[2023-06-08 12:26:45,471] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:26:45,484] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:26:45,484] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf18b5ae-5174-4d5c-9a84-83de4f524027/dqc_reference
[2023-06-08 12:26:46,694] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:26:46,696] [INFO] Task started: Prodigal
[2023-06-08 12:26:46,696] [INFO] Running command: gunzip -c /var/lib/cwl/stgea68a8de-535d-49d9-b283-dd0e83fa6296/GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:26:49,610] [INFO] Task succeeded: Prodigal
[2023-06-08 12:26:49,611] [INFO] Task started: HMMsearch
[2023-06-08 12:26:49,611] [INFO] Running command: hmmsearch --tblout GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf18b5ae-5174-4d5c-9a84-83de4f524027/dqc_reference/reference_markers.hmm GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:26:49,802] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:26:49,803] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgea68a8de-535d-49d9-b283-dd0e83fa6296/GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 12:26:49,822] [INFO] Query marker FASTA was written to GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 12:26:49,823] [INFO] Task started: Blastn
[2023-06-08 12:26:49,823] [INFO] Running command: blastn -query GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf18b5ae-5174-4d5c-9a84-83de4f524027/dqc_reference/reference_markers.fasta -out GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:26:50,419] [INFO] Task succeeded: Blastn
[2023-06-08 12:26:50,427] [INFO] Selected 23 target genomes.
[2023-06-08 12:26:50,427] [INFO] Target genome list was writen to GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 12:26:50,432] [INFO] Task started: fastANI
[2023-06-08 12:26:50,432] [INFO] Running command: fastANI --query /var/lib/cwl/stgea68a8de-535d-49d9-b283-dd0e83fa6296/GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:27:02,971] [INFO] Task succeeded: fastANI
[2023-06-08 12:27:02,972] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf18b5ae-5174-4d5c-9a84-83de4f524027/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:27:02,972] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf18b5ae-5174-4d5c-9a84-83de4f524027/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:27:02,976] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:27:02,977] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 12:27:02,977] [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
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	76.9285	63	323	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	76.2691	51	323	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 12:27:02,981] [INFO] DFAST Taxonomy check result was written to GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 12:27:02,982] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:27:02,982] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:27:02,982] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf18b5ae-5174-4d5c-9a84-83de4f524027/dqc_reference/checkm_data
[2023-06-08 12:27:02,984] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:27:03,001] [INFO] Task started: CheckM
[2023-06-08 12:27:03,001] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 12:27:21,270] [INFO] Task succeeded: CheckM
[2023-06-08 12:27:21,271] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.39%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:27:21,308] [INFO] ===== Completeness check finished =====
[2023-06-08 12:27:21,308] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:27:21,309] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 12:27:21,309] [INFO] Task started: Blastn
[2023-06-08 12:27:21,309] [INFO] Running command: blastn -query GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf18b5ae-5174-4d5c-9a84-83de4f524027/dqc_reference/reference_markers_gtdb.fasta -out GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:27:22,084] [INFO] Task succeeded: Blastn
[2023-06-08 12:27:22,088] [INFO] Selected 26 target genomes.
[2023-06-08 12:27:22,088] [INFO] Target genome list was writen to GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:27:22,096] [INFO] Task started: fastANI
[2023-06-08 12:27:22,097] [INFO] Running command: fastANI --query /var/lib/cwl/stgea68a8de-535d-49d9-b283-dd0e83fa6296/GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:27:34,890] [INFO] Task succeeded: fastANI
[2023-06-08 12:27:34,895] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 12:27:34,895] [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_009695765.1	s__VUNI01 sp009695765	76.9678	62	323	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__VUNI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363675.1	s__Agathobacter sp000434275	76.4812	52	323	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	99.18	99.14	0.93	0.89	5	-
GCF_001406815.1	s__Agathobacter faecis	76.2675	51	323	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.10	97.07	0.85	0.62	43	-
--------------------------------------------------------------------------------
[2023-06-08 12:27:34,897] [INFO] GTDB search result was written to GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 12:27:34,897] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:27:34,899] [INFO] DFAST_QC result json was written to GCA_945788065.1_SRR3178347_bin.51_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 12:27:34,900] [INFO] DFAST_QC completed!
[2023-06-08 12:27:34,900] [INFO] Total running time: 0h0m49s