_028278545.1_ASM2827854v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028278545.1_ASM2827854v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 14:19:14,427] [INFO] Task succeeded: fastANI
[2023-06-17 14:19:14,437] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 14:19:14,438] [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_016783125.1	s__NIOZ-UU35 sp016783125	78.9646	485	1221	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11858;g__NIOZ-UU35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016865865.1	s__NIOZ-UU35 sp016865865	78.1462	334	1221	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11858;g__NIOZ-UU35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016785015.1	s__NIOZ-UU35 sp016785015	77.4454	284	1221	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11858;g__NIOZ-UU35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015485245.1	s__J130 sp015485245	76.4883	75	1221	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11858;g__J130	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003694235.1	s__J130 sp003694235	76.2972	60	1221	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11858;g__J130	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018648225.1	s__NIOZ-UU35 sp018648225	76.1621	125	1221	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11858;g__NIOZ-UU35	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 14:19:14,440] [INFO] GTDB search result was written to GCA_028278545.1_ASM2827854v1_genomic.fna/result_gtdb.tsv
[2023-06-17 14:19:14,440] [INFO] ===== GTDB Search completed =====
[2023-06-17 14:19:14,443] [INFO] DFAST_QC result json was written to GCA_028278545.1_ASM2827854v1_genomic.fna/dqc_result.json
[2023-06-17 14:19:14,443] [INFO] DFAST_QC completed!
[2023-06-17 14:19:14,444] [INFO] Total running time: 0h1m23s