[2023-06-04 20:01:50,057] [INFO] DFAST_QC pipeline started.
[2023-06-04 20:01:50,066] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 20:01:50,066] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c082c66-6729-4dac-9922-3f7d4b3d9d6c/dqc_reference
[2023-06-04 20:01:53,104] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 20:01:53,105] [INFO] Task started: Prodigal
[2023-06-04 20:01:53,106] [INFO] Running command: gunzip -c /var/lib/cwl/stg431734a9-1b21-4b19-9593-72d8696fe65b/GCA_934331055.1_ERR7738661_bin.399_genomic.fna.gz | prodigal -d GCA_934331055.1_ERR7738661_bin.399_genomic.fna/cds.fna -a GCA_934331055.1_ERR7738661_bin.399_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 20:01:57,758] [INFO] Task succeeded: Prodigal
[2023-06-04 20:01:57,758] [INFO] Task started: HMMsearch
[2023-06-04 20:01:57,759] [INFO] Running command: hmmsearch --tblout GCA_934331055.1_ERR7738661_bin.399_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c082c66-6729-4dac-9922-3f7d4b3d9d6c/dqc_reference/reference_markers.hmm GCA_934331055.1_ERR7738661_bin.399_genomic.fna/protein.faa > /dev/null
[2023-06-04 20:01:57,971] [INFO] Task succeeded: HMMsearch
[2023-06-04 20:01:57,973] [INFO] Found 6/6 markers.
[2023-06-04 20:01:57,998] [INFO] Query marker FASTA was written to GCA_934331055.1_ERR7738661_bin.399_genomic.fna/markers.fasta
[2023-06-04 20:01:57,998] [INFO] Task started: Blastn
[2023-06-04 20:01:57,998] [INFO] Running command: blastn -query GCA_934331055.1_ERR7738661_bin.399_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c082c66-6729-4dac-9922-3f7d4b3d9d6c/dqc_reference/reference_markers.fasta -out GCA_934331055.1_ERR7738661_bin.399_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:01:58,600] [INFO] Task succeeded: Blastn
[2023-06-04 20:01:58,604] [INFO] Selected 20 target genomes.
[2023-06-04 20:01:58,605] [INFO] Target genome list was writen to GCA_934331055.1_ERR7738661_bin.399_genomic.fna/target_genomes.txt
[2023-06-04 20:01:58,609] [INFO] Task started: fastANI
[2023-06-04 20:01:58,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg431734a9-1b21-4b19-9593-72d8696fe65b/GCA_934331055.1_ERR7738661_bin.399_genomic.fna.gz --refList GCA_934331055.1_ERR7738661_bin.399_genomic.fna/target_genomes.txt --output GCA_934331055.1_ERR7738661_bin.399_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 20:02:08,712] [INFO] Task succeeded: fastANI
[2023-06-04 20:02:08,713] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c082c66-6729-4dac-9922-3f7d4b3d9d6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 20:02:08,713] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c082c66-6729-4dac-9922-3f7d4b3d9d6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 20:02:08,721] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 20:02:08,721] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 20:02:08,722] [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
Eubacterium ventriosum	strain=ATCC 27560	GCA_000153885.1	39496	39496	suspected-type	True	80.3279	279	740	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_025150745.1	39496	39496	suspected-type	True	80.2988	281	740	95	below_threshold
Eubacterium uniforme	strain=ATCC 35992	GCA_900167115.1	39495	39495	type	True	77.9844	96	740	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	77.2405	60	740	95	below_threshold
Lachnotalea glycerini	strain=DSM 28816	GCA_003201285.1	1763509	1763509	type	True	76.3719	59	740	95	below_threshold
[Clostridium] polysaccharolyticum	strain=DSM 1801	GCA_900111595.1	29364	29364	type	True	76.3386	51	740	95	below_threshold
Anaerosacchariphilus polymeriproducens	strain=MCWD5	GCA_003363435.1	1812858	1812858	type	True	76.034	50	740	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 20:02:08,724] [INFO] DFAST Taxonomy check result was written to GCA_934331055.1_ERR7738661_bin.399_genomic.fna/tc_result.tsv
[2023-06-04 20:02:08,725] [INFO] ===== Taxonomy check completed =====
[2023-06-04 20:02:08,725] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 20:02:08,725] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c082c66-6729-4dac-9922-3f7d4b3d9d6c/dqc_reference/checkm_data
[2023-06-04 20:02:08,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 20:02:08,751] [INFO] Task started: CheckM
[2023-06-04 20:02:08,751] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934331055.1_ERR7738661_bin.399_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934331055.1_ERR7738661_bin.399_genomic.fna/checkm_input GCA_934331055.1_ERR7738661_bin.399_genomic.fna/checkm_result
[2023-06-04 20:02:29,061] [INFO] Task succeeded: CheckM
[2023-06-04 20:02:29,062] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 20:02:29,087] [INFO] ===== Completeness check finished =====
[2023-06-04 20:02:29,087] [INFO] ===== Start GTDB Search =====
[2023-06-04 20:02:29,088] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934331055.1_ERR7738661_bin.399_genomic.fna/markers.fasta)
[2023-06-04 20:02:29,088] [INFO] Task started: Blastn
[2023-06-04 20:02:29,088] [INFO] Running command: blastn -query GCA_934331055.1_ERR7738661_bin.399_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c082c66-6729-4dac-9922-3f7d4b3d9d6c/dqc_reference/reference_markers_gtdb.fasta -out GCA_934331055.1_ERR7738661_bin.399_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:02:30,056] [INFO] Task succeeded: Blastn
[2023-06-04 20:02:30,060] [INFO] Selected 11 target genomes.
[2023-06-04 20:02:30,061] [INFO] Target genome list was writen to GCA_934331055.1_ERR7738661_bin.399_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 20:02:30,078] [INFO] Task started: fastANI
[2023-06-04 20:02:30,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg431734a9-1b21-4b19-9593-72d8696fe65b/GCA_934331055.1_ERR7738661_bin.399_genomic.fna.gz --refList GCA_934331055.1_ERR7738661_bin.399_genomic.fna/target_genomes_gtdb.txt --output GCA_934331055.1_ERR7738661_bin.399_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 20:02:34,911] [INFO] Task succeeded: fastANI
[2023-06-04 20:02:34,921] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 20:02:34,921] [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_900550135.1	s__Eubacterium_G sp900550135	95.7607	526	740	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.87	97.32	0.76	0.74	4	conclusive
GCF_003460505.1	s__Eubacterium_G sp000435815	82.5928	399	740	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.79	97.65	0.84	0.54	8	-
GCA_900548465.1	s__Eubacterium_G sp900548465	80.6929	309	740	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	97.75	97.64	0.80	0.72	3	-
GCF_000153885.1	s__Eubacterium_G ventriosum	80.3279	279	740	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.27	97.67	0.81	0.64	20	-
GCF_003479405.1	s__Eubacterium_G sp000432355	80.1195	297	740	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	99.22	97.56	0.94	0.86	9	-
GCA_910584795.1	s__Eubacterium_G sp910584795	79.5524	280	740	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578975.1	s__Eubacterium_G sp910578975	79.5029	283	740	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910574895.1	s__Eubacterium_G sp910574895	79.481	299	740	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363805.1	s__Eubacterium_G sp000434315	79.3999	211	740	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.27	98.14	0.87	0.84	6	-
GCF_900111595.1	s__Clostridium_AI polysaccharolyticum	76.304	52	740	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_AI	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 20:02:34,923] [INFO] GTDB search result was written to GCA_934331055.1_ERR7738661_bin.399_genomic.fna/result_gtdb.tsv
[2023-06-04 20:02:34,924] [INFO] ===== GTDB Search completed =====
[2023-06-04 20:02:34,927] [INFO] DFAST_QC result json was written to GCA_934331055.1_ERR7738661_bin.399_genomic.fna/dqc_result.json
[2023-06-04 20:02:34,928] [INFO] DFAST_QC completed!
[2023-06-04 20:02:34,928] [INFO] Total running time: 0h0m45s