[2023-06-19 00:25:46,417] [INFO] DFAST_QC pipeline started.
[2023-06-19 00:25:46,420] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 00:25:46,420] [INFO] DQC Reference Directory: /var/lib/cwl/stg69c48799-b93e-48c1-af7e-31bfd910071b/dqc_reference
[2023-06-19 00:25:47,711] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 00:25:47,714] [INFO] Task started: Prodigal
[2023-06-19 00:25:47,714] [INFO] Running command: gunzip -c /var/lib/cwl/stgf61a3c51-7d06-444e-a5c8-7dd2a39cb802/GCA_018054345.1_ASM1805434v1_genomic.fna.gz | prodigal -d GCA_018054345.1_ASM1805434v1_genomic.fna/cds.fna -a GCA_018054345.1_ASM1805434v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 00:25:50,975] [INFO] Task succeeded: Prodigal
[2023-06-19 00:25:50,975] [INFO] Task started: HMMsearch
[2023-06-19 00:25:50,975] [INFO] Running command: hmmsearch --tblout GCA_018054345.1_ASM1805434v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69c48799-b93e-48c1-af7e-31bfd910071b/dqc_reference/reference_markers.hmm GCA_018054345.1_ASM1805434v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 00:25:51,256] [INFO] Task succeeded: HMMsearch
[2023-06-19 00:25:51,257] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgf61a3c51-7d06-444e-a5c8-7dd2a39cb802/GCA_018054345.1_ASM1805434v1_genomic.fna.gz]
[2023-06-19 00:25:51,315] [INFO] Query marker FASTA was written to GCA_018054345.1_ASM1805434v1_genomic.fna/markers.fasta
[2023-06-19 00:25:51,315] [INFO] Task started: Blastn
[2023-06-19 00:25:51,315] [INFO] Running command: blastn -query GCA_018054345.1_ASM1805434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69c48799-b93e-48c1-af7e-31bfd910071b/dqc_reference/reference_markers.fasta -out GCA_018054345.1_ASM1805434v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:25:51,886] [INFO] Task succeeded: Blastn
[2023-06-19 00:25:51,892] [INFO] Selected 6 target genomes.
[2023-06-19 00:25:51,892] [INFO] Target genome list was writen to GCA_018054345.1_ASM1805434v1_genomic.fna/target_genomes.txt
[2023-06-19 00:25:51,895] [INFO] Task started: fastANI
[2023-06-19 00:25:51,896] [INFO] Running command: fastANI --query /var/lib/cwl/stgf61a3c51-7d06-444e-a5c8-7dd2a39cb802/GCA_018054345.1_ASM1805434v1_genomic.fna.gz --refList GCA_018054345.1_ASM1805434v1_genomic.fna/target_genomes.txt --output GCA_018054345.1_ASM1805434v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 00:25:54,811] [INFO] Task succeeded: fastANI
[2023-06-19 00:25:54,811] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69c48799-b93e-48c1-af7e-31bfd910071b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 00:25:54,812] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69c48799-b93e-48c1-af7e-31bfd910071b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 00:25:54,817] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 00:25:54,817] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 00:25:54,817] [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
Coprococcus eutactus	strain=ATCC 27759	GCA_000154425.1	33043	33043	suspected-type	True	86.9879	307	384	95	below_threshold
Coprococcus eutactus	strain=ATCC 27759	GCA_025149915.1	33043	33043	suspected-type	True	86.7655	317	384	95	below_threshold
Wujia chipingensis	strain=NSJ-4	GCA_014337155.1	2763670	2763670	type	True	77.9093	57	384	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 00:25:54,818] [INFO] DFAST Taxonomy check result was written to GCA_018054345.1_ASM1805434v1_genomic.fna/tc_result.tsv
[2023-06-19 00:25:54,819] [INFO] ===== Taxonomy check completed =====
[2023-06-19 00:25:54,819] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 00:25:54,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69c48799-b93e-48c1-af7e-31bfd910071b/dqc_reference/checkm_data
[2023-06-19 00:25:54,820] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 00:25:54,841] [INFO] Task started: CheckM
[2023-06-19 00:25:54,841] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018054345.1_ASM1805434v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018054345.1_ASM1805434v1_genomic.fna/checkm_input GCA_018054345.1_ASM1805434v1_genomic.fna/checkm_result
[2023-06-19 00:26:12,844] [INFO] Task succeeded: CheckM
[2023-06-19 00:26:12,845] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 00:26:12,883] [INFO] ===== Completeness check finished =====
[2023-06-19 00:26:12,883] [INFO] ===== Start GTDB Search =====
[2023-06-19 00:26:12,883] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018054345.1_ASM1805434v1_genomic.fna/markers.fasta)
[2023-06-19 00:26:12,884] [INFO] Task started: Blastn
[2023-06-19 00:26:12,884] [INFO] Running command: blastn -query GCA_018054345.1_ASM1805434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69c48799-b93e-48c1-af7e-31bfd910071b/dqc_reference/reference_markers_gtdb.fasta -out GCA_018054345.1_ASM1805434v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:26:13,472] [INFO] Task succeeded: Blastn
[2023-06-19 00:26:13,482] [INFO] Selected 6 target genomes.
[2023-06-19 00:26:13,482] [INFO] Target genome list was writen to GCA_018054345.1_ASM1805434v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 00:26:13,542] [INFO] Task started: fastANI
[2023-06-19 00:26:13,542] [INFO] Running command: fastANI --query /var/lib/cwl/stgf61a3c51-7d06-444e-a5c8-7dd2a39cb802/GCA_018054345.1_ASM1805434v1_genomic.fna.gz --refList GCA_018054345.1_ASM1805434v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018054345.1_ASM1805434v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 00:26:16,368] [INFO] Task succeeded: fastANI
[2023-06-19 00:26:16,375] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 00:26:16,376] [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_001404675.1	s__Coprococcus eutactus_A	99.3634	382	384	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	98.33	97.53	0.90	0.82	34	conclusive
GCF_000154425.1	s__Coprococcus eutactus	86.9879	307	384	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	98.55	98.02	0.90	0.86	8	-
GCA_900548215.1	s__Coprococcus sp900548215	85.9653	277	384	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	98.00	97.92	0.89	0.88	3	-
GCA_900548315.1	s__Coprococcus sp900548315	85.761	251	384	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016297325.1	s__Coprococcus sp016297325	84.3305	280	384	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017624085.1	s__Coprococcus sp017624085	80.0829	66	384	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 00:26:16,378] [INFO] GTDB search result was written to GCA_018054345.1_ASM1805434v1_genomic.fna/result_gtdb.tsv
[2023-06-19 00:26:16,378] [INFO] ===== GTDB Search completed =====
[2023-06-19 00:26:16,383] [INFO] DFAST_QC result json was written to GCA_018054345.1_ASM1805434v1_genomic.fna/dqc_result.json
[2023-06-19 00:26:16,383] [INFO] DFAST_QC completed!
[2023-06-19 00:26:16,383] [INFO] Total running time: 0h0m30s