[2023-06-05 05:36:43,106] [INFO] DFAST_QC pipeline started.
[2023-06-05 05:36:43,111] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 05:36:43,114] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8fd471a-975d-4ae7-afed-164710e3a318/dqc_reference
[2023-06-05 05:36:45,418] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 05:36:45,419] [INFO] Task started: Prodigal
[2023-06-05 05:36:45,419] [INFO] Running command: gunzip -c /var/lib/cwl/stg77876b6d-ee38-401d-9bbe-bedf292c1e67/GCA_934317455.1_ERR7737622_bin.35_genomic.fna.gz | prodigal -d GCA_934317455.1_ERR7737622_bin.35_genomic.fna/cds.fna -a GCA_934317455.1_ERR7737622_bin.35_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 05:36:51,702] [INFO] Task succeeded: Prodigal
[2023-06-05 05:36:51,702] [INFO] Task started: HMMsearch
[2023-06-05 05:36:51,703] [INFO] Running command: hmmsearch --tblout GCA_934317455.1_ERR7737622_bin.35_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8fd471a-975d-4ae7-afed-164710e3a318/dqc_reference/reference_markers.hmm GCA_934317455.1_ERR7737622_bin.35_genomic.fna/protein.faa > /dev/null
[2023-06-05 05:36:52,030] [INFO] Task succeeded: HMMsearch
[2023-06-05 05:36:52,031] [INFO] Found 6/6 markers.
[2023-06-05 05:36:52,078] [INFO] Query marker FASTA was written to GCA_934317455.1_ERR7737622_bin.35_genomic.fna/markers.fasta
[2023-06-05 05:36:52,078] [INFO] Task started: Blastn
[2023-06-05 05:36:52,078] [INFO] Running command: blastn -query GCA_934317455.1_ERR7737622_bin.35_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8fd471a-975d-4ae7-afed-164710e3a318/dqc_reference/reference_markers.fasta -out GCA_934317455.1_ERR7737622_bin.35_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:36:54,599] [INFO] Task succeeded: Blastn
[2023-06-05 05:36:54,607] [INFO] Selected 25 target genomes.
[2023-06-05 05:36:54,607] [INFO] Target genome list was writen to GCA_934317455.1_ERR7737622_bin.35_genomic.fna/target_genomes.txt
[2023-06-05 05:36:54,613] [INFO] Task started: fastANI
[2023-06-05 05:36:54,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg77876b6d-ee38-401d-9bbe-bedf292c1e67/GCA_934317455.1_ERR7737622_bin.35_genomic.fna.gz --refList GCA_934317455.1_ERR7737622_bin.35_genomic.fna/target_genomes.txt --output GCA_934317455.1_ERR7737622_bin.35_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 05:37:09,950] [INFO] Task succeeded: fastANI
[2023-06-05 05:37:09,950] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8fd471a-975d-4ae7-afed-164710e3a318/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 05:37:09,950] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8fd471a-975d-4ae7-afed-164710e3a318/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 05:37:09,956] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 05:37:09,956] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 05:37:09,956] [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	78.4648	159	784	95	below_threshold
Butyrivibrio crossotus	strain=DSM 2876	GCA_000156015.1	45851	45851	type	True	78.3403	156	784	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	76.997	52	784	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 05:37:09,958] [INFO] DFAST Taxonomy check result was written to GCA_934317455.1_ERR7737622_bin.35_genomic.fna/tc_result.tsv
[2023-06-05 05:37:09,959] [INFO] ===== Taxonomy check completed =====
[2023-06-05 05:37:09,959] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 05:37:09,959] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8fd471a-975d-4ae7-afed-164710e3a318/dqc_reference/checkm_data
[2023-06-05 05:37:09,960] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 05:37:10,002] [INFO] Task started: CheckM
[2023-06-05 05:37:10,002] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934317455.1_ERR7737622_bin.35_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934317455.1_ERR7737622_bin.35_genomic.fna/checkm_input GCA_934317455.1_ERR7737622_bin.35_genomic.fna/checkm_result
[2023-06-05 05:37:34,723] [INFO] Task succeeded: CheckM
[2023-06-05 05:37:34,725] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 05:37:34,745] [INFO] ===== Completeness check finished =====
[2023-06-05 05:37:34,746] [INFO] ===== Start GTDB Search =====
[2023-06-05 05:37:34,746] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934317455.1_ERR7737622_bin.35_genomic.fna/markers.fasta)
[2023-06-05 05:37:34,746] [INFO] Task started: Blastn
[2023-06-05 05:37:34,747] [INFO] Running command: blastn -query GCA_934317455.1_ERR7737622_bin.35_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8fd471a-975d-4ae7-afed-164710e3a318/dqc_reference/reference_markers_gtdb.fasta -out GCA_934317455.1_ERR7737622_bin.35_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:37:35,783] [INFO] Task succeeded: Blastn
[2023-06-05 05:37:35,788] [INFO] Selected 24 target genomes.
[2023-06-05 05:37:35,788] [INFO] Target genome list was writen to GCA_934317455.1_ERR7737622_bin.35_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 05:37:35,799] [INFO] Task started: fastANI
[2023-06-05 05:37:35,800] [INFO] Running command: fastANI --query /var/lib/cwl/stg77876b6d-ee38-401d-9bbe-bedf292c1e67/GCA_934317455.1_ERR7737622_bin.35_genomic.fna.gz --refList GCA_934317455.1_ERR7737622_bin.35_genomic.fna/target_genomes_gtdb.txt --output GCA_934317455.1_ERR7737622_bin.35_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 05:37:46,874] [INFO] Task succeeded: fastANI
[2023-06-05 05:37:46,890] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 05:37:46,890] [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_000431815.1	s__Butyrivibrio_A sp000431815	97.364	660	784	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	conclusive
GCF_000156015.1	s__Butyrivibrio_A crossotus	78.3512	155	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio_A	95.0	98.48	97.83	0.85	0.60	12	-
GCA_900771195.1	s__Butyrivibrio_A sp900771195	78.1271	131	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016297265.1	s__Butyrivibrio_A sp016297265	78.117	90	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio_A	95.0	98.79	98.79	0.89	0.89	2	-
GCA_900768755.1	s__Butyrivibrio_A sp900768755	77.9891	119	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577605.1	s__Butyrivibrio_A sp910577605	77.5223	88	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003486385.1	s__CAG-882 sp003486385	77.4563	73	784	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	-
GCA_900545175.1	s__CAG-882 sp900545175	77.4057	73	784	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_902763335.1	s__UBA2821 sp902763335	77.3904	58	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2821	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545455.1	s__CAG-882 sp900545455	76.6696	61	784	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	-
--------------------------------------------------------------------------------
[2023-06-05 05:37:46,893] [INFO] GTDB search result was written to GCA_934317455.1_ERR7737622_bin.35_genomic.fna/result_gtdb.tsv
[2023-06-05 05:37:46,893] [INFO] ===== GTDB Search completed =====
[2023-06-05 05:37:46,896] [INFO] DFAST_QC result json was written to GCA_934317455.1_ERR7737622_bin.35_genomic.fna/dqc_result.json
[2023-06-05 05:37:46,896] [INFO] DFAST_QC completed!
[2023-06-05 05:37:46,897] [INFO] Total running time: 0h1m4s