[2023-06-05 10:46:57,469] [INFO] DFAST_QC pipeline started.
[2023-06-05 10:46:57,471] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 10:46:57,472] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b56f093-9562-4e88-a4a3-d1f71b42f9ca/dqc_reference
[2023-06-05 10:46:58,802] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 10:46:58,803] [INFO] Task started: Prodigal
[2023-06-05 10:46:58,804] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ead86f4-7187-4f70-90ae-7d96f2f281ba/GCA_934834445.1_MTG229_bin.53.fa_genomic.fna.gz | prodigal -d GCA_934834445.1_MTG229_bin.53.fa_genomic.fna/cds.fna -a GCA_934834445.1_MTG229_bin.53.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 10:47:04,150] [INFO] Task succeeded: Prodigal
[2023-06-05 10:47:04,151] [INFO] Task started: HMMsearch
[2023-06-05 10:47:04,151] [INFO] Running command: hmmsearch --tblout GCA_934834445.1_MTG229_bin.53.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b56f093-9562-4e88-a4a3-d1f71b42f9ca/dqc_reference/reference_markers.hmm GCA_934834445.1_MTG229_bin.53.fa_genomic.fna/protein.faa > /dev/null
[2023-06-05 10:47:04,456] [INFO] Task succeeded: HMMsearch
[2023-06-05 10:47:04,457] [INFO] Found 6/6 markers.
[2023-06-05 10:47:04,488] [INFO] Query marker FASTA was written to GCA_934834445.1_MTG229_bin.53.fa_genomic.fna/markers.fasta
[2023-06-05 10:47:04,489] [INFO] Task started: Blastn
[2023-06-05 10:47:04,489] [INFO] Running command: blastn -query GCA_934834445.1_MTG229_bin.53.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b56f093-9562-4e88-a4a3-d1f71b42f9ca/dqc_reference/reference_markers.fasta -out GCA_934834445.1_MTG229_bin.53.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:47:05,202] [INFO] Task succeeded: Blastn
[2023-06-05 10:47:05,209] [INFO] Selected 24 target genomes.
[2023-06-05 10:47:05,210] [INFO] Target genome list was writen to GCA_934834445.1_MTG229_bin.53.fa_genomic.fna/target_genomes.txt
[2023-06-05 10:47:05,214] [INFO] Task started: fastANI
[2023-06-05 10:47:05,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ead86f4-7187-4f70-90ae-7d96f2f281ba/GCA_934834445.1_MTG229_bin.53.fa_genomic.fna.gz --refList GCA_934834445.1_MTG229_bin.53.fa_genomic.fna/target_genomes.txt --output GCA_934834445.1_MTG229_bin.53.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 10:47:20,740] [INFO] Task succeeded: fastANI
[2023-06-05 10:47:20,741] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b56f093-9562-4e88-a4a3-d1f71b42f9ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 10:47:20,741] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b56f093-9562-4e88-a4a3-d1f71b42f9ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 10:47:20,749] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 10:47:20,750] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 10:47:20,750] [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
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	78.455	235	787	95	below_threshold
Lachnospira multipara	strain=ATCC 19207	GCA_000424105.1	28051	28051	type	True	77.8889	89	787	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_025150745.1	39496	39496	suspected-type	True	77.2898	58	787	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_000153885.1	39496	39496	suspected-type	True	77.2728	56	787	95	below_threshold
Butyrivibrio crossotus	strain=DSM 2876	GCA_025148445.1	45851	45851	type	True	76.8297	75	787	95	below_threshold
Butyrivibrio crossotus	strain=DSM 2876	GCA_000156015.1	45851	45851	type	True	76.7945	78	787	95	below_threshold
[Clostridium] fimetarium	strain=DSM 9179	GCA_900111235.1	99656	99656	type	True	76.1175	60	787	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 10:47:20,753] [INFO] DFAST Taxonomy check result was written to GCA_934834445.1_MTG229_bin.53.fa_genomic.fna/tc_result.tsv
[2023-06-05 10:47:20,753] [INFO] ===== Taxonomy check completed =====
[2023-06-05 10:47:20,753] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 10:47:20,754] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b56f093-9562-4e88-a4a3-d1f71b42f9ca/dqc_reference/checkm_data
[2023-06-05 10:47:20,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 10:47:20,785] [INFO] Task started: CheckM
[2023-06-05 10:47:20,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934834445.1_MTG229_bin.53.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934834445.1_MTG229_bin.53.fa_genomic.fna/checkm_input GCA_934834445.1_MTG229_bin.53.fa_genomic.fna/checkm_result
[2023-06-05 10:47:43,861] [INFO] Task succeeded: CheckM
[2023-06-05 10:47:43,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.82%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 10:47:43,883] [INFO] ===== Completeness check finished =====
[2023-06-05 10:47:43,883] [INFO] ===== Start GTDB Search =====
[2023-06-05 10:47:43,884] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934834445.1_MTG229_bin.53.fa_genomic.fna/markers.fasta)
[2023-06-05 10:47:43,884] [INFO] Task started: Blastn
[2023-06-05 10:47:43,884] [INFO] Running command: blastn -query GCA_934834445.1_MTG229_bin.53.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b56f093-9562-4e88-a4a3-d1f71b42f9ca/dqc_reference/reference_markers_gtdb.fasta -out GCA_934834445.1_MTG229_bin.53.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:47:44,898] [INFO] Task succeeded: Blastn
[2023-06-05 10:47:44,903] [INFO] Selected 21 target genomes.
[2023-06-05 10:47:44,903] [INFO] Target genome list was writen to GCA_934834445.1_MTG229_bin.53.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 10:47:44,915] [INFO] Task started: fastANI
[2023-06-05 10:47:44,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ead86f4-7187-4f70-90ae-7d96f2f281ba/GCA_934834445.1_MTG229_bin.53.fa_genomic.fna.gz --refList GCA_934834445.1_MTG229_bin.53.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934834445.1_MTG229_bin.53.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 10:47:54,202] [INFO] Task succeeded: fastANI
[2023-06-05 10:47:54,221] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 10:47:54,221] [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_014287955.1	s__Lachnospira sp900316325	99.0809	734	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.86	98.35	0.93	0.88	10	conclusive
GCF_003464165.1	s__Lachnospira sp003451515	78.7585	208	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	97.95	97.44	0.88	0.84	9	-
GCA_900112995.1	s__Lachnospira rogosae_A	78.62	232	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	99.05	98.51	0.91	0.85	17	-
GCF_003458705.1	s__Lachnospira sp003537285	78.6065	224	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.4867	98.01	96.87	0.87	0.80	8	-
GCA_900772425.1	s__Lachnospira sp900772425	78.5946	120	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547255.1	s__Lachnospira sp900547255	78.4413	231	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	99.87	99.87	0.91	0.91	2	-
GCA_000436535.1	s__Lachnospira sp000436535	78.4	200	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.91	98.77	0.95	0.93	6	-
GCA_000437735.1	s__Lachnospira sp000437735	78.3389	156	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.81	98.12	0.91	0.82	10	-
GCA_900552795.1	s__Lachnospira sp900552795	78.2606	187	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	99.54	99.07	0.90	0.84	3	-
GCA_900545725.1	s__Lachnospira sp900545725	78.2314	212	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.88	98.45	0.88	0.87	3	-
GCA_000436475.1	s__Lachnospira sp000436475	78.2239	212	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	97.97	97.42	0.90	0.86	10	-
GCA_017397445.1	s__Lachnospira sp017397445	78.1872	129	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002394205.1	s__Lachnospira sp002394205	78.119	122	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	99.96	99.94	0.94	0.91	3	-
GCA_002435585.1	s__Lachnospira sp002435585	77.9399	166	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017626275.1	s__Lachnospira sp017626275	77.6173	95	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585095.1	s__Lachnospira sp910585095	77.4626	121	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551945.1	s__Lachnospira sp900551945	77.3613	173	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	99.31	99.16	0.89	0.87	3	-
GCF_018918265.1	s__Falcatimonas sp018918265	77.2991	110	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Falcatimonas	95.0	98.30	98.30	0.93	0.93	2	-
GCA_910587485.1	s__Lachnospira sp910587485	77.2569	136	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363805.1	s__Eubacterium_G sp000434315	76.6373	66	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.27	98.14	0.87	0.84	6	-
--------------------------------------------------------------------------------
[2023-06-05 10:47:54,223] [INFO] GTDB search result was written to GCA_934834445.1_MTG229_bin.53.fa_genomic.fna/result_gtdb.tsv
[2023-06-05 10:47:54,224] [INFO] ===== GTDB Search completed =====
[2023-06-05 10:47:54,228] [INFO] DFAST_QC result json was written to GCA_934834445.1_MTG229_bin.53.fa_genomic.fna/dqc_result.json
[2023-06-05 10:47:54,228] [INFO] DFAST_QC completed!
[2023-06-05 10:47:54,228] [INFO] Total running time: 0h0m57s