[2023-06-28 01:17:49,797] [INFO] DFAST_QC pipeline started.
[2023-06-28 01:17:49,799] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 01:17:49,800] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6782fdf-7886-4ee4-828a-c6008ca3b569/dqc_reference
[2023-06-28 01:17:52,617] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 01:17:52,618] [INFO] Task started: Prodigal
[2023-06-28 01:17:52,619] [INFO] Running command: gunzip -c /var/lib/cwl/stg2657eabf-86a8-406b-9754-d49deb527952/GCA_017476345.1_ASM1747634v1_genomic.fna.gz | prodigal -d GCA_017476345.1_ASM1747634v1_genomic.fna/cds.fna -a GCA_017476345.1_ASM1747634v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 01:17:57,553] [INFO] Task succeeded: Prodigal
[2023-06-28 01:17:57,554] [INFO] Task started: HMMsearch
[2023-06-28 01:17:57,554] [INFO] Running command: hmmsearch --tblout GCA_017476345.1_ASM1747634v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6782fdf-7886-4ee4-828a-c6008ca3b569/dqc_reference/reference_markers.hmm GCA_017476345.1_ASM1747634v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 01:17:57,752] [INFO] Task succeeded: HMMsearch
[2023-06-28 01:17:57,754] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2657eabf-86a8-406b-9754-d49deb527952/GCA_017476345.1_ASM1747634v1_genomic.fna.gz]
[2023-06-28 01:17:57,783] [INFO] Query marker FASTA was written to GCA_017476345.1_ASM1747634v1_genomic.fna/markers.fasta
[2023-06-28 01:17:57,783] [INFO] Task started: Blastn
[2023-06-28 01:17:57,783] [INFO] Running command: blastn -query GCA_017476345.1_ASM1747634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6782fdf-7886-4ee4-828a-c6008ca3b569/dqc_reference/reference_markers.fasta -out GCA_017476345.1_ASM1747634v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:17:58,371] [INFO] Task succeeded: Blastn
[2023-06-28 01:17:58,375] [INFO] Selected 11 target genomes.
[2023-06-28 01:17:58,376] [INFO] Target genome list was writen to GCA_017476345.1_ASM1747634v1_genomic.fna/target_genomes.txt
[2023-06-28 01:17:58,377] [INFO] Task started: fastANI
[2023-06-28 01:17:58,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg2657eabf-86a8-406b-9754-d49deb527952/GCA_017476345.1_ASM1747634v1_genomic.fna.gz --refList GCA_017476345.1_ASM1747634v1_genomic.fna/target_genomes.txt --output GCA_017476345.1_ASM1747634v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 01:18:05,828] [INFO] Task succeeded: fastANI
[2023-06-28 01:18:05,828] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6782fdf-7886-4ee4-828a-c6008ca3b569/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 01:18:05,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6782fdf-7886-4ee4-828a-c6008ca3b569/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 01:18:05,834] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 01:18:05,834] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 01:18:05,834] [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
Fibrobacter succinogenes subsp. succinogenes	strain=S85	GCA_000146505.1	834	833	type	True	79.2359	133	288	95	below_threshold
Fibrobacter succinogenes subsp. succinogenes	strain=S85	GCA_000024665.1	834	833	type	True	79.2359	133	288	95	below_threshold
Hallerella succinigenes	strain=UWS3	GCA_002797675.1	1896222	1896222	type	True	78.755	50	288	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 01:18:05,836] [INFO] DFAST Taxonomy check result was written to GCA_017476345.1_ASM1747634v1_genomic.fna/tc_result.tsv
[2023-06-28 01:18:05,837] [INFO] ===== Taxonomy check completed =====
[2023-06-28 01:18:05,837] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 01:18:05,837] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6782fdf-7886-4ee4-828a-c6008ca3b569/dqc_reference/checkm_data
[2023-06-28 01:18:05,839] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 01:18:05,866] [INFO] Task started: CheckM
[2023-06-28 01:18:05,867] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017476345.1_ASM1747634v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017476345.1_ASM1747634v1_genomic.fna/checkm_input GCA_017476345.1_ASM1747634v1_genomic.fna/checkm_result
[2023-06-28 01:18:27,233] [INFO] Task succeeded: CheckM
[2023-06-28 01:18:27,235] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.19%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 01:18:27,255] [INFO] ===== Completeness check finished =====
[2023-06-28 01:18:27,256] [INFO] ===== Start GTDB Search =====
[2023-06-28 01:18:27,256] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017476345.1_ASM1747634v1_genomic.fna/markers.fasta)
[2023-06-28 01:18:27,257] [INFO] Task started: Blastn
[2023-06-28 01:18:27,257] [INFO] Running command: blastn -query GCA_017476345.1_ASM1747634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6782fdf-7886-4ee4-828a-c6008ca3b569/dqc_reference/reference_markers_gtdb.fasta -out GCA_017476345.1_ASM1747634v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:18:28,070] [INFO] Task succeeded: Blastn
[2023-06-28 01:18:28,074] [INFO] Selected 10 target genomes.
[2023-06-28 01:18:28,075] [INFO] Target genome list was writen to GCA_017476345.1_ASM1747634v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 01:18:28,090] [INFO] Task started: fastANI
[2023-06-28 01:18:28,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg2657eabf-86a8-406b-9754-d49deb527952/GCA_017476345.1_ASM1747634v1_genomic.fna.gz --refList GCA_017476345.1_ASM1747634v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017476345.1_ASM1747634v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 01:18:33,472] [INFO] Task succeeded: fastANI
[2023-06-28 01:18:33,484] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 01:18:33,484] [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_900143055.1	s__Fibrobacter sp900143055	95.4971	249	288	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	96.51	95.61	0.84	0.74	8	conclusive
GCA_902800815.1	s__Fibrobacter succinogenes_B	88.9833	227	288	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.10	97.10	0.90	0.90	2	-
GCA_002449765.1	s__Fibrobacter sp002449765	88.1089	216	288	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	98.21	96.54	0.93	0.89	8	-
GCA_017615055.1	s__Fibrobacter sp017615055	87.368	189	288	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902762305.1	s__Fibrobacter succinogenes_I	84.1657	203	288	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902771595.1	s__Fibrobacter succinogenes_C	83.7496	197	288	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	98.72	98.72	0.91	0.91	2	-
GCA_017551775.1	s__Fibrobacter sp017551775	82.6377	184	288	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017412605.1	s__Fibrobacter sp017412605	81.7429	156	288	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642335.1	s__Fibrobacter sp017642335	81.6909	156	288	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	98.30	98.30	0.90	0.90	2	-
GCA_017649565.1	s__Fibrobacter sp017649565	81.114	140	288	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 01:18:33,486] [INFO] GTDB search result was written to GCA_017476345.1_ASM1747634v1_genomic.fna/result_gtdb.tsv
[2023-06-28 01:18:33,487] [INFO] ===== GTDB Search completed =====
[2023-06-28 01:18:33,489] [INFO] DFAST_QC result json was written to GCA_017476345.1_ASM1747634v1_genomic.fna/dqc_result.json
[2023-06-28 01:18:33,489] [INFO] DFAST_QC completed!
[2023-06-28 01:18:33,489] [INFO] Total running time: 0h0m44s