[2024-01-24 13:10:19,571] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:19,573] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:19,573] [INFO] DQC Reference Directory: /var/lib/cwl/stg424016cb-c999-4dce-93aa-50334a7ea17a/dqc_reference
[2024-01-24 13:10:20,855] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:20,856] [INFO] Task started: Prodigal
[2024-01-24 13:10:20,857] [INFO] Running command: gunzip -c /var/lib/cwl/stg2da6c9af-7974-4df0-b002-44b873e465fd/GCF_025149915.1_ASM2514991v1_genomic.fna.gz | prodigal -d GCF_025149915.1_ASM2514991v1_genomic.fna/cds.fna -a GCF_025149915.1_ASM2514991v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:28,926] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:28,926] [INFO] Task started: HMMsearch
[2024-01-24 13:10:28,927] [INFO] Running command: hmmsearch --tblout GCF_025149915.1_ASM2514991v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg424016cb-c999-4dce-93aa-50334a7ea17a/dqc_reference/reference_markers.hmm GCF_025149915.1_ASM2514991v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:29,205] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:29,207] [INFO] Found 6/6 markers.
[2024-01-24 13:10:29,235] [INFO] Query marker FASTA was written to GCF_025149915.1_ASM2514991v1_genomic.fna/markers.fasta
[2024-01-24 13:10:29,235] [INFO] Task started: Blastn
[2024-01-24 13:10:29,235] [INFO] Running command: blastn -query GCF_025149915.1_ASM2514991v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg424016cb-c999-4dce-93aa-50334a7ea17a/dqc_reference/reference_markers.fasta -out GCF_025149915.1_ASM2514991v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:29,857] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:29,860] [INFO] Selected 15 target genomes.
[2024-01-24 13:10:29,861] [INFO] Target genome list was writen to GCF_025149915.1_ASM2514991v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:29,871] [INFO] Task started: fastANI
[2024-01-24 13:10:29,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg2da6c9af-7974-4df0-b002-44b873e465fd/GCF_025149915.1_ASM2514991v1_genomic.fna.gz --refList GCF_025149915.1_ASM2514991v1_genomic.fna/target_genomes.txt --output GCF_025149915.1_ASM2514991v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:37,928] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:37,928] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg424016cb-c999-4dce-93aa-50334a7ea17a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:37,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg424016cb-c999-4dce-93aa-50334a7ea17a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:37,939] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:10:37,939] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:37,939] [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	100.0	1035	1037	95	conclusive
Coprococcus eutactus	strain=ATCC 27759	GCA_000154425.1	33043	33043	suspected-type	True	99.9809	1013	1037	95	conclusive
Wujia chipingensis	strain=NSJ-4	GCA_014337155.1	2763670	2763670	type	True	81.5294	129	1037	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	80.8984	79	1037	95	below_threshold
Butyrivibrio crossotus	strain=DSM 2876	GCA_000156015.1	45851	45851	type	True	79.2558	50	1037	95	below_threshold
Eubacterium ruminantium	strain=ATCC 17233	GCA_900167085.1	42322	42322	type	True	77.5343	62	1037	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:37,944] [INFO] DFAST Taxonomy check result was written to GCF_025149915.1_ASM2514991v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:37,944] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:37,945] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:37,945] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg424016cb-c999-4dce-93aa-50334a7ea17a/dqc_reference/checkm_data
[2024-01-24 13:10:37,946] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:37,984] [INFO] Task started: CheckM
[2024-01-24 13:10:37,984] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025149915.1_ASM2514991v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025149915.1_ASM2514991v1_genomic.fna/checkm_input GCF_025149915.1_ASM2514991v1_genomic.fna/checkm_result
[2024-01-24 13:11:08,414] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:08,416] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:08,436] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:08,436] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:08,437] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025149915.1_ASM2514991v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:08,437] [INFO] Task started: Blastn
[2024-01-24 13:11:08,437] [INFO] Running command: blastn -query GCF_025149915.1_ASM2514991v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg424016cb-c999-4dce-93aa-50334a7ea17a/dqc_reference/reference_markers_gtdb.fasta -out GCF_025149915.1_ASM2514991v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:09,415] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:09,426] [INFO] Selected 9 target genomes.
[2024-01-24 13:11:09,426] [INFO] Target genome list was writen to GCF_025149915.1_ASM2514991v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:09,449] [INFO] Task started: fastANI
[2024-01-24 13:11:09,449] [INFO] Running command: fastANI --query /var/lib/cwl/stg2da6c9af-7974-4df0-b002-44b873e465fd/GCF_025149915.1_ASM2514991v1_genomic.fna.gz --refList GCF_025149915.1_ASM2514991v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025149915.1_ASM2514991v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:14,501] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:14,516] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:14,517] [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_000154425.1	s__Coprococcus eutactus	99.9809	1013	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	98.55	98.02	0.90	0.86	8	conclusive
GCA_900767685.1	s__Coprococcus sp900767685	91.1717	605	1037	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_900557435.1	s__Coprococcus sp900557435	90.7019	499	1037	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_900548315.1	s__Coprococcus sp900548315	90.2984	553	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001404675.1	s__Coprococcus eutactus_A	89.4823	724	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	98.33	97.53	0.90	0.82	34	-
GCA_900548215.1	s__Coprococcus sp900548215	87.818	587	1037	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_016297325.1	s__Coprococcus sp016297325	84.9503	531	1037	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	79.4148	119	1037	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_016296785.1	s__Coprococcus sp016296785	77.9351	133	1037	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:14,523] [INFO] GTDB search result was written to GCF_025149915.1_ASM2514991v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:14,523] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:14,526] [INFO] DFAST_QC result json was written to GCF_025149915.1_ASM2514991v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:14,526] [INFO] DFAST_QC completed!
[2024-01-24 13:11:14,527] [INFO] Total running time: 0h0m55s