[2023-06-13 02:18:19,874] [INFO] DFAST_QC pipeline started.
[2023-06-13 02:18:19,877] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 02:18:19,877] [INFO] DQC Reference Directory: /var/lib/cwl/stgedb8cb4c-67e3-45de-a758-9da3052402b4/dqc_reference
[2023-06-13 02:18:21,151] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 02:18:21,152] [INFO] Task started: Prodigal
[2023-06-13 02:18:21,152] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f96f239-5fd8-478c-a4db-cb9fd00742c8/GCA_022790895.1_ASM2279089v1_genomic.fna.gz | prodigal -d GCA_022790895.1_ASM2279089v1_genomic.fna/cds.fna -a GCA_022790895.1_ASM2279089v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 02:18:28,068] [INFO] Task succeeded: Prodigal
[2023-06-13 02:18:28,069] [INFO] Task started: HMMsearch
[2023-06-13 02:18:28,069] [INFO] Running command: hmmsearch --tblout GCA_022790895.1_ASM2279089v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgedb8cb4c-67e3-45de-a758-9da3052402b4/dqc_reference/reference_markers.hmm GCA_022790895.1_ASM2279089v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 02:18:28,396] [INFO] Task succeeded: HMMsearch
[2023-06-13 02:18:28,397] [INFO] Found 6/6 markers.
[2023-06-13 02:18:28,434] [INFO] Query marker FASTA was written to GCA_022790895.1_ASM2279089v1_genomic.fna/markers.fasta
[2023-06-13 02:18:28,435] [INFO] Task started: Blastn
[2023-06-13 02:18:28,435] [INFO] Running command: blastn -query GCA_022790895.1_ASM2279089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedb8cb4c-67e3-45de-a758-9da3052402b4/dqc_reference/reference_markers.fasta -out GCA_022790895.1_ASM2279089v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:18:29,146] [INFO] Task succeeded: Blastn
[2023-06-13 02:18:29,149] [INFO] Selected 29 target genomes.
[2023-06-13 02:18:29,149] [INFO] Target genome list was writen to GCA_022790895.1_ASM2279089v1_genomic.fna/target_genomes.txt
[2023-06-13 02:18:29,152] [INFO] Task started: fastANI
[2023-06-13 02:18:29,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f96f239-5fd8-478c-a4db-cb9fd00742c8/GCA_022790895.1_ASM2279089v1_genomic.fna.gz --refList GCA_022790895.1_ASM2279089v1_genomic.fna/target_genomes.txt --output GCA_022790895.1_ASM2279089v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 02:18:47,817] [INFO] Task succeeded: fastANI
[2023-06-13 02:18:47,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgedb8cb4c-67e3-45de-a758-9da3052402b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 02:18:47,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgedb8cb4c-67e3-45de-a758-9da3052402b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 02:18:47,824] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 02:18:47,825] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 02:18:47,825] [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
Sporofaciens musculi	strain=WCA-9-b2	GCA_009830285.1	2681861	2681861	type	True	77.123	52	970	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	76.8065	52	970	95	below_threshold
Blautia argi	strain=KCTC 15426	GCA_003287895.1	1912897	1912897	type	True	76.6865	51	970	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	76.6247	52	970	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 02:18:47,827] [INFO] DFAST Taxonomy check result was written to GCA_022790895.1_ASM2279089v1_genomic.fna/tc_result.tsv
[2023-06-13 02:18:47,828] [INFO] ===== Taxonomy check completed =====
[2023-06-13 02:18:47,828] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 02:18:47,828] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgedb8cb4c-67e3-45de-a758-9da3052402b4/dqc_reference/checkm_data
[2023-06-13 02:18:47,829] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 02:18:47,869] [INFO] Task started: CheckM
[2023-06-13 02:18:47,869] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022790895.1_ASM2279089v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022790895.1_ASM2279089v1_genomic.fna/checkm_input GCA_022790895.1_ASM2279089v1_genomic.fna/checkm_result
[2023-06-13 02:19:15,626] [INFO] Task succeeded: CheckM
[2023-06-13 02:19:15,628] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.84%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 02:19:15,651] [INFO] ===== Completeness check finished =====
[2023-06-13 02:19:15,652] [INFO] ===== Start GTDB Search =====
[2023-06-13 02:19:15,652] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022790895.1_ASM2279089v1_genomic.fna/markers.fasta)
[2023-06-13 02:19:15,652] [INFO] Task started: Blastn
[2023-06-13 02:19:15,653] [INFO] Running command: blastn -query GCA_022790895.1_ASM2279089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedb8cb4c-67e3-45de-a758-9da3052402b4/dqc_reference/reference_markers_gtdb.fasta -out GCA_022790895.1_ASM2279089v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:19:16,673] [INFO] Task succeeded: Blastn
[2023-06-13 02:19:16,676] [INFO] Selected 22 target genomes.
[2023-06-13 02:19:16,676] [INFO] Target genome list was writen to GCA_022790895.1_ASM2279089v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 02:19:16,684] [INFO] Task started: fastANI
[2023-06-13 02:19:16,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f96f239-5fd8-478c-a4db-cb9fd00742c8/GCA_022790895.1_ASM2279089v1_genomic.fna.gz --refList GCA_022790895.1_ASM2279089v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022790895.1_ASM2279089v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 02:19:29,354] [INFO] Task succeeded: fastANI
[2023-06-13 02:19:29,370] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 02:19:29,370] [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_910575445.1	s__Choladocola sp910575445	98.9277	935	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	99.04	98.55	0.92	0.85	5	conclusive
GCA_910585995.1	s__Choladocola sp910585995	80.3759	571	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579225.1	s__Choladocola sp910579225	78.0548	260	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910574805.1	s__Choladocola sp009774135	78.0381	225	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	99.38	99.01	0.92	0.88	3	-
GCA_910583895.1	s__Choladocola sp910583895	78.0083	214	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009774145.1	s__Choladocola sp009774145	78.0028	234	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	98.49	98.49	0.80	0.80	2	-
GCA_910585465.1	s__Choladocola sp910585465	77.9444	192	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584945.1	s__Choladocola sp910584945	77.884	193	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009774155.1	s__Choladocola sp009774155	77.6425	161	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	98.91	98.91	0.77	0.77	2	-
GCA_002491115.1	s__Choladocola sp002491115	77.5944	179	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	99.92	99.92	0.92	0.92	2	-
GCA_910587765.1	s__Choladocola sp910587765	77.4528	181	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018376135.1	s__Choladocola sp018376135	77.4333	174	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018228645.1	s__Choladocola sp003481535	77.3054	130	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	97.90	97.68	0.80	0.76	5	-
GCA_910587495.1	s__Choladocola sp910587495	77.2942	160	970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 02:19:29,372] [INFO] GTDB search result was written to GCA_022790895.1_ASM2279089v1_genomic.fna/result_gtdb.tsv
[2023-06-13 02:19:29,373] [INFO] ===== GTDB Search completed =====
[2023-06-13 02:19:29,378] [INFO] DFAST_QC result json was written to GCA_022790895.1_ASM2279089v1_genomic.fna/dqc_result.json
[2023-06-13 02:19:29,378] [INFO] DFAST_QC completed!
[2023-06-13 02:19:29,378] [INFO] Total running time: 0h1m10s