[2023-06-08 11:33:35,159] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:33:35,168] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:33:35,168] [INFO] DQC Reference Directory: /var/lib/cwl/stg804ad9a6-0bd8-454a-b29d-790daaddb508/dqc_reference
[2023-06-08 11:33:36,341] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:33:36,342] [INFO] Task started: Prodigal
[2023-06-08 11:33:36,342] [INFO] Running command: gunzip -c /var/lib/cwl/stg372bb277-9bd9-4824-b2e1-46af70c93737/GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:33:41,201] [INFO] Task succeeded: Prodigal
[2023-06-08 11:33:41,201] [INFO] Task started: HMMsearch
[2023-06-08 11:33:41,202] [INFO] Running command: hmmsearch --tblout GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg804ad9a6-0bd8-454a-b29d-790daaddb508/dqc_reference/reference_markers.hmm GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:33:41,430] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:33:41,432] [INFO] Found 6/6 markers.
[2023-06-08 11:33:41,456] [INFO] Query marker FASTA was written to GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 11:33:41,457] [INFO] Task started: Blastn
[2023-06-08 11:33:41,457] [INFO] Running command: blastn -query GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg804ad9a6-0bd8-454a-b29d-790daaddb508/dqc_reference/reference_markers.fasta -out GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:33:42,156] [INFO] Task succeeded: Blastn
[2023-06-08 11:33:42,161] [INFO] Selected 19 target genomes.
[2023-06-08 11:33:42,161] [INFO] Target genome list was writen to GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 11:33:42,163] [INFO] Task started: fastANI
[2023-06-08 11:33:42,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg372bb277-9bd9-4824-b2e1-46af70c93737/GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 11:33:49,124] [INFO] Task succeeded: fastANI
[2023-06-08 11:33:49,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg804ad9a6-0bd8-454a-b29d-790daaddb508/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 11:33:49,125] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg804ad9a6-0bd8-454a-b29d-790daaddb508/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 11:33:49,134] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 11:33:49,134] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 11:33:49,134] [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
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.5844	92	554	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.4611	63	554	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.2554	105	554	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	76.9673	69	554	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	76.6728	51	554	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	76.6543	92	554	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	76.5819	72	554	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	76.5781	68	554	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 11:33:49,136] [INFO] DFAST Taxonomy check result was written to GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 11:33:49,137] [INFO] ===== Taxonomy check completed =====
[2023-06-08 11:33:49,137] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:33:49,137] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg804ad9a6-0bd8-454a-b29d-790daaddb508/dqc_reference/checkm_data
[2023-06-08 11:33:49,138] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:33:49,159] [INFO] Task started: CheckM
[2023-06-08 11:33:49,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 11:34:10,455] [INFO] Task succeeded: CheckM
[2023-06-08 11:34:10,456] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.46%
Contamintation: 11.34%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-06-08 11:34:10,481] [INFO] ===== Completeness check finished =====
[2023-06-08 11:34:10,482] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:34:10,482] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 11:34:10,482] [INFO] Task started: Blastn
[2023-06-08 11:34:10,483] [INFO] Running command: blastn -query GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg804ad9a6-0bd8-454a-b29d-790daaddb508/dqc_reference/reference_markers_gtdb.fasta -out GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:34:11,666] [INFO] Task succeeded: Blastn
[2023-06-08 11:34:11,670] [INFO] Selected 10 target genomes.
[2023-06-08 11:34:11,671] [INFO] Target genome list was writen to GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:34:11,672] [INFO] Task started: fastANI
[2023-06-08 11:34:11,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg372bb277-9bd9-4824-b2e1-46af70c93737/GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:34:15,874] [INFO] Task succeeded: fastANI
[2023-06-08 11:34:15,884] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 11:34:15,885] [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_000765235.1	s__ER4 sp000765235	97.0928	495	554	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	96.82	96.40	0.83	0.70	19	conclusive
GCA_900552015.1	s__ER4 sp900552015	90.8478	394	554	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900550165.1	s__ER4 sp900550165	89.0181	374	554	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	96.79	96.53	0.85	0.84	4	-
GCA_900763705.1	s__ER4 sp900763705	88.2657	326	554	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003522105.1	s__ER4 sp003522105	88.2002	362	554	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	97.35	97.09	0.78	0.74	7	-
GCA_900546295.1	s__ER4 sp900546295	87.3308	367	554	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	98.01	98.01	0.87	0.87	2	-
GCA_900556145.1	s__ER4 sp900556145	86.0766	251	554	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002405995.1	s__ER4 sp002405995	85.5248	343	554	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	99.39	99.39	0.82	0.82	2	-
GCA_900549405.1	s__Lawsonibacter sp900549405	77.199	65	554	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	97.96	97.96	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-08 11:34:15,887] [INFO] GTDB search result was written to GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 11:34:15,887] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:34:15,891] [INFO] DFAST_QC result json was written to GCA_945877165.1_SRR17382106_bin.6_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 11:34:15,891] [INFO] DFAST_QC completed!
[2023-06-08 11:34:15,891] [INFO] Total running time: 0h0m41s