[2023-06-04 22:52:12,175] [INFO] DFAST_QC pipeline started.
[2023-06-04 22:52:12,182] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 22:52:12,182] [INFO] DQC Reference Directory: /var/lib/cwl/stgca3c7c9a-9f7c-4b9f-89ba-83bb8d10fdd2/dqc_reference
[2023-06-04 22:52:13,605] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 22:52:13,606] [INFO] Task started: Prodigal
[2023-06-04 22:52:13,606] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f962255-8e42-4990-8e02-2b8009118f80/GCA_934320855.1_ERR7745389_bin.97_genomic.fna.gz | prodigal -d GCA_934320855.1_ERR7745389_bin.97_genomic.fna/cds.fna -a GCA_934320855.1_ERR7745389_bin.97_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 22:52:21,611] [INFO] Task succeeded: Prodigal
[2023-06-04 22:52:21,611] [INFO] Task started: HMMsearch
[2023-06-04 22:52:21,611] [INFO] Running command: hmmsearch --tblout GCA_934320855.1_ERR7745389_bin.97_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca3c7c9a-9f7c-4b9f-89ba-83bb8d10fdd2/dqc_reference/reference_markers.hmm GCA_934320855.1_ERR7745389_bin.97_genomic.fna/protein.faa > /dev/null
[2023-06-04 22:52:21,893] [INFO] Task succeeded: HMMsearch
[2023-06-04 22:52:21,894] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5f962255-8e42-4990-8e02-2b8009118f80/GCA_934320855.1_ERR7745389_bin.97_genomic.fna.gz]
[2023-06-04 22:52:21,926] [INFO] Query marker FASTA was written to GCA_934320855.1_ERR7745389_bin.97_genomic.fna/markers.fasta
[2023-06-04 22:52:21,926] [INFO] Task started: Blastn
[2023-06-04 22:52:21,926] [INFO] Running command: blastn -query GCA_934320855.1_ERR7745389_bin.97_genomic.fna/markers.fasta -db /var/lib/cwl/stgca3c7c9a-9f7c-4b9f-89ba-83bb8d10fdd2/dqc_reference/reference_markers.fasta -out GCA_934320855.1_ERR7745389_bin.97_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:52:22,558] [INFO] Task succeeded: Blastn
[2023-06-04 22:52:22,562] [INFO] Selected 18 target genomes.
[2023-06-04 22:52:22,562] [INFO] Target genome list was writen to GCA_934320855.1_ERR7745389_bin.97_genomic.fna/target_genomes.txt
[2023-06-04 22:52:22,564] [INFO] Task started: fastANI
[2023-06-04 22:52:22,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f962255-8e42-4990-8e02-2b8009118f80/GCA_934320855.1_ERR7745389_bin.97_genomic.fna.gz --refList GCA_934320855.1_ERR7745389_bin.97_genomic.fna/target_genomes.txt --output GCA_934320855.1_ERR7745389_bin.97_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 22:52:32,890] [INFO] Task succeeded: fastANI
[2023-06-04 22:52:32,891] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca3c7c9a-9f7c-4b9f-89ba-83bb8d10fdd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 22:52:32,891] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca3c7c9a-9f7c-4b9f-89ba-83bb8d10fdd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 22:52:32,901] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 22:52:32,902] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 22:52:32,902] [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
Butyrivibrio crossotus	strain=DSM 2876	GCA_025148445.1	45851	45851	type	True	78.0308	70	1060	95	below_threshold
Butyrivibrio crossotus	strain=DSM 2876	GCA_000156015.1	45851	45851	type	True	78.0196	70	1060	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	77.5388	60	1060	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	77.4879	63	1060	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	77.3676	77	1060	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	77.2805	62	1060	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 22:52:32,904] [INFO] DFAST Taxonomy check result was written to GCA_934320855.1_ERR7745389_bin.97_genomic.fna/tc_result.tsv
[2023-06-04 22:52:32,904] [INFO] ===== Taxonomy check completed =====
[2023-06-04 22:52:32,905] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 22:52:32,905] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca3c7c9a-9f7c-4b9f-89ba-83bb8d10fdd2/dqc_reference/checkm_data
[2023-06-04 22:52:32,906] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 22:52:32,944] [INFO] Task started: CheckM
[2023-06-04 22:52:32,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934320855.1_ERR7745389_bin.97_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934320855.1_ERR7745389_bin.97_genomic.fna/checkm_input GCA_934320855.1_ERR7745389_bin.97_genomic.fna/checkm_result
[2023-06-04 22:53:02,169] [INFO] Task succeeded: CheckM
[2023-06-04 22:53:02,170] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 22:53:02,193] [INFO] ===== Completeness check finished =====
[2023-06-04 22:53:02,194] [INFO] ===== Start GTDB Search =====
[2023-06-04 22:53:02,194] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934320855.1_ERR7745389_bin.97_genomic.fna/markers.fasta)
[2023-06-04 22:53:02,194] [INFO] Task started: Blastn
[2023-06-04 22:53:02,195] [INFO] Running command: blastn -query GCA_934320855.1_ERR7745389_bin.97_genomic.fna/markers.fasta -db /var/lib/cwl/stgca3c7c9a-9f7c-4b9f-89ba-83bb8d10fdd2/dqc_reference/reference_markers_gtdb.fasta -out GCA_934320855.1_ERR7745389_bin.97_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:53:02,938] [INFO] Task succeeded: Blastn
[2023-06-04 22:53:02,943] [INFO] Selected 11 target genomes.
[2023-06-04 22:53:02,943] [INFO] Target genome list was writen to GCA_934320855.1_ERR7745389_bin.97_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 22:53:02,956] [INFO] Task started: fastANI
[2023-06-04 22:53:02,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f962255-8e42-4990-8e02-2b8009118f80/GCA_934320855.1_ERR7745389_bin.97_genomic.fna.gz --refList GCA_934320855.1_ERR7745389_bin.97_genomic.fna/target_genomes_gtdb.txt --output GCA_934320855.1_ERR7745389_bin.97_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 22:53:08,844] [INFO] Task succeeded: fastANI
[2023-06-04 22:53:08,850] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 22:53:08,851] [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_003486385.1	s__CAG-882 sp003486385	95.9416	807	1060	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-882	95.0	98.36	97.90	0.89	0.87	6	conclusive
GCA_900545175.1	s__CAG-882 sp900545175	83.7899	582	1060	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-882	95.0	99.03	98.05	0.94	0.87	3	-
GCA_900545455.1	s__CAG-882 sp900545455	81.5907	410	1060	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-882	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000435595.1	s__CAG-882 sp000435595	81.5554	501	1060	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-882	95.0	98.75	98.61	0.86	0.85	4	-
GCA_015057505.1	s__SIG300 sp015057505	77.4706	51	1060	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG300	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000431815.1	s__Butyrivibrio_A sp000431815	77.1135	67	1060	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio_A	95.0	98.85	98.85	0.94	0.94	3	-
GCA_900545725.1	s__Lachnospira sp900545725	76.4212	51	1060	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.88	98.45	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2023-06-04 22:53:08,853] [INFO] GTDB search result was written to GCA_934320855.1_ERR7745389_bin.97_genomic.fna/result_gtdb.tsv
[2023-06-04 22:53:08,854] [INFO] ===== GTDB Search completed =====
[2023-06-04 22:53:08,871] [INFO] DFAST_QC result json was written to GCA_934320855.1_ERR7745389_bin.97_genomic.fna/dqc_result.json
[2023-06-04 22:53:08,872] [INFO] DFAST_QC completed!
[2023-06-04 22:53:08,872] [INFO] Total running time: 0h0m57s