[2023-06-05 18:56:57,927] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:56:57,929] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:56:57,929] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a47502f-8417-4292-b6c6-e3de0c09f4f2/dqc_reference
[2023-06-05 18:56:59,059] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:56:59,060] [INFO] Task started: Prodigal
[2023-06-05 18:56:59,060] [INFO] Running command: gunzip -c /var/lib/cwl/stgc7ff87ce-3ab8-4f39-a746-92d43e55b445/GCA_934879375.1_MTG247_bin.38.fa_genomic.fna.gz | prodigal -d GCA_934879375.1_MTG247_bin.38.fa_genomic.fna/cds.fna -a GCA_934879375.1_MTG247_bin.38.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:57:02,397] [INFO] Task succeeded: Prodigal
[2023-06-05 18:57:02,397] [INFO] Task started: HMMsearch
[2023-06-05 18:57:02,398] [INFO] Running command: hmmsearch --tblout GCA_934879375.1_MTG247_bin.38.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a47502f-8417-4292-b6c6-e3de0c09f4f2/dqc_reference/reference_markers.hmm GCA_934879375.1_MTG247_bin.38.fa_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:57:02,578] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:57:02,579] [INFO] Found 6/6 markers.
[2023-06-05 18:57:02,597] [INFO] Query marker FASTA was written to GCA_934879375.1_MTG247_bin.38.fa_genomic.fna/markers.fasta
[2023-06-05 18:57:02,597] [INFO] Task started: Blastn
[2023-06-05 18:57:02,597] [INFO] Running command: blastn -query GCA_934879375.1_MTG247_bin.38.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a47502f-8417-4292-b6c6-e3de0c09f4f2/dqc_reference/reference_markers.fasta -out GCA_934879375.1_MTG247_bin.38.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:57:03,204] [INFO] Task succeeded: Blastn
[2023-06-05 18:57:03,208] [INFO] Selected 20 target genomes.
[2023-06-05 18:57:03,208] [INFO] Target genome list was writen to GCA_934879375.1_MTG247_bin.38.fa_genomic.fna/target_genomes.txt
[2023-06-05 18:57:03,213] [INFO] Task started: fastANI
[2023-06-05 18:57:03,213] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7ff87ce-3ab8-4f39-a746-92d43e55b445/GCA_934879375.1_MTG247_bin.38.fa_genomic.fna.gz --refList GCA_934879375.1_MTG247_bin.38.fa_genomic.fna/target_genomes.txt --output GCA_934879375.1_MTG247_bin.38.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:57:15,220] [INFO] Task succeeded: fastANI
[2023-06-05 18:57:15,220] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a47502f-8417-4292-b6c6-e3de0c09f4f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:57:15,220] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a47502f-8417-4292-b6c6-e3de0c09f4f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:57:15,222] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:57:15,222] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:57:15,222] [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 18:57:15,224] [INFO] DFAST Taxonomy check result was written to GCA_934879375.1_MTG247_bin.38.fa_genomic.fna/tc_result.tsv
[2023-06-05 18:57:15,224] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:57:15,224] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:57:15,224] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a47502f-8417-4292-b6c6-e3de0c09f4f2/dqc_reference/checkm_data
[2023-06-05 18:57:15,227] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:57:15,247] [INFO] Task started: CheckM
[2023-06-05 18:57:15,247] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934879375.1_MTG247_bin.38.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934879375.1_MTG247_bin.38.fa_genomic.fna/checkm_input GCA_934879375.1_MTG247_bin.38.fa_genomic.fna/checkm_result
[2023-06-05 18:57:30,812] [INFO] Task succeeded: CheckM
[2023-06-05 18:57:30,815] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:57:30,842] [INFO] ===== Completeness check finished =====
[2023-06-05 18:57:30,842] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:57:30,843] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934879375.1_MTG247_bin.38.fa_genomic.fna/markers.fasta)
[2023-06-05 18:57:30,843] [INFO] Task started: Blastn
[2023-06-05 18:57:30,843] [INFO] Running command: blastn -query GCA_934879375.1_MTG247_bin.38.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a47502f-8417-4292-b6c6-e3de0c09f4f2/dqc_reference/reference_markers_gtdb.fasta -out GCA_934879375.1_MTG247_bin.38.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:57:31,822] [INFO] Task succeeded: Blastn
[2023-06-05 18:57:31,825] [INFO] Selected 11 target genomes.
[2023-06-05 18:57:31,826] [INFO] Target genome list was writen to GCA_934879375.1_MTG247_bin.38.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:57:31,849] [INFO] Task started: fastANI
[2023-06-05 18:57:31,849] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7ff87ce-3ab8-4f39-a746-92d43e55b445/GCA_934879375.1_MTG247_bin.38.fa_genomic.fna.gz --refList GCA_934879375.1_MTG247_bin.38.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934879375.1_MTG247_bin.38.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:57:35,475] [INFO] Task succeeded: fastANI
[2023-06-05 18:57:35,482] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:57:35,482] [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_900549005.1	s__Coproplasma stercorigallinarum	97.1736	381	488	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	97.42	97.40	0.87	0.83	4	conclusive
GCA_018713165.1	s__Coproplasma stercoravium	81.4955	323	488	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	98.55	98.33	0.89	0.85	3	-
GCA_018712405.1	s__Coproplasma stercoripullorum	80.5702	259	488	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905207385.1	s__Coproplasma sp905207385	80.1042	195	488	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715195.1	s__Coproplasma excrementavium	80.0982	242	488	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	99.98	99.98	0.97	0.97	2	-
GCA_018714625.1	s__Coproplasma excrementigallinarum	80.0631	228	488	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	99.92	99.92	0.92	0.92	2	-
GCA_018711385.1	s__Coproplasma avistercoris	79.8533	213	488	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	98.46	98.39	0.92	0.92	3	-
GCA_910585705.1	s__Coproplasma sp910585705	77.2944	67	488	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578145.1	s__Coproplasma sp910578145	76.5267	80	488	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119395.1	s__Borkfalkia stercoripullorum	76.2814	50	488	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	99.97	99.97	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-05 18:57:35,484] [INFO] GTDB search result was written to GCA_934879375.1_MTG247_bin.38.fa_genomic.fna/result_gtdb.tsv
[2023-06-05 18:57:35,484] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:57:35,487] [INFO] DFAST_QC result json was written to GCA_934879375.1_MTG247_bin.38.fa_genomic.fna/dqc_result.json
[2023-06-05 18:57:35,487] [INFO] DFAST_QC completed!
[2023-06-05 18:57:35,487] [INFO] Total running time: 0h0m38s