[2023-06-30 11:36:08,621] [INFO] DFAST_QC pipeline started.
[2023-06-30 11:36:08,623] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 11:36:08,623] [INFO] DQC Reference Directory: /var/lib/cwl/stgb10acf05-44f0-47f0-b35a-d7d209b5a848/dqc_reference
[2023-06-30 11:36:10,932] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 11:36:10,933] [INFO] Task started: Prodigal
[2023-06-30 11:36:10,933] [INFO] Running command: gunzip -c /var/lib/cwl/stg778da22a-e0d4-4a6e-b1c5-9c9d58a30306/GCA_943355005.1_MsH-01oct19-133_genomic.fna.gz | prodigal -d GCA_943355005.1_MsH-01oct19-133_genomic.fna/cds.fna -a GCA_943355005.1_MsH-01oct19-133_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 11:36:16,135] [INFO] Task succeeded: Prodigal
[2023-06-30 11:36:16,136] [INFO] Task started: HMMsearch
[2023-06-30 11:36:16,136] [INFO] Running command: hmmsearch --tblout GCA_943355005.1_MsH-01oct19-133_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb10acf05-44f0-47f0-b35a-d7d209b5a848/dqc_reference/reference_markers.hmm GCA_943355005.1_MsH-01oct19-133_genomic.fna/protein.faa > /dev/null
[2023-06-30 11:36:16,308] [INFO] Task succeeded: HMMsearch
[2023-06-30 11:36:16,310] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg778da22a-e0d4-4a6e-b1c5-9c9d58a30306/GCA_943355005.1_MsH-01oct19-133_genomic.fna.gz]
[2023-06-30 11:36:16,348] [INFO] Query marker FASTA was written to GCA_943355005.1_MsH-01oct19-133_genomic.fna/markers.fasta
[2023-06-30 11:36:16,348] [INFO] Task started: Blastn
[2023-06-30 11:36:16,349] [INFO] Running command: blastn -query GCA_943355005.1_MsH-01oct19-133_genomic.fna/markers.fasta -db /var/lib/cwl/stgb10acf05-44f0-47f0-b35a-d7d209b5a848/dqc_reference/reference_markers.fasta -out GCA_943355005.1_MsH-01oct19-133_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:36:16,942] [INFO] Task succeeded: Blastn
[2023-06-30 11:36:16,946] [INFO] Selected 12 target genomes.
[2023-06-30 11:36:16,946] [INFO] Target genome list was writen to GCA_943355005.1_MsH-01oct19-133_genomic.fna/target_genomes.txt
[2023-06-30 11:36:16,951] [INFO] Task started: fastANI
[2023-06-30 11:36:16,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg778da22a-e0d4-4a6e-b1c5-9c9d58a30306/GCA_943355005.1_MsH-01oct19-133_genomic.fna.gz --refList GCA_943355005.1_MsH-01oct19-133_genomic.fna/target_genomes.txt --output GCA_943355005.1_MsH-01oct19-133_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 11:36:22,131] [INFO] Task succeeded: fastANI
[2023-06-30 11:36:22,132] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb10acf05-44f0-47f0-b35a-d7d209b5a848/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 11:36:22,132] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb10acf05-44f0-47f0-b35a-d7d209b5a848/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 11:36:22,134] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 11:36:22,134] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 11:36:22,134] [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
--------------------------------------------------------------------------------
[2023-06-30 11:36:22,136] [INFO] DFAST Taxonomy check result was written to GCA_943355005.1_MsH-01oct19-133_genomic.fna/tc_result.tsv
[2023-06-30 11:36:22,137] [INFO] ===== Taxonomy check completed =====
[2023-06-30 11:36:22,137] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 11:36:22,137] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb10acf05-44f0-47f0-b35a-d7d209b5a848/dqc_reference/checkm_data
[2023-06-30 11:36:22,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 11:36:22,155] [INFO] Task started: CheckM
[2023-06-30 11:36:22,156] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_943355005.1_MsH-01oct19-133_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_943355005.1_MsH-01oct19-133_genomic.fna/checkm_input GCA_943355005.1_MsH-01oct19-133_genomic.fna/checkm_result
[2023-06-30 11:36:43,213] [INFO] Task succeeded: CheckM
[2023-06-30 11:36:43,214] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.49%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 11:36:43,231] [INFO] ===== Completeness check finished =====
[2023-06-30 11:36:43,232] [INFO] ===== Start GTDB Search =====
[2023-06-30 11:36:43,232] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_943355005.1_MsH-01oct19-133_genomic.fna/markers.fasta)
[2023-06-30 11:36:43,232] [INFO] Task started: Blastn
[2023-06-30 11:36:43,232] [INFO] Running command: blastn -query GCA_943355005.1_MsH-01oct19-133_genomic.fna/markers.fasta -db /var/lib/cwl/stgb10acf05-44f0-47f0-b35a-d7d209b5a848/dqc_reference/reference_markers_gtdb.fasta -out GCA_943355005.1_MsH-01oct19-133_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:36:43,955] [INFO] Task succeeded: Blastn
[2023-06-30 11:36:43,960] [INFO] Selected 16 target genomes.
[2023-06-30 11:36:43,960] [INFO] Target genome list was writen to GCA_943355005.1_MsH-01oct19-133_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 11:36:43,969] [INFO] Task started: fastANI
[2023-06-30 11:36:43,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg778da22a-e0d4-4a6e-b1c5-9c9d58a30306/GCA_943355005.1_MsH-01oct19-133_genomic.fna.gz --refList GCA_943355005.1_MsH-01oct19-133_genomic.fna/target_genomes_gtdb.txt --output GCA_943355005.1_MsH-01oct19-133_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 11:36:49,815] [INFO] Task succeeded: fastANI
[2023-06-30 11:36:49,820] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 11:36:49,820] [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_001774685.1	s__UBA10133 sp001774685	77.5169	75	407	d__Bacteria;p__Patescibacteria;c__Microgenomatia;o__UBA1400;f__MFAQ01;g__UBA10133	95.0	99.99	99.98	0.99	0.97	7	-
GCA_003531665.1	s__UBA10133 sp003531665	77.0253	51	407	d__Bacteria;p__Patescibacteria;c__Microgenomatia;o__UBA1400;f__MFAQ01;g__UBA10133	95.0	99.84	99.79	0.92	0.85	7	-
GCA_001000865.1	s__UBA10133 sp001000865	76.6199	63	407	d__Bacteria;p__Patescibacteria;c__Microgenomatia;o__UBA1400;f__MFAQ01;g__UBA10133	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 11:36:49,823] [INFO] GTDB search result was written to GCA_943355005.1_MsH-01oct19-133_genomic.fna/result_gtdb.tsv
[2023-06-30 11:36:49,824] [INFO] ===== GTDB Search completed =====
[2023-06-30 11:36:49,826] [INFO] DFAST_QC result json was written to GCA_943355005.1_MsH-01oct19-133_genomic.fna/dqc_result.json
[2023-06-30 11:36:49,827] [INFO] DFAST_QC completed!
[2023-06-30 11:36:49,827] [INFO] Total running time: 0h0m41s