[2023-06-30 09:06:44,093] [INFO] DFAST_QC pipeline started.
[2023-06-30 09:06:44,095] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 09:06:44,095] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c734c95-6e33-407c-a653-5b69b6b3d4c2/dqc_reference
[2023-06-30 09:06:45,346] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 09:06:45,347] [INFO] Task started: Prodigal
[2023-06-30 09:06:45,347] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c118f64-707d-4e6a-9d77-c3656d4f9451/GCA_024399135.1_ASM2439913v1_genomic.fna.gz | prodigal -d GCA_024399135.1_ASM2439913v1_genomic.fna/cds.fna -a GCA_024399135.1_ASM2439913v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 09:06:51,503] [INFO] Task succeeded: Prodigal
[2023-06-30 09:06:51,504] [INFO] Task started: HMMsearch
[2023-06-30 09:06:51,505] [INFO] Running command: hmmsearch --tblout GCA_024399135.1_ASM2439913v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c734c95-6e33-407c-a653-5b69b6b3d4c2/dqc_reference/reference_markers.hmm GCA_024399135.1_ASM2439913v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 09:06:51,784] [INFO] Task succeeded: HMMsearch
[2023-06-30 09:06:51,786] [INFO] Found 6/6 markers.
[2023-06-30 09:06:51,818] [INFO] Query marker FASTA was written to GCA_024399135.1_ASM2439913v1_genomic.fna/markers.fasta
[2023-06-30 09:06:51,818] [INFO] Task started: Blastn
[2023-06-30 09:06:51,819] [INFO] Running command: blastn -query GCA_024399135.1_ASM2439913v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c734c95-6e33-407c-a653-5b69b6b3d4c2/dqc_reference/reference_markers.fasta -out GCA_024399135.1_ASM2439913v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:06:52,462] [INFO] Task succeeded: Blastn
[2023-06-30 09:06:52,466] [INFO] Selected 30 target genomes.
[2023-06-30 09:06:52,467] [INFO] Target genome list was writen to GCA_024399135.1_ASM2439913v1_genomic.fna/target_genomes.txt
[2023-06-30 09:06:52,480] [INFO] Task started: fastANI
[2023-06-30 09:06:52,481] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c118f64-707d-4e6a-9d77-c3656d4f9451/GCA_024399135.1_ASM2439913v1_genomic.fna.gz --refList GCA_024399135.1_ASM2439913v1_genomic.fna/target_genomes.txt --output GCA_024399135.1_ASM2439913v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 09:07:10,021] [INFO] Task succeeded: fastANI
[2023-06-30 09:07:10,022] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c734c95-6e33-407c-a653-5b69b6b3d4c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 09:07:10,023] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c734c95-6e33-407c-a653-5b69b6b3d4c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 09:07:10,034] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 09:07:10,035] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 09:07:10,035] [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 proteoclasticus	strain=B316	GCA_000145035.1	43305	43305	type	True	77.4959	55	1006	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_025150745.1	39496	39496	suspected-type	True	77.1177	55	1006	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_000153885.1	39496	39496	suspected-type	True	77.1006	55	1006	95	below_threshold
Butyrivibrio hungatei	strain=DSM 14810	GCA_900143205.1	185008	185008	type	True	76.7637	73	1006	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	76.6797	56	1006	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 09:07:10,037] [INFO] DFAST Taxonomy check result was written to GCA_024399135.1_ASM2439913v1_genomic.fna/tc_result.tsv
[2023-06-30 09:07:10,038] [INFO] ===== Taxonomy check completed =====
[2023-06-30 09:07:10,038] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 09:07:10,038] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c734c95-6e33-407c-a653-5b69b6b3d4c2/dqc_reference/checkm_data
[2023-06-30 09:07:10,039] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 09:07:10,078] [INFO] Task started: CheckM
[2023-06-30 09:07:10,078] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024399135.1_ASM2439913v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024399135.1_ASM2439913v1_genomic.fna/checkm_input GCA_024399135.1_ASM2439913v1_genomic.fna/checkm_result
[2023-06-30 09:07:34,816] [INFO] Task succeeded: CheckM
[2023-06-30 09:07:34,817] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 09:07:34,839] [INFO] ===== Completeness check finished =====
[2023-06-30 09:07:34,840] [INFO] ===== Start GTDB Search =====
[2023-06-30 09:07:34,840] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024399135.1_ASM2439913v1_genomic.fna/markers.fasta)
[2023-06-30 09:07:34,840] [INFO] Task started: Blastn
[2023-06-30 09:07:34,841] [INFO] Running command: blastn -query GCA_024399135.1_ASM2439913v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c734c95-6e33-407c-a653-5b69b6b3d4c2/dqc_reference/reference_markers_gtdb.fasta -out GCA_024399135.1_ASM2439913v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:07:35,880] [INFO] Task succeeded: Blastn
[2023-06-30 09:07:35,885] [INFO] Selected 34 target genomes.
[2023-06-30 09:07:35,886] [INFO] Target genome list was writen to GCA_024399135.1_ASM2439913v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 09:07:35,903] [INFO] Task started: fastANI
[2023-06-30 09:07:35,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c118f64-707d-4e6a-9d77-c3656d4f9451/GCA_024399135.1_ASM2439913v1_genomic.fna.gz --refList GCA_024399135.1_ASM2439913v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024399135.1_ASM2439913v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 09:07:53,409] [INFO] Task succeeded: fastANI
[2023-06-30 09:07:53,423] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 09:07:53,424] [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_002317175.1	s__UBA1712 sp002317175	77.6815	83	1006	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779505.1	s__UBA1712 sp902779505	77.6219	53	1006	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	98.45	98.04	0.85	0.80	3	-
GCA_017467805.1	s__COE1 sp017467805	77.61	63	1006	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018064425.1	s__UBA1712 sp018064425	77.5586	58	1006	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000687675.1	s__NK4A136 sp000687675	77.3926	92	1006	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__NK4A136	95.0	96.46	96.24	0.90	0.87	4	-
GCA_015056925.1	s__COE1 sp015056925	77.1576	64	1006	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153885.1	s__Eubacterium_G ventriosum	77.1006	55	1006	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.27	97.67	0.81	0.64	20	-
GCF_000420945.1	s__Butyrivibrio sp000420945	76.985	63	1006	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103635.1	s__Butyrivibrio sp900103635	76.9478	55	1006	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	95.99	95.99	0.85	0.85	2	-
GCF_018918265.1	s__Falcatimonas sp018918265	76.7732	56	1006	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Falcatimonas	95.0	98.30	98.30	0.93	0.93	2	-
GCF_900143205.1	s__Butyrivibrio hungatei	76.7637	73	1006	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	97.43	97.43	0.86	0.86	2	-
GCA_017437065.1	s__RGIG3002 sp017437065	76.688	54	1006	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG3002	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102515.1	s__Butyrivibrio sp900102515	76.6811	66	1006	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	95.65	95.65	0.82	0.82	2	-
GCA_017424235.1	s__COE1 sp017424235	76.6229	65	1006	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	98.29	98.29	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-06-30 09:07:53,426] [INFO] GTDB search result was written to GCA_024399135.1_ASM2439913v1_genomic.fna/result_gtdb.tsv
[2023-06-30 09:07:53,427] [INFO] ===== GTDB Search completed =====
[2023-06-30 09:07:53,430] [INFO] DFAST_QC result json was written to GCA_024399135.1_ASM2439913v1_genomic.fna/dqc_result.json
[2023-06-30 09:07:53,430] [INFO] DFAST_QC completed!
[2023-06-30 09:07:53,430] [INFO] Total running time: 0h1m9s