[2023-06-08 20:04:30,355] [INFO] DFAST_QC pipeline started.
[2023-06-08 20:04:30,359] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 20:04:30,359] [INFO] DQC Reference Directory: /var/lib/cwl/stgb06af8d9-e0ce-4598-8813-4b5353017570/dqc_reference
[2023-06-08 20:04:33,037] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 20:04:33,038] [INFO] Task started: Prodigal
[2023-06-08 20:04:33,039] [INFO] Running command: gunzip -c /var/lib/cwl/stg3fc1e74d-3fc2-4a9a-b55f-50f31928c8f3/GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 20:04:36,118] [INFO] Task succeeded: Prodigal
[2023-06-08 20:04:36,119] [INFO] Task started: HMMsearch
[2023-06-08 20:04:36,119] [INFO] Running command: hmmsearch --tblout GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb06af8d9-e0ce-4598-8813-4b5353017570/dqc_reference/reference_markers.hmm GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 20:04:36,333] [INFO] Task succeeded: HMMsearch
[2023-06-08 20:04:36,335] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3fc1e74d-3fc2-4a9a-b55f-50f31928c8f3/GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 20:04:36,357] [INFO] Query marker FASTA was written to GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 20:04:36,358] [INFO] Task started: Blastn
[2023-06-08 20:04:36,358] [INFO] Running command: blastn -query GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb06af8d9-e0ce-4598-8813-4b5353017570/dqc_reference/reference_markers.fasta -out GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:04:36,907] [INFO] Task succeeded: Blastn
[2023-06-08 20:04:36,911] [INFO] Selected 12 target genomes.
[2023-06-08 20:04:36,912] [INFO] Target genome list was writen to GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 20:04:36,914] [INFO] Task started: fastANI
[2023-06-08 20:04:36,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fc1e74d-3fc2-4a9a-b55f-50f31928c8f3/GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 20:04:42,274] [INFO] Task succeeded: fastANI
[2023-06-08 20:04:42,275] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb06af8d9-e0ce-4598-8813-4b5353017570/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 20:04:42,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb06af8d9-e0ce-4598-8813-4b5353017570/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 20:04:42,284] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 20:04:42,284] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 20:04:42,284] [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
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	80.5493	211	320	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	78.6908	67	320	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	78.5571	142	320	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.0201	78	320	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.9704	134	320	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.9039	75	320	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.8036	88	320	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	77.5132	122	320	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.1912	75	320	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 20:04:42,286] [INFO] DFAST Taxonomy check result was written to GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 20:04:42,287] [INFO] ===== Taxonomy check completed =====
[2023-06-08 20:04:42,287] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 20:04:42,287] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb06af8d9-e0ce-4598-8813-4b5353017570/dqc_reference/checkm_data
[2023-06-08 20:04:42,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 20:04:42,308] [INFO] Task started: CheckM
[2023-06-08 20:04:42,308] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 20:04:58,720] [INFO] Task succeeded: CheckM
[2023-06-08 20:04:58,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.53%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 20:04:58,742] [INFO] ===== Completeness check finished =====
[2023-06-08 20:04:58,743] [INFO] ===== Start GTDB Search =====
[2023-06-08 20:04:58,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 20:04:58,744] [INFO] Task started: Blastn
[2023-06-08 20:04:58,744] [INFO] Running command: blastn -query GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb06af8d9-e0ce-4598-8813-4b5353017570/dqc_reference/reference_markers_gtdb.fasta -out GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:04:59,423] [INFO] Task succeeded: Blastn
[2023-06-08 20:04:59,427] [INFO] Selected 11 target genomes.
[2023-06-08 20:04:59,427] [INFO] Target genome list was writen to GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 20:04:59,463] [INFO] Task started: fastANI
[2023-06-08 20:04:59,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fc1e74d-3fc2-4a9a-b55f-50f31928c8f3/GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 20:05:04,340] [INFO] Task succeeded: fastANI
[2023-06-08 20:05:04,350] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 20:05:04,351] [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_017937405.1	s__Dysosmobacter sp017937405	87.2841	260	320	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770295.1	s__Dysosmobacter sp900770295	83.3215	262	320	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004558115.1	s__Dysosmobacter sp004558115	82.5052	199	320	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544955.1	s__Dysosmobacter sp900544955	81.7593	211	320	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118245.1	s__Dysosmobacter excrementigallinarum	81.5491	207	320	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018228705.1	s__Dysosmobacter sp018228705	81.4591	235	320	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551885.1	s__Dysosmobacter sp900551885	80.5592	174	320	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	99.92	99.85	0.92	0.84	3	-
GCA_900548505.1	s__Dysosmobacter sp900548505	80.4326	186	320	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017469475.1	s__Dysosmobacter sp017469475	80.3721	182	320	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	97.68	97.62	0.84	0.82	4	-
GCA_900546705.1	s__Dysosmobacter sp900546705	80.1859	184	320	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017482345.1	s__Dysosmobacter sp017482345	80.1732	137	320	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 20:05:04,353] [INFO] GTDB search result was written to GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 20:05:04,354] [INFO] ===== GTDB Search completed =====
[2023-06-08 20:05:04,357] [INFO] DFAST_QC result json was written to GCA_945836855.1_SRR5665903_bin.60_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 20:05:04,358] [INFO] DFAST_QC completed!
[2023-06-08 20:05:04,358] [INFO] Total running time: 0h0m34s