[2023-06-08 17:09:11,622] [INFO] DFAST_QC pipeline started.
[2023-06-08 17:09:11,624] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 17:09:11,624] [INFO] DQC Reference Directory: /var/lib/cwl/stg947af39b-0546-458f-a833-919d97a95b34/dqc_reference
[2023-06-08 17:09:12,801] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 17:09:12,802] [INFO] Task started: Prodigal
[2023-06-08 17:09:12,802] [INFO] Running command: gunzip -c /var/lib/cwl/stg478fb394-dd2c-4b24-bc9f-3aaf98a231e5/GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 17:09:18,183] [INFO] Task succeeded: Prodigal
[2023-06-08 17:09:18,184] [INFO] Task started: HMMsearch
[2023-06-08 17:09:18,184] [INFO] Running command: hmmsearch --tblout GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg947af39b-0546-458f-a833-919d97a95b34/dqc_reference/reference_markers.hmm GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 17:09:18,437] [INFO] Task succeeded: HMMsearch
[2023-06-08 17:09:18,439] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg478fb394-dd2c-4b24-bc9f-3aaf98a231e5/GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 17:09:18,472] [INFO] Query marker FASTA was written to GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 17:09:18,472] [INFO] Task started: Blastn
[2023-06-08 17:09:18,472] [INFO] Running command: blastn -query GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg947af39b-0546-458f-a833-919d97a95b34/dqc_reference/reference_markers.fasta -out GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:09:19,057] [INFO] Task succeeded: Blastn
[2023-06-08 17:09:19,061] [INFO] Selected 15 target genomes.
[2023-06-08 17:09:19,061] [INFO] Target genome list was writen to GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 17:09:19,062] [INFO] Task started: fastANI
[2023-06-08 17:09:19,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg478fb394-dd2c-4b24-bc9f-3aaf98a231e5/GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 17:09:27,828] [INFO] Task succeeded: fastANI
[2023-06-08 17:09:27,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg947af39b-0546-458f-a833-919d97a95b34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 17:09:27,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg947af39b-0546-458f-a833-919d97a95b34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 17:09:27,841] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 17:09:27,842] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 17:09:27,842] [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
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	86.9955	568	763	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	86.9269	544	763	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	86.2575	494	763	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	78.8096	218	763	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	78.7579	227	763	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	77.8228	161	763	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	77.3539	107	763	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	76.603	61	763	95	below_threshold
Blautia coccoides	strain=NCTC11035	GCA_900461125.1	1532	1532	type	True	76.3335	60	763	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	76.2695	59	763	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 17:09:27,844] [INFO] DFAST Taxonomy check result was written to GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 17:09:27,844] [INFO] ===== Taxonomy check completed =====
[2023-06-08 17:09:27,844] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 17:09:27,845] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg947af39b-0546-458f-a833-919d97a95b34/dqc_reference/checkm_data
[2023-06-08 17:09:27,846] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 17:09:27,874] [INFO] Task started: CheckM
[2023-06-08 17:09:27,874] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 17:09:51,414] [INFO] Task succeeded: CheckM
[2023-06-08 17:09:51,416] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.23%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 17:09:51,440] [INFO] ===== Completeness check finished =====
[2023-06-08 17:09:51,440] [INFO] ===== Start GTDB Search =====
[2023-06-08 17:09:51,441] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 17:09:51,441] [INFO] Task started: Blastn
[2023-06-08 17:09:51,442] [INFO] Running command: blastn -query GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg947af39b-0546-458f-a833-919d97a95b34/dqc_reference/reference_markers_gtdb.fasta -out GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:09:52,321] [INFO] Task succeeded: Blastn
[2023-06-08 17:09:52,326] [INFO] Selected 8 target genomes.
[2023-06-08 17:09:52,326] [INFO] Target genome list was writen to GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 17:09:52,328] [INFO] Task started: fastANI
[2023-06-08 17:09:52,329] [INFO] Running command: fastANI --query /var/lib/cwl/stg478fb394-dd2c-4b24-bc9f-3aaf98a231e5/GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 17:09:58,117] [INFO] Task succeeded: fastANI
[2023-06-08 17:09:58,130] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 17:09:58,130] [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_018919065.1	s__Blautia_A sp018919065	96.8614	616	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905209435.1	s__Blautia_A sp905209435	87.1423	530	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000484655.1	s__Blautia_A wexlerae	86.9121	545	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.38	96.15	0.76	0.65	140	-
GCF_013300825.1	s__Blautia_A wexlerae_B	86.2881	536	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.68	98.07	0.89	0.86	5	-
GCF_009707925.1	s__Blautia_A luti	86.2379	495	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.33	97.04	0.87	0.84	5	-
GCF_003471165.1	s__Blautia_A sp003471165	86.1282	576	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.40	97.74	0.83	0.79	20	-
GCF_003477525.1	s__Blautia_A sp003477525	85.4279	556	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.30	98.60	0.90	0.81	3	-
GCF_000210015.1	s__Blautia_A obeum_B	78.6401	214	763	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.64	98.44	0.85	0.84	7	-
--------------------------------------------------------------------------------
[2023-06-08 17:09:58,132] [INFO] GTDB search result was written to GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 17:09:58,133] [INFO] ===== GTDB Search completed =====
[2023-06-08 17:09:58,136] [INFO] DFAST_QC result json was written to GCA_945831645.1_SRR5240730_bin.9_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 17:09:58,136] [INFO] DFAST_QC completed!
[2023-06-08 17:09:58,136] [INFO] Total running time: 0h0m47s