[2023-06-29 01:46:03,284] [INFO] DFAST_QC pipeline started.
[2023-06-29 01:46:03,286] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 01:46:03,286] [INFO] DQC Reference Directory: /var/lib/cwl/stg499c7e53-c5ce-44c1-ae69-81fb923de7f5/dqc_reference
[2023-06-29 01:46:06,325] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 01:46:06,327] [INFO] Task started: Prodigal
[2023-06-29 01:46:06,327] [INFO] Running command: gunzip -c /var/lib/cwl/stgf6788fae-502d-41f1-86f9-9563601de51a/GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 01:46:13,138] [INFO] Task succeeded: Prodigal
[2023-06-29 01:46:13,138] [INFO] Task started: HMMsearch
[2023-06-29 01:46:13,138] [INFO] Running command: hmmsearch --tblout GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg499c7e53-c5ce-44c1-ae69-81fb923de7f5/dqc_reference/reference_markers.hmm GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 01:46:13,417] [INFO] Task succeeded: HMMsearch
[2023-06-29 01:46:13,418] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf6788fae-502d-41f1-86f9-9563601de51a/GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-29 01:46:13,457] [INFO] Query marker FASTA was written to GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-29 01:46:13,457] [INFO] Task started: Blastn
[2023-06-29 01:46:13,458] [INFO] Running command: blastn -query GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg499c7e53-c5ce-44c1-ae69-81fb923de7f5/dqc_reference/reference_markers.fasta -out GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 01:46:14,120] [INFO] Task succeeded: Blastn
[2023-06-29 01:46:14,124] [INFO] Selected 27 target genomes.
[2023-06-29 01:46:14,124] [INFO] Target genome list was writen to GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-29 01:46:14,125] [INFO] Task started: fastANI
[2023-06-29 01:46:14,126] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6788fae-502d-41f1-86f9-9563601de51a/GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 01:46:30,160] [INFO] Task succeeded: fastANI
[2023-06-29 01:46:30,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg499c7e53-c5ce-44c1-ae69-81fb923de7f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 01:46:30,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg499c7e53-c5ce-44c1-ae69-81fb923de7f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 01:46:30,163] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 01:46:30,163] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 01:46:30,163] [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
--------------------------------------------------------------------------------
[2023-06-29 01:46:30,165] [INFO] DFAST Taxonomy check result was written to GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-29 01:46:30,165] [INFO] ===== Taxonomy check completed =====
[2023-06-29 01:46:30,166] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 01:46:30,166] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg499c7e53-c5ce-44c1-ae69-81fb923de7f5/dqc_reference/checkm_data
[2023-06-29 01:46:30,169] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 01:46:30,199] [INFO] Task started: CheckM
[2023-06-29 01:46:30,199] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-29 01:46:56,362] [INFO] Task succeeded: CheckM
[2023-06-29 01:46:56,364] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 01:46:56,383] [INFO] ===== Completeness check finished =====
[2023-06-29 01:46:56,383] [INFO] ===== Start GTDB Search =====
[2023-06-29 01:46:56,384] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-29 01:46:56,384] [INFO] Task started: Blastn
[2023-06-29 01:46:56,385] [INFO] Running command: blastn -query GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg499c7e53-c5ce-44c1-ae69-81fb923de7f5/dqc_reference/reference_markers_gtdb.fasta -out GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 01:46:57,325] [INFO] Task succeeded: Blastn
[2023-06-29 01:46:57,330] [INFO] Selected 21 target genomes.
[2023-06-29 01:46:57,330] [INFO] Target genome list was writen to GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 01:46:57,345] [INFO] Task started: fastANI
[2023-06-29 01:46:57,345] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6788fae-502d-41f1-86f9-9563601de51a/GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 01:47:08,470] [INFO] Task succeeded: fastANI
[2023-06-29 01:47:08,481] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 01:47:08,482] [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_910574015.1	s__Eubacterium_F sp910574015	99.3644	783	834	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F	95.0	99.61	98.86	0.93	0.82	4	conclusive
GCA_910584875.1	s__Eubacterium_F sp910584875	79.5129	402	834	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F	95.0	98.24	98.24	0.92	0.92	2	-
GCA_910575665.1	s__Eubacterium_F sp910575665	77.6263	113	834	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F	95.0	98.59	95.46	0.90	0.84	7	-
GCA_900319095.1	s__Eubacterium_F sp900319095	77.2722	81	834	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F	95.0	99.89	99.89	0.98	0.98	2	-
GCA_002362575.1	s__Eubacterium_F sp002362575	77.2555	119	834	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F	95.0	99.97	99.97	0.97	0.97	2	-
GCA_000433735.1	s__Eubacterium_F sp000433735	76.9792	108	834	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F	95.0	98.51	97.83	0.95	0.95	3	-
GCA_910583555.1	s__Eubacterium_F sp910583555	76.8934	80	834	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002490465.1	s__Eubacterium_F sp002490465	76.863	86	834	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584065.1	s__Eubacterium_F sp910584065	76.7516	71	834	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 01:47:08,484] [INFO] GTDB search result was written to GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 01:47:08,484] [INFO] ===== GTDB Search completed =====
[2023-06-29 01:47:08,486] [INFO] DFAST_QC result json was written to GCA_948433995.1_SRR15604595_bin.33_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-29 01:47:08,487] [INFO] DFAST_QC completed!
[2023-06-29 01:47:08,487] [INFO] Total running time: 0h1m5s