[2023-06-07 22:13:22,555] [INFO] DFAST_QC pipeline started.
[2023-06-07 22:13:22,558] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 22:13:22,558] [INFO] DQC Reference Directory: /var/lib/cwl/stg1936bb6a-ed46-4aa4-a69e-440df612d8e7/dqc_reference
[2023-06-07 22:13:23,795] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 22:13:23,796] [INFO] Task started: Prodigal
[2023-06-07 22:13:23,796] [INFO] Running command: gunzip -c /var/lib/cwl/stg729cb252-d2dd-4f4d-aceb-9aad5e28073e/GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna.gz | prodigal -d GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna/cds.fna -a GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 22:13:25,980] [INFO] Task succeeded: Prodigal
[2023-06-07 22:13:25,980] [INFO] Task started: HMMsearch
[2023-06-07 22:13:25,980] [INFO] Running command: hmmsearch --tblout GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1936bb6a-ed46-4aa4-a69e-440df612d8e7/dqc_reference/reference_markers.hmm GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna/protein.faa > /dev/null
[2023-06-07 22:13:26,145] [INFO] Task succeeded: HMMsearch
[2023-06-07 22:13:26,147] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg729cb252-d2dd-4f4d-aceb-9aad5e28073e/GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna.gz]
[2023-06-07 22:13:26,164] [INFO] Query marker FASTA was written to GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna/markers.fasta
[2023-06-07 22:13:26,164] [INFO] Task started: Blastn
[2023-06-07 22:13:26,164] [INFO] Running command: blastn -query GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna/markers.fasta -db /var/lib/cwl/stg1936bb6a-ed46-4aa4-a69e-440df612d8e7/dqc_reference/reference_markers.fasta -out GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:13:26,722] [INFO] Task succeeded: Blastn
[2023-06-07 22:13:26,726] [INFO] Selected 23 target genomes.
[2023-06-07 22:13:26,726] [INFO] Target genome list was writen to GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna/target_genomes.txt
[2023-06-07 22:13:26,730] [INFO] Task started: fastANI
[2023-06-07 22:13:26,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg729cb252-d2dd-4f4d-aceb-9aad5e28073e/GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna.gz --refList GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna/target_genomes.txt --output GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 22:13:35,234] [INFO] Task succeeded: fastANI
[2023-06-07 22:13:35,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1936bb6a-ed46-4aa4-a69e-440df612d8e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 22:13:35,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1936bb6a-ed46-4aa4-a69e-440df612d8e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 22:13:35,239] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 22:13:35,240] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 22:13:35,240] [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
Clostridium ihumii	strain=AP5	GCA_000612845.1	1470356	1470356	type	True	74.8379	64	430	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_000473995.1	169679	169679	type	True	74.6756	53	430	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 22:13:35,246] [INFO] DFAST Taxonomy check result was written to GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna/tc_result.tsv
[2023-06-07 22:13:35,252] [INFO] ===== Taxonomy check completed =====
[2023-06-07 22:13:35,252] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 22:13:35,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1936bb6a-ed46-4aa4-a69e-440df612d8e7/dqc_reference/checkm_data
[2023-06-07 22:13:35,253] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 22:13:35,270] [INFO] Task started: CheckM
[2023-06-07 22:13:35,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna/checkm_input GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna/checkm_result
[2023-06-07 22:13:49,361] [INFO] Task succeeded: CheckM
[2023-06-07 22:13:49,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 22:13:49,378] [INFO] ===== Completeness check finished =====
[2023-06-07 22:13:49,378] [INFO] ===== Start GTDB Search =====
[2023-06-07 22:13:49,378] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna/markers.fasta)
[2023-06-07 22:13:49,379] [INFO] Task started: Blastn
[2023-06-07 22:13:49,379] [INFO] Running command: blastn -query GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna/markers.fasta -db /var/lib/cwl/stg1936bb6a-ed46-4aa4-a69e-440df612d8e7/dqc_reference/reference_markers_gtdb.fasta -out GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:13:50,141] [INFO] Task succeeded: Blastn
[2023-06-07 22:13:50,145] [INFO] Selected 14 target genomes.
[2023-06-07 22:13:50,145] [INFO] Target genome list was writen to GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 22:13:50,151] [INFO] Task started: fastANI
[2023-06-07 22:13:50,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg729cb252-d2dd-4f4d-aceb-9aad5e28073e/GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna.gz --refList GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna/target_genomes_gtdb.txt --output GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 22:13:53,674] [INFO] Task succeeded: fastANI
[2023-06-07 22:13:53,686] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 22:13:53,687] [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_003507395.1	s__CAG-273 sp003507395	99.9629	423	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	99.04	98.89	0.89	0.87	5	conclusive
GCA_003534295.1	s__CAG-273 sp003534295	82.9296	295	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	98.76	98.52	0.84	0.83	5	-
GCA_000437855.1	s__CAG-273 sp000437855	78.981	159	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	98.80	98.79	0.86	0.86	3	-
GCA_017937285.1	s__CAG-492 sp017937285	78.2624	136	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000438355.1	s__CAG-273 sp000438355	78.2591	149	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	98.50	98.37	0.86	0.79	3	-
GCA_900753245.1	s__UMGS1663 sp900753245	78.1246	140	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1663	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214245.1	s__CAG-273 sp905214245	77.8854	125	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905198755.1	s__HGM13634 sp905198755	77.7479	112	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__HGM13634	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000434035.1	s__CAG-452 sp000434035	77.7269	123	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-452	95.0	98.46	98.21	0.89	0.89	3	-
GCA_905215615.1	s__CAG-273 sp905215615	77.5711	83	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553405.1	s__UMGS1663 sp900553405	77.4393	154	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1663	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017469445.1	s__UMGS1864 sp017469445	77.4239	104	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1864	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017886645.1	s__CAG-273 sp017886645	77.2005	146	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000437215.1	s__CAG-269 sp000437215	76.9613	131	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.98	98.94	0.85	0.85	3	-
--------------------------------------------------------------------------------
[2023-06-07 22:13:53,689] [INFO] GTDB search result was written to GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna/result_gtdb.tsv
[2023-06-07 22:13:53,690] [INFO] ===== GTDB Search completed =====
[2023-06-07 22:13:53,693] [INFO] DFAST_QC result json was written to GCA_902461835.1_UHGG-TPA_MGYG-HGUT-00372_genomic.fna/dqc_result.json
[2023-06-07 22:13:53,693] [INFO] DFAST_QC completed!
[2023-06-07 22:13:53,693] [INFO] Total running time: 0h0m31s