[2023-06-08 17:09:19,009] [INFO] DFAST_QC pipeline started.
[2023-06-08 17:09:19,014] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 17:09:19,014] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e27385e-e14f-4e05-9c89-14a272611db1/dqc_reference
[2023-06-08 17:09:20,362] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 17:09:20,363] [INFO] Task started: Prodigal
[2023-06-08 17:09:20,363] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ffed452-b094-4894-82d8-f4d6a02a6746/GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 17:09:23,259] [INFO] Task succeeded: Prodigal
[2023-06-08 17:09:23,259] [INFO] Task started: HMMsearch
[2023-06-08 17:09:23,259] [INFO] Running command: hmmsearch --tblout GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e27385e-e14f-4e05-9c89-14a272611db1/dqc_reference/reference_markers.hmm GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 17:09:23,485] [INFO] Task succeeded: HMMsearch
[2023-06-08 17:09:23,486] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8ffed452-b094-4894-82d8-f4d6a02a6746/GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 17:09:23,506] [INFO] Query marker FASTA was written to GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 17:09:23,506] [INFO] Task started: Blastn
[2023-06-08 17:09:23,506] [INFO] Running command: blastn -query GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e27385e-e14f-4e05-9c89-14a272611db1/dqc_reference/reference_markers.fasta -out GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:09:24,123] [INFO] Task succeeded: Blastn
[2023-06-08 17:09:24,127] [INFO] Selected 17 target genomes.
[2023-06-08 17:09:24,127] [INFO] Target genome list was writen to GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 17:09:24,133] [INFO] Task started: fastANI
[2023-06-08 17:09:24,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ffed452-b094-4894-82d8-f4d6a02a6746/GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 17:09:33,467] [INFO] Task succeeded: fastANI
[2023-06-08 17:09:33,468] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e27385e-e14f-4e05-9c89-14a272611db1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 17:09:33,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e27385e-e14f-4e05-9c89-14a272611db1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 17:09:33,473] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2023-06-08 17:09:33,473] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 17:09:33,473] [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
Turicibacter bilis	strain=MMM721	GCA_024499055.1	2735723	2735723	type	True	98.6783	415	435	95	conclusive
Turicibacter bilis	strain=MMM721	GCA_018305205.1	2735723	2735723	type	True	98.6721	413	435	95	conclusive
Turicibacter sanguinis	strain=MOL361	GCA_013046825.1	154288	154288	type	True	80.9532	240	435	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 17:09:33,477] [INFO] DFAST Taxonomy check result was written to GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 17:09:33,479] [INFO] ===== Taxonomy check completed =====
[2023-06-08 17:09:33,479] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 17:09:33,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e27385e-e14f-4e05-9c89-14a272611db1/dqc_reference/checkm_data
[2023-06-08 17:09:33,481] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 17:09:33,505] [INFO] Task started: CheckM
[2023-06-08 17:09:33,505] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 17:09:50,531] [INFO] Task succeeded: CheckM
[2023-06-08 17:09:50,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 17:09:50,557] [INFO] ===== Completeness check finished =====
[2023-06-08 17:09:50,557] [INFO] ===== Start GTDB Search =====
[2023-06-08 17:09:50,558] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 17:09:50,558] [INFO] Task started: Blastn
[2023-06-08 17:09:50,558] [INFO] Running command: blastn -query GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e27385e-e14f-4e05-9c89-14a272611db1/dqc_reference/reference_markers_gtdb.fasta -out GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:09:51,453] [INFO] Task succeeded: Blastn
[2023-06-08 17:09:51,457] [INFO] Selected 17 target genomes.
[2023-06-08 17:09:51,457] [INFO] Target genome list was writen to GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 17:09:51,464] [INFO] Task started: fastANI
[2023-06-08 17:09:51,465] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ffed452-b094-4894-82d8-f4d6a02a6746/GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 17:09:59,855] [INFO] Task succeeded: fastANI
[2023-06-08 17:09:59,864] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 17:09:59,864] [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_001543345.1	s__Turicibacter sp001543345	99.1893	417	435	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	98.30	97.82	0.87	0.78	10	conclusive
GCA_017888305.1	s__Turicibacter sp017888305	82.9945	255	435	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013046825.1	s__Turicibacter sanguinis	80.9532	240	435	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	99.52	99.21	0.94	0.89	18	-
GCA_002493395.1	s__Turicibacter sp002493395	80.4531	186	435	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009935875.1	s__Turicibacter sp002311155	80.2363	198	435	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	99.25	99.25	0.93	0.91	3	-
GCA_003486705.1	s__Turicibacter sp003486705	78.1876	111	435	d__Bacteria;p__Firmicutes;c__Bacilli;o__Haloplasmatales_A;f__Turicibacteraceae;g__Turicibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 17:09:59,866] [INFO] GTDB search result was written to GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 17:09:59,867] [INFO] ===== GTDB Search completed =====
[2023-06-08 17:09:59,870] [INFO] DFAST_QC result json was written to GCA_945971345.1_SRR15725430_bin.26_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 17:09:59,870] [INFO] DFAST_QC completed!
[2023-06-08 17:09:59,870] [INFO] Total running time: 0h0m41s