[2023-06-05 12:22:54,205] [INFO] DFAST_QC pipeline started.
[2023-06-05 12:22:54,208] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 12:22:54,208] [INFO] DQC Reference Directory: /var/lib/cwl/stg1da157d5-6cd9-43fc-b187-bc3cedf73bcc/dqc_reference
[2023-06-05 12:22:55,314] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 12:22:55,315] [INFO] Task started: Prodigal
[2023-06-05 12:22:55,315] [INFO] Running command: gunzip -c /var/lib/cwl/stg79e88994-544d-411b-945a-56d8944ec90e/GCA_934852095.1_MTG235_bin.43.fa_genomic.fna.gz | prodigal -d GCA_934852095.1_MTG235_bin.43.fa_genomic.fna/cds.fna -a GCA_934852095.1_MTG235_bin.43.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 12:22:59,038] [INFO] Task succeeded: Prodigal
[2023-06-05 12:22:59,038] [INFO] Task started: HMMsearch
[2023-06-05 12:22:59,038] [INFO] Running command: hmmsearch --tblout GCA_934852095.1_MTG235_bin.43.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1da157d5-6cd9-43fc-b187-bc3cedf73bcc/dqc_reference/reference_markers.hmm GCA_934852095.1_MTG235_bin.43.fa_genomic.fna/protein.faa > /dev/null
[2023-06-05 12:22:59,199] [INFO] Task succeeded: HMMsearch
[2023-06-05 12:22:59,200] [INFO] Found 6/6 markers.
[2023-06-05 12:22:59,215] [INFO] Query marker FASTA was written to GCA_934852095.1_MTG235_bin.43.fa_genomic.fna/markers.fasta
[2023-06-05 12:22:59,216] [INFO] Task started: Blastn
[2023-06-05 12:22:59,216] [INFO] Running command: blastn -query GCA_934852095.1_MTG235_bin.43.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg1da157d5-6cd9-43fc-b187-bc3cedf73bcc/dqc_reference/reference_markers.fasta -out GCA_934852095.1_MTG235_bin.43.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:22:59,923] [INFO] Task succeeded: Blastn
[2023-06-05 12:22:59,927] [INFO] Selected 29 target genomes.
[2023-06-05 12:22:59,927] [INFO] Target genome list was writen to GCA_934852095.1_MTG235_bin.43.fa_genomic.fna/target_genomes.txt
[2023-06-05 12:22:59,933] [INFO] Task started: fastANI
[2023-06-05 12:22:59,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg79e88994-544d-411b-945a-56d8944ec90e/GCA_934852095.1_MTG235_bin.43.fa_genomic.fna.gz --refList GCA_934852095.1_MTG235_bin.43.fa_genomic.fna/target_genomes.txt --output GCA_934852095.1_MTG235_bin.43.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 12:23:14,291] [INFO] Task succeeded: fastANI
[2023-06-05 12:23:14,291] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1da157d5-6cd9-43fc-b187-bc3cedf73bcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 12:23:14,292] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1da157d5-6cd9-43fc-b187-bc3cedf73bcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 12:23:14,293] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 12:23:14,293] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 12:23:14,293] [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
--------------------------------------------------------------------------------
[2023-06-05 12:23:14,295] [INFO] DFAST Taxonomy check result was written to GCA_934852095.1_MTG235_bin.43.fa_genomic.fna/tc_result.tsv
[2023-06-05 12:23:14,295] [INFO] ===== Taxonomy check completed =====
[2023-06-05 12:23:14,295] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 12:23:14,295] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1da157d5-6cd9-43fc-b187-bc3cedf73bcc/dqc_reference/checkm_data
[2023-06-05 12:23:14,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 12:23:14,326] [INFO] Task started: CheckM
[2023-06-05 12:23:14,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934852095.1_MTG235_bin.43.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934852095.1_MTG235_bin.43.fa_genomic.fna/checkm_input GCA_934852095.1_MTG235_bin.43.fa_genomic.fna/checkm_result
[2023-06-05 12:23:30,499] [INFO] Task succeeded: CheckM
[2023-06-05 12:23:30,500] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 12:23:30,514] [INFO] ===== Completeness check finished =====
[2023-06-05 12:23:30,514] [INFO] ===== Start GTDB Search =====
[2023-06-05 12:23:30,515] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934852095.1_MTG235_bin.43.fa_genomic.fna/markers.fasta)
[2023-06-05 12:23:30,515] [INFO] Task started: Blastn
[2023-06-05 12:23:30,515] [INFO] Running command: blastn -query GCA_934852095.1_MTG235_bin.43.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg1da157d5-6cd9-43fc-b187-bc3cedf73bcc/dqc_reference/reference_markers_gtdb.fasta -out GCA_934852095.1_MTG235_bin.43.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:23:31,888] [INFO] Task succeeded: Blastn
[2023-06-05 12:23:31,892] [INFO] Selected 6 target genomes.
[2023-06-05 12:23:31,892] [INFO] Target genome list was writen to GCA_934852095.1_MTG235_bin.43.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 12:23:31,896] [INFO] Task started: fastANI
[2023-06-05 12:23:31,896] [INFO] Running command: fastANI --query /var/lib/cwl/stg79e88994-544d-411b-945a-56d8944ec90e/GCA_934852095.1_MTG235_bin.43.fa_genomic.fna.gz --refList GCA_934852095.1_MTG235_bin.43.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934852095.1_MTG235_bin.43.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 12:23:34,499] [INFO] Task succeeded: fastANI
[2023-06-05 12:23:34,504] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 12:23:34,504] [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_900543625.1	s__CAG-103 sp900543625	97.0369	402	437	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	96.93	95.23	0.89	0.87	12	conclusive
GCA_900757655.1	s__CAG-103 sp900757655	90.5415	358	437	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	96.74	95.66	0.88	0.82	7	-
GCA_000432375.1	s__CAG-103 sp000432375	90.3567	337	437	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	98.15	97.87	0.87	0.82	10	-
GCA_900317855.1	s__CAG-103 sp900317855	90.179	357	437	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	97.11	95.56	0.88	0.84	11	-
GCA_004556965.1	s__CAG-103 sp004556965	80.257	240	437	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	98.49	98.32	0.91	0.88	6	-
GCA_018265835.1	s__CAG-103 sp018265835	80.195	247	437	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 12:23:34,506] [INFO] GTDB search result was written to GCA_934852095.1_MTG235_bin.43.fa_genomic.fna/result_gtdb.tsv
[2023-06-05 12:23:34,506] [INFO] ===== GTDB Search completed =====
[2023-06-05 12:23:34,509] [INFO] DFAST_QC result json was written to GCA_934852095.1_MTG235_bin.43.fa_genomic.fna/dqc_result.json
[2023-06-05 12:23:34,509] [INFO] DFAST_QC completed!
[2023-06-05 12:23:34,509] [INFO] Total running time: 0h0m40s