[2023-07-01 06:01:33,544] [INFO] DFAST_QC pipeline started.
[2023-07-01 06:01:33,547] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 06:01:33,547] [INFO] DQC Reference Directory: /var/lib/cwl/stgd06dc9af-98da-4e6e-80a5-2b595f55d491/dqc_reference
[2023-07-01 06:01:34,911] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 06:01:34,912] [INFO] Task started: Prodigal
[2023-07-01 06:01:34,912] [INFO] Running command: gunzip -c /var/lib/cwl/stg54c05f20-9578-4952-9231-10a338d13e47/GCA_024698145.1_ASM2469814v1_genomic.fna.gz | prodigal -d GCA_024698145.1_ASM2469814v1_genomic.fna/cds.fna -a GCA_024698145.1_ASM2469814v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 06:01:41,532] [INFO] Task succeeded: Prodigal
[2023-07-01 06:01:41,532] [INFO] Task started: HMMsearch
[2023-07-01 06:01:41,532] [INFO] Running command: hmmsearch --tblout GCA_024698145.1_ASM2469814v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd06dc9af-98da-4e6e-80a5-2b595f55d491/dqc_reference/reference_markers.hmm GCA_024698145.1_ASM2469814v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 06:01:41,787] [INFO] Task succeeded: HMMsearch
[2023-07-01 06:01:41,788] [INFO] Found 6/6 markers.
[2023-07-01 06:01:41,817] [INFO] Query marker FASTA was written to GCA_024698145.1_ASM2469814v1_genomic.fna/markers.fasta
[2023-07-01 06:01:41,817] [INFO] Task started: Blastn
[2023-07-01 06:01:41,817] [INFO] Running command: blastn -query GCA_024698145.1_ASM2469814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd06dc9af-98da-4e6e-80a5-2b595f55d491/dqc_reference/reference_markers.fasta -out GCA_024698145.1_ASM2469814v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 06:01:42,402] [INFO] Task succeeded: Blastn
[2023-07-01 06:01:42,424] [INFO] Selected 20 target genomes.
[2023-07-01 06:01:42,425] [INFO] Target genome list was writen to GCA_024698145.1_ASM2469814v1_genomic.fna/target_genomes.txt
[2023-07-01 06:01:42,434] [INFO] Task started: fastANI
[2023-07-01 06:01:42,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg54c05f20-9578-4952-9231-10a338d13e47/GCA_024698145.1_ASM2469814v1_genomic.fna.gz --refList GCA_024698145.1_ASM2469814v1_genomic.fna/target_genomes.txt --output GCA_024698145.1_ASM2469814v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 06:01:53,061] [INFO] Task succeeded: fastANI
[2023-07-01 06:01:53,061] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd06dc9af-98da-4e6e-80a5-2b595f55d491/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 06:01:53,062] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd06dc9af-98da-4e6e-80a5-2b595f55d491/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 06:01:53,067] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 06:01:53,067] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 06:01:53,068] [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
Wujia chipingensis	strain=NSJ-4	GCA_014337155.1	2763670	2763670	type	True	77.9875	61	929	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	77.2265	54	929	95	below_threshold
Eubacterium uniforme	strain=ATCC 35992	GCA_900167115.1	39495	39495	type	True	76.684	62	929	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 06:01:53,094] [INFO] DFAST Taxonomy check result was written to GCA_024698145.1_ASM2469814v1_genomic.fna/tc_result.tsv
[2023-07-01 06:01:53,095] [INFO] ===== Taxonomy check completed =====
[2023-07-01 06:01:53,095] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 06:01:53,095] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd06dc9af-98da-4e6e-80a5-2b595f55d491/dqc_reference/checkm_data
[2023-07-01 06:01:53,097] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 06:01:53,128] [INFO] Task started: CheckM
[2023-07-01 06:01:53,128] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024698145.1_ASM2469814v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024698145.1_ASM2469814v1_genomic.fna/checkm_input GCA_024698145.1_ASM2469814v1_genomic.fna/checkm_result
[2023-07-01 06:02:19,091] [INFO] Task succeeded: CheckM
[2023-07-01 06:02:19,093] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 06:02:19,115] [INFO] ===== Completeness check finished =====
[2023-07-01 06:02:19,115] [INFO] ===== Start GTDB Search =====
[2023-07-01 06:02:19,115] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024698145.1_ASM2469814v1_genomic.fna/markers.fasta)
[2023-07-01 06:02:19,116] [INFO] Task started: Blastn
[2023-07-01 06:02:19,116] [INFO] Running command: blastn -query GCA_024698145.1_ASM2469814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd06dc9af-98da-4e6e-80a5-2b595f55d491/dqc_reference/reference_markers_gtdb.fasta -out GCA_024698145.1_ASM2469814v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 06:02:19,967] [INFO] Task succeeded: Blastn
[2023-07-01 06:02:19,971] [INFO] Selected 17 target genomes.
[2023-07-01 06:02:19,972] [INFO] Target genome list was writen to GCA_024698145.1_ASM2469814v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 06:02:19,979] [INFO] Task started: fastANI
[2023-07-01 06:02:19,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg54c05f20-9578-4952-9231-10a338d13e47/GCA_024698145.1_ASM2469814v1_genomic.fna.gz --refList GCA_024698145.1_ASM2469814v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024698145.1_ASM2469814v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 06:02:28,159] [INFO] Task succeeded: fastANI
[2023-07-01 06:02:28,171] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 06:02:28,172] [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_015057325.1	s__CAG-590 sp015057325	89.4874	695	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902793335.1	s__CAG-590 sp902793335	79.5506	309	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900313855.1	s__CAG-590 sp900313855	79.2372	212	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	99.22	99.22	0.85	0.85	2	-
GCA_905235345.1	s__CAG-590 sp905235345	78.8539	174	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017469275.1	s__CAG-590 sp017469275	78.6707	221	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017470935.1	s__CAG-590 sp017470935	78.6079	201	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902762905.1	s__CAG-590 sp003530125	78.0884	138	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	99.91	99.91	0.89	0.89	2	-
GCA_015057435.1	s__CAG-590 sp015057435	77.8098	147	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552885.1	s__CAG-590 sp900552885	77.6275	100	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	97.66	97.66	0.76	0.76	2	-
GCA_017439675.1	s__CAG-590 sp017439675	77.3268	99	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000146185.1	s__Lachnospira eligens	77.2265	54	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.6336	96.66	95.71	0.87	0.85	3	-
GCF_009680455.1	s__Lachnospira eligens_A	77.2019	59	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.6336	97.83	97.23	0.89	0.81	35	-
GCA_017625335.1	s__CAG-127 sp017625335	76.9749	62	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548855.1	s__CAG-590 sp900548855	76.9408	102	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-590	95.0	99.80	99.61	0.88	0.84	3	-
GCA_017456585.1	s__SIG300 sp017456585	76.7189	51	929	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG300	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 06:02:28,173] [INFO] GTDB search result was written to GCA_024698145.1_ASM2469814v1_genomic.fna/result_gtdb.tsv
[2023-07-01 06:02:28,174] [INFO] ===== GTDB Search completed =====
[2023-07-01 06:02:28,177] [INFO] DFAST_QC result json was written to GCA_024698145.1_ASM2469814v1_genomic.fna/dqc_result.json
[2023-07-01 06:02:28,177] [INFO] DFAST_QC completed!
[2023-07-01 06:02:28,178] [INFO] Total running time: 0h0m55s