[2023-06-05 00:38:09,087] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:38:09,090] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:38:09,090] [INFO] DQC Reference Directory: /var/lib/cwl/stg3319b2c4-05a4-4898-a551-e1a356306b0f/dqc_reference
[2023-06-05 00:38:10,744] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:38:10,746] [INFO] Task started: Prodigal
[2023-06-05 00:38:10,746] [INFO] Running command: gunzip -c /var/lib/cwl/stg85275dee-acfe-4f2e-ba55-3f725d26b107/GCA_934552565.1_ERR7738553_bin.264_genomic.fna.gz | prodigal -d GCA_934552565.1_ERR7738553_bin.264_genomic.fna/cds.fna -a GCA_934552565.1_ERR7738553_bin.264_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:38:13,841] [INFO] Task succeeded: Prodigal
[2023-06-05 00:38:13,841] [INFO] Task started: HMMsearch
[2023-06-05 00:38:13,841] [INFO] Running command: hmmsearch --tblout GCA_934552565.1_ERR7738553_bin.264_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3319b2c4-05a4-4898-a551-e1a356306b0f/dqc_reference/reference_markers.hmm GCA_934552565.1_ERR7738553_bin.264_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:38:14,114] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:38:14,116] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg85275dee-acfe-4f2e-ba55-3f725d26b107/GCA_934552565.1_ERR7738553_bin.264_genomic.fna.gz]
[2023-06-05 00:38:14,134] [INFO] Query marker FASTA was written to GCA_934552565.1_ERR7738553_bin.264_genomic.fna/markers.fasta
[2023-06-05 00:38:14,134] [INFO] Task started: Blastn
[2023-06-05 00:38:14,135] [INFO] Running command: blastn -query GCA_934552565.1_ERR7738553_bin.264_genomic.fna/markers.fasta -db /var/lib/cwl/stg3319b2c4-05a4-4898-a551-e1a356306b0f/dqc_reference/reference_markers.fasta -out GCA_934552565.1_ERR7738553_bin.264_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:38:14,768] [INFO] Task succeeded: Blastn
[2023-06-05 00:38:14,784] [INFO] Selected 20 target genomes.
[2023-06-05 00:38:14,784] [INFO] Target genome list was writen to GCA_934552565.1_ERR7738553_bin.264_genomic.fna/target_genomes.txt
[2023-06-05 00:38:14,788] [INFO] Task started: fastANI
[2023-06-05 00:38:14,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg85275dee-acfe-4f2e-ba55-3f725d26b107/GCA_934552565.1_ERR7738553_bin.264_genomic.fna.gz --refList GCA_934552565.1_ERR7738553_bin.264_genomic.fna/target_genomes.txt --output GCA_934552565.1_ERR7738553_bin.264_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:38:27,980] [INFO] Task succeeded: fastANI
[2023-06-05 00:38:27,980] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3319b2c4-05a4-4898-a551-e1a356306b0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:38:27,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3319b2c4-05a4-4898-a551-e1a356306b0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:38:27,987] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-06-05 00:38:27,987] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 00:38:27,987] [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
Eubacterium coprostanoligenes	strain=ATCC 51222	GCA_900167205.1	290054	290054	type	True	96.5576	262	277	95	conclusive
--------------------------------------------------------------------------------
[2023-06-05 00:38:27,990] [INFO] DFAST Taxonomy check result was written to GCA_934552565.1_ERR7738553_bin.264_genomic.fna/tc_result.tsv
[2023-06-05 00:38:27,991] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:38:27,991] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:38:27,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3319b2c4-05a4-4898-a551-e1a356306b0f/dqc_reference/checkm_data
[2023-06-05 00:38:27,994] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:38:28,017] [INFO] Task started: CheckM
[2023-06-05 00:38:28,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934552565.1_ERR7738553_bin.264_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934552565.1_ERR7738553_bin.264_genomic.fna/checkm_input GCA_934552565.1_ERR7738553_bin.264_genomic.fna/checkm_result
[2023-06-05 00:38:45,444] [INFO] Task succeeded: CheckM
[2023-06-05 00:38:45,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.94%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:38:45,467] [INFO] ===== Completeness check finished =====
[2023-06-05 00:38:45,468] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:38:45,468] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934552565.1_ERR7738553_bin.264_genomic.fna/markers.fasta)
[2023-06-05 00:38:45,469] [INFO] Task started: Blastn
[2023-06-05 00:38:45,469] [INFO] Running command: blastn -query GCA_934552565.1_ERR7738553_bin.264_genomic.fna/markers.fasta -db /var/lib/cwl/stg3319b2c4-05a4-4898-a551-e1a356306b0f/dqc_reference/reference_markers_gtdb.fasta -out GCA_934552565.1_ERR7738553_bin.264_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:38:46,273] [INFO] Task succeeded: Blastn
[2023-06-05 00:38:46,278] [INFO] Selected 7 target genomes.
[2023-06-05 00:38:46,279] [INFO] Target genome list was writen to GCA_934552565.1_ERR7738553_bin.264_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:38:46,281] [INFO] Task started: fastANI
[2023-06-05 00:38:46,281] [INFO] Running command: fastANI --query /var/lib/cwl/stg85275dee-acfe-4f2e-ba55-3f725d26b107/GCA_934552565.1_ERR7738553_bin.264_genomic.fna.gz --refList GCA_934552565.1_ERR7738553_bin.264_genomic.fna/target_genomes_gtdb.txt --output GCA_934552565.1_ERR7738553_bin.264_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:38:48,419] [INFO] Task succeeded: fastANI
[2023-06-05 00:38:48,429] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 00:38:48,430] [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_900167205.1	s__Eubacterium_R coprostanoligenes	96.5576	262	277	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.02	97.98	0.90	0.89	4	conclusive
GCA_900539325.1	s__Eubacterium_R sp900539325	89.0277	243	277	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	97.44	97.34	0.90	0.87	4	-
GCA_900766895.1	s__Eubacterium_R sp900766895	79.9552	170	277	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539165.1	s__Eubacterium_R sp900539165	78.9636	139	277	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	99.98	99.98	0.94	0.94	2	-
GCA_900542875.1	s__Eubacterium_R sp900542875	78.7676	119	277	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	97.37	97.10	0.91	0.86	6	-
GCA_900772705.1	s__Eubacterium_R sp900772705	78.4552	98	277	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 00:38:48,432] [INFO] GTDB search result was written to GCA_934552565.1_ERR7738553_bin.264_genomic.fna/result_gtdb.tsv
[2023-06-05 00:38:48,432] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:38:48,435] [INFO] DFAST_QC result json was written to GCA_934552565.1_ERR7738553_bin.264_genomic.fna/dqc_result.json
[2023-06-05 00:38:48,435] [INFO] DFAST_QC completed!
[2023-06-05 00:38:48,435] [INFO] Total running time: 0h0m39s