[2024-01-25 17:39:50,571] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:39:50,572] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:39:50,573] [INFO] DQC Reference Directory: /var/lib/cwl/stgb87fffb0-21bf-4f3a-9f53-6ae98a350c4b/dqc_reference
[2024-01-25 17:39:51,671] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:39:51,671] [INFO] Task started: Prodigal
[2024-01-25 17:39:51,672] [INFO] Running command: gunzip -c /var/lib/cwl/stg893e2b2c-c8f6-4162-b06a-7a6ab5f3610c/GCF_025567285.1_ASM2556728v1_genomic.fna.gz | prodigal -d GCF_025567285.1_ASM2556728v1_genomic.fna/cds.fna -a GCF_025567285.1_ASM2556728v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:59,001] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:59,001] [INFO] Task started: HMMsearch
[2024-01-25 17:39:59,002] [INFO] Running command: hmmsearch --tblout GCF_025567285.1_ASM2556728v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb87fffb0-21bf-4f3a-9f53-6ae98a350c4b/dqc_reference/reference_markers.hmm GCF_025567285.1_ASM2556728v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:59,228] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:59,229] [INFO] Found 6/6 markers.
[2024-01-25 17:39:59,256] [INFO] Query marker FASTA was written to GCF_025567285.1_ASM2556728v1_genomic.fna/markers.fasta
[2024-01-25 17:39:59,256] [INFO] Task started: Blastn
[2024-01-25 17:39:59,256] [INFO] Running command: blastn -query GCF_025567285.1_ASM2556728v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb87fffb0-21bf-4f3a-9f53-6ae98a350c4b/dqc_reference/reference_markers.fasta -out GCF_025567285.1_ASM2556728v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:59,847] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:59,855] [INFO] Selected 17 target genomes.
[2024-01-25 17:39:59,855] [INFO] Target genome list was writen to GCF_025567285.1_ASM2556728v1_genomic.fna/target_genomes.txt
[2024-01-25 17:39:59,867] [INFO] Task started: fastANI
[2024-01-25 17:39:59,867] [INFO] Running command: fastANI --query /var/lib/cwl/stg893e2b2c-c8f6-4162-b06a-7a6ab5f3610c/GCF_025567285.1_ASM2556728v1_genomic.fna.gz --refList GCF_025567285.1_ASM2556728v1_genomic.fna/target_genomes.txt --output GCF_025567285.1_ASM2556728v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:09,503] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:09,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb87fffb0-21bf-4f3a-9f53-6ae98a350c4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:09,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb87fffb0-21bf-4f3a-9f53-6ae98a350c4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:09,509] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:40:09,509] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:40:09,509] [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_025149915.1	33043	33043	suspected-type	True	89.1468	725	1067	95	below_threshold
Coprococcus eutactus	strain=ATCC 27759	GCA_000154425.1	33043	33043	suspected-type	True	88.9787	740	1067	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	82.4999	52	1067	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	79.6637	62	1067	95	below_threshold
Wujia chipingensis	strain=NSJ-4	GCA_014337155.1	2763670	2763670	type	True	79.3259	103	1067	95	below_threshold
Eubacterium ruminantium	strain=ATCC 17233	GCA_900167085.1	42322	42322	type	True	77.4877	56	1067	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:09,511] [INFO] DFAST Taxonomy check result was written to GCF_025567285.1_ASM2556728v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:09,511] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:09,511] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:09,512] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb87fffb0-21bf-4f3a-9f53-6ae98a350c4b/dqc_reference/checkm_data
[2024-01-25 17:40:09,513] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:09,547] [INFO] Task started: CheckM
[2024-01-25 17:40:09,547] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025567285.1_ASM2556728v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025567285.1_ASM2556728v1_genomic.fna/checkm_input GCF_025567285.1_ASM2556728v1_genomic.fna/checkm_result
[2024-01-25 17:40:36,277] [INFO] Task succeeded: CheckM
[2024-01-25 17:40:36,278] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:40:36,297] [INFO] ===== Completeness check finished =====
[2024-01-25 17:40:36,297] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:40:36,298] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025567285.1_ASM2556728v1_genomic.fna/markers.fasta)
[2024-01-25 17:40:36,298] [INFO] Task started: Blastn
[2024-01-25 17:40:36,298] [INFO] Running command: blastn -query GCF_025567285.1_ASM2556728v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb87fffb0-21bf-4f3a-9f53-6ae98a350c4b/dqc_reference/reference_markers_gtdb.fasta -out GCF_025567285.1_ASM2556728v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:37,358] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:37,361] [INFO] Selected 8 target genomes.
[2024-01-25 17:40:37,362] [INFO] Target genome list was writen to GCF_025567285.1_ASM2556728v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:40:37,375] [INFO] Task started: fastANI
[2024-01-25 17:40:37,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg893e2b2c-c8f6-4162-b06a-7a6ab5f3610c/GCF_025567285.1_ASM2556728v1_genomic.fna.gz --refList GCF_025567285.1_ASM2556728v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025567285.1_ASM2556728v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:41,986] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:41,991] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:41,992] [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	98.6405	915	1067	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	88.9787	740	1067	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_900557435.1	s__Coprococcus sp900557435	88.3579	456	1067	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_900548215.1	s__Coprococcus sp900548215	87.7808	576	1067	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	87.6246	490	1067	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_900767685.1	s__Coprococcus sp900767685	87.3356	538	1067	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	85.3531	554	1067	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	79.5239	120	1067	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:41,993] [INFO] GTDB search result was written to GCF_025567285.1_ASM2556728v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:41,993] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:41,995] [INFO] DFAST_QC result json was written to GCF_025567285.1_ASM2556728v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:41,996] [INFO] DFAST_QC completed!
[2024-01-25 17:40:41,996] [INFO] Total running time: 0h0m51s