[2023-06-29 11:06:57,719] [INFO] DFAST_QC pipeline started.
[2023-06-29 11:06:57,721] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 11:06:57,721] [INFO] DQC Reference Directory: /var/lib/cwl/stg09cc553e-b80a-4673-b097-e3ebdf50f5d6/dqc_reference
[2023-06-29 11:07:01,502] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 11:07:01,503] [INFO] Task started: Prodigal
[2023-06-29 11:07:01,503] [INFO] Running command: gunzip -c /var/lib/cwl/stg5925c5da-ab85-4061-9277-11938f2a406a/GCA_027347145.1_ASM2734714v1_genomic.fna.gz | prodigal -d GCA_027347145.1_ASM2734714v1_genomic.fna/cds.fna -a GCA_027347145.1_ASM2734714v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 11:07:34,568] [INFO] Task succeeded: Prodigal
[2023-06-29 11:07:34,568] [INFO] Task started: HMMsearch
[2023-06-29 11:07:34,568] [INFO] Running command: hmmsearch --tblout GCA_027347145.1_ASM2734714v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09cc553e-b80a-4673-b097-e3ebdf50f5d6/dqc_reference/reference_markers.hmm GCA_027347145.1_ASM2734714v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 11:07:34,836] [INFO] Task succeeded: HMMsearch
[2023-06-29 11:07:34,838] [INFO] Found 6/6 markers.
[2023-06-29 11:07:34,883] [INFO] Query marker FASTA was written to GCA_027347145.1_ASM2734714v1_genomic.fna/markers.fasta
[2023-06-29 11:07:34,884] [INFO] Task started: Blastn
[2023-06-29 11:07:34,884] [INFO] Running command: blastn -query GCA_027347145.1_ASM2734714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09cc553e-b80a-4673-b097-e3ebdf50f5d6/dqc_reference/reference_markers.fasta -out GCA_027347145.1_ASM2734714v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 11:07:35,559] [INFO] Task succeeded: Blastn
[2023-06-29 11:07:35,567] [INFO] Selected 27 target genomes.
[2023-06-29 11:07:35,568] [INFO] Target genome list was writen to GCA_027347145.1_ASM2734714v1_genomic.fna/target_genomes.txt
[2023-06-29 11:07:35,580] [INFO] Task started: fastANI
[2023-06-29 11:07:35,580] [INFO] Running command: fastANI --query /var/lib/cwl/stg5925c5da-ab85-4061-9277-11938f2a406a/GCA_027347145.1_ASM2734714v1_genomic.fna.gz --refList GCA_027347145.1_ASM2734714v1_genomic.fna/target_genomes.txt --output GCA_027347145.1_ASM2734714v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 11:07:52,303] [INFO] Task succeeded: fastANI
[2023-06-29 11:07:52,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09cc553e-b80a-4673-b097-e3ebdf50f5d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 11:07:52,304] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09cc553e-b80a-4673-b097-e3ebdf50f5d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 11:07:52,307] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 11:07:52,307] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 11:07:52,308] [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
Limisphaera ngatamarikiensis	strain=NGM72.4	GCA_011044775.1	1324935	1324935	type	True	75.5497	59	1441	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 11:07:52,309] [INFO] DFAST Taxonomy check result was written to GCA_027347145.1_ASM2734714v1_genomic.fna/tc_result.tsv
[2023-06-29 11:07:52,310] [INFO] ===== Taxonomy check completed =====
[2023-06-29 11:07:52,310] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 11:07:52,310] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09cc553e-b80a-4673-b097-e3ebdf50f5d6/dqc_reference/checkm_data
[2023-06-29 11:07:52,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 11:07:52,352] [INFO] Task started: CheckM
[2023-06-29 11:07:52,352] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027347145.1_ASM2734714v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027347145.1_ASM2734714v1_genomic.fna/checkm_input GCA_027347145.1_ASM2734714v1_genomic.fna/checkm_result
[2023-06-29 11:09:20,867] [INFO] Task succeeded: CheckM
[2023-06-29 11:09:20,868] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 11:09:20,890] [INFO] ===== Completeness check finished =====
[2023-06-29 11:09:20,890] [INFO] ===== Start GTDB Search =====
[2023-06-29 11:09:20,890] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027347145.1_ASM2734714v1_genomic.fna/markers.fasta)
[2023-06-29 11:09:20,891] [INFO] Task started: Blastn
[2023-06-29 11:09:20,891] [INFO] Running command: blastn -query GCA_027347145.1_ASM2734714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09cc553e-b80a-4673-b097-e3ebdf50f5d6/dqc_reference/reference_markers_gtdb.fasta -out GCA_027347145.1_ASM2734714v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 11:09:22,054] [INFO] Task succeeded: Blastn
[2023-06-29 11:09:22,059] [INFO] Selected 19 target genomes.
[2023-06-29 11:09:22,060] [INFO] Target genome list was writen to GCA_027347145.1_ASM2734714v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 11:09:22,083] [INFO] Task started: fastANI
[2023-06-29 11:09:22,083] [INFO] Running command: fastANI --query /var/lib/cwl/stg5925c5da-ab85-4061-9277-11938f2a406a/GCA_027347145.1_ASM2734714v1_genomic.fna.gz --refList GCA_027347145.1_ASM2734714v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027347145.1_ASM2734714v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 11:09:35,361] [INFO] Task succeeded: fastANI
[2023-06-29 11:09:35,380] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 11:09:35,381] [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_903918885.1	s__UBA11358 sp903918885	78.4512	289	1441	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.76	99.61	0.88	0.86	5	-
GCA_903870815.1	s__UBA11358 sp903870815	78.2745	281	1441	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.83	99.83	0.93	0.93	2	-
GCA_903944085.1	s__UBA11358 sp903944085	78.2744	420	1441	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.64	99.63	0.93	0.93	3	-
GCA_903921455.1	s__UBA11358 sp903921455	78.2651	367	1441	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903889895.1	s__UBA11358 sp903889895	78.2421	295	1441	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903922735.1	s__UBA11358 sp903922735	78.2408	358	1441	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858275.1	s__UBA11358 sp903858275	78.2348	329	1441	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.00	98.19	0.88	0.83	3	-
GCA_903861445.1	s__UBA11358 sp903861445	78.2253	242	1441	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903878805.1	s__UBA11358 sp903878805	78.1004	239	1441	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.90	99.90	0.92	0.92	2	-
GCA_903850425.1	s__UBA11358 sp903850425	78.0792	383	1441	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903917705.1	s__UBA11358 sp903917705	77.83	226	1441	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151855.1	s__UBA11358 sp003151855	77.7713	288	1441	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842235.1	s__UBA11358 sp903842235	77.7582	326	1441	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003455565.1	s__UBA11358 sp003455565	77.7462	281	1441	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903872345.1	s__UBA11358 sp903872345	77.3696	291	1441	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	100.00	100.00	0.99	0.99	3	-
GCA_903820285.1	s__UBA11358 sp903820285	77.1312	235	1441	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	98.56	98.53	0.77	0.76	3	-
GCA_903911825.1	s__UBA11358 sp903911825	77.0069	219	1441	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.63	99.63	0.91	0.91	2	-
GCA_016235585.1	s__JACRJY01 sp016235585	76.7289	125	1441	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__JACRJY01;g__JACRJY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 11:09:35,383] [INFO] GTDB search result was written to GCA_027347145.1_ASM2734714v1_genomic.fna/result_gtdb.tsv
[2023-06-29 11:09:35,383] [INFO] ===== GTDB Search completed =====
[2023-06-29 11:09:35,387] [INFO] DFAST_QC result json was written to GCA_027347145.1_ASM2734714v1_genomic.fna/dqc_result.json
[2023-06-29 11:09:35,387] [INFO] DFAST_QC completed!
[2023-06-29 11:09:35,387] [INFO] Total running time: 0h2m38s