[2023-06-13 10:50:09,763] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:50:09,765] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:50:09,765] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b8e53c5-eea5-42b1-806a-a632c007aea1/dqc_reference
[2023-06-13 10:50:11,327] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:50:11,328] [INFO] Task started: Prodigal
[2023-06-13 10:50:11,328] [INFO] Running command: gunzip -c /var/lib/cwl/stg59854f9d-f81d-4875-9d27-bc75b38af4ca/GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:50:15,208] [INFO] Task succeeded: Prodigal
[2023-06-13 10:50:15,208] [INFO] Task started: HMMsearch
[2023-06-13 10:50:15,208] [INFO] Running command: hmmsearch --tblout GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b8e53c5-eea5-42b1-806a-a632c007aea1/dqc_reference/reference_markers.hmm GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:50:15,374] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:50:15,377] [INFO] Found 6/6 markers.
[2023-06-13 10:50:15,396] [INFO] Query marker FASTA was written to GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 10:50:15,397] [INFO] Task started: Blastn
[2023-06-13 10:50:15,397] [INFO] Running command: blastn -query GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b8e53c5-eea5-42b1-806a-a632c007aea1/dqc_reference/reference_markers.fasta -out GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:50:15,966] [INFO] Task succeeded: Blastn
[2023-06-13 10:50:15,972] [INFO] Selected 15 target genomes.
[2023-06-13 10:50:15,972] [INFO] Target genome list was writen to GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 10:50:15,975] [INFO] Task started: fastANI
[2023-06-13 10:50:15,976] [INFO] Running command: fastANI --query /var/lib/cwl/stg59854f9d-f81d-4875-9d27-bc75b38af4ca/GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:50:20,361] [INFO] Task succeeded: fastANI
[2023-06-13 10:50:20,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b8e53c5-eea5-42b1-806a-a632c007aea1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:50:20,362] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b8e53c5-eea5-42b1-806a-a632c007aea1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:50:20,369] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 10:50:20,369] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 10:50:20,369] [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
Lancefieldella parvula	strain=DSM 20469	GCA_000024225.1	1382	1382	type	True	88.6349	422	492	95	below_threshold
Lancefieldella rimae	strain=DSM 7090	GCA_001438885.1	1383	1383	type	True	80.3515	113	492	95	below_threshold
Lancefieldella rimae	strain=ATCC 49626	GCA_000174015.1	1383	1383	type	True	80.3261	113	492	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 10:50:20,372] [INFO] DFAST Taxonomy check result was written to GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 10:50:20,373] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:50:20,373] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:50:20,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b8e53c5-eea5-42b1-806a-a632c007aea1/dqc_reference/checkm_data
[2023-06-13 10:50:20,375] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:50:20,394] [INFO] Task started: CheckM
[2023-06-13 10:50:20,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 10:50:38,441] [INFO] Task succeeded: CheckM
[2023-06-13 10:50:38,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 10:50:38,468] [INFO] ===== Completeness check finished =====
[2023-06-13 10:50:38,469] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:50:38,469] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 10:50:38,469] [INFO] Task started: Blastn
[2023-06-13 10:50:38,469] [INFO] Running command: blastn -query GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b8e53c5-eea5-42b1-806a-a632c007aea1/dqc_reference/reference_markers_gtdb.fasta -out GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:50:39,234] [INFO] Task succeeded: Blastn
[2023-06-13 10:50:39,238] [INFO] Selected 7 target genomes.
[2023-06-13 10:50:39,239] [INFO] Target genome list was writen to GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:50:39,242] [INFO] Task started: fastANI
[2023-06-13 10:50:39,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg59854f9d-f81d-4875-9d27-bc75b38af4ca/GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:50:41,483] [INFO] Task succeeded: fastANI
[2023-06-13 10:50:41,490] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 10:50:41,490] [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
GCF_000564995.1	s__Lancefieldella sp000564995	94.2681	434	492	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	95.37	95.06	0.93	0.85	23	-
GCA_900555335.1	s__Lancefieldella sp900555335	93.8757	308	492	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015259035.1	s__Lancefieldella sp015259035	93.8333	288	492	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	95.13	95.13	0.67	0.67	2	-
GCA_015258605.1	s__Lancefieldella sp015258605	93.6024	289	492	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015259045.1	s__Lancefieldella sp015259045	93.5412	276	492	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	95.43	95.43	0.88	0.88	2	-
GCA_015259105.1	s__Lancefieldella sp015259105	93.4559	348	492	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	95.21	95.21	0.86	0.86	2	-
GCA_015258715.1	s__Lancefieldella sp015258715	93.2263	413	492	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 10:50:41,492] [INFO] GTDB search result was written to GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 10:50:41,493] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:50:41,496] [INFO] DFAST_QC result json was written to GCA_938028565.1_ERR589464_bin.22_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 10:50:41,496] [INFO] DFAST_QC completed!
[2023-06-13 10:50:41,496] [INFO] Total running time: 0h0m32s