[2023-06-08 09:53:45,600] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:53:45,606] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:53:45,607] [INFO] DQC Reference Directory: /var/lib/cwl/stg87ed2fe5-f04f-4d1c-94de-75213793b4ab/dqc_reference
[2023-06-08 09:53:47,180] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:53:47,185] [INFO] Task started: Prodigal
[2023-06-08 09:53:47,185] [INFO] Running command: gunzip -c /var/lib/cwl/stga6d2c2d6-ffdd-459b-a3e1-136f4c380427/GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:53:50,546] [INFO] Task succeeded: Prodigal
[2023-06-08 09:53:50,547] [INFO] Task started: HMMsearch
[2023-06-08 09:53:50,547] [INFO] Running command: hmmsearch --tblout GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87ed2fe5-f04f-4d1c-94de-75213793b4ab/dqc_reference/reference_markers.hmm GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:53:50,755] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:53:50,756] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga6d2c2d6-ffdd-459b-a3e1-136f4c380427/GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 09:53:50,776] [INFO] Query marker FASTA was written to GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 09:53:50,777] [INFO] Task started: Blastn
[2023-06-08 09:53:50,777] [INFO] Running command: blastn -query GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg87ed2fe5-f04f-4d1c-94de-75213793b4ab/dqc_reference/reference_markers.fasta -out GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:53:51,407] [INFO] Task succeeded: Blastn
[2023-06-08 09:53:51,411] [INFO] Selected 13 target genomes.
[2023-06-08 09:53:51,411] [INFO] Target genome list was writen to GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 09:53:51,414] [INFO] Task started: fastANI
[2023-06-08 09:53:51,414] [INFO] Running command: fastANI --query /var/lib/cwl/stga6d2c2d6-ffdd-459b-a3e1-136f4c380427/GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:54:02,731] [INFO] Task succeeded: fastANI
[2023-06-08 09:54:02,732] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87ed2fe5-f04f-4d1c-94de-75213793b4ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:54:02,732] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87ed2fe5-f04f-4d1c-94de-75213793b4ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:54:02,736] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2023-06-08 09:54:02,736] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 09:54:02,736] [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
Butyricicoccus porcorum	strain=BB10	GCA_002157465.1	1945634	1945634	type	True	99.7313	285	290	95	conclusive
Butyricicoccus intestinisimiae	strain=MSJd-7	GCA_018918345.1	2841509	2841509	type	True	79.6797	150	290	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 09:54:02,738] [INFO] DFAST Taxonomy check result was written to GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 09:54:02,739] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:54:02,739] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:54:02,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87ed2fe5-f04f-4d1c-94de-75213793b4ab/dqc_reference/checkm_data
[2023-06-08 09:54:02,740] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:54:02,756] [INFO] Task started: CheckM
[2023-06-08 09:54:02,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 09:54:20,846] [INFO] Task succeeded: CheckM
[2023-06-08 09:54:20,848] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.10%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:54:20,870] [INFO] ===== Completeness check finished =====
[2023-06-08 09:54:20,870] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:54:20,871] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 09:54:20,871] [INFO] Task started: Blastn
[2023-06-08 09:54:20,871] [INFO] Running command: blastn -query GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg87ed2fe5-f04f-4d1c-94de-75213793b4ab/dqc_reference/reference_markers_gtdb.fasta -out GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:54:21,689] [INFO] Task succeeded: Blastn
[2023-06-08 09:54:21,694] [INFO] Selected 9 target genomes.
[2023-06-08 09:54:21,694] [INFO] Target genome list was writen to GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:54:21,700] [INFO] Task started: fastANI
[2023-06-08 09:54:21,700] [INFO] Running command: fastANI --query /var/lib/cwl/stga6d2c2d6-ffdd-459b-a3e1-136f4c380427/GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:54:25,308] [INFO] Task succeeded: fastANI
[2023-06-08 09:54:25,319] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 09:54:25,320] [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_002157465.1	s__Butyricicoccus_A porcorum	99.7313	285	290	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A	95.0	99.36	99.36	0.89	0.89	2	conclusive
GCA_019112985.1	s__Butyricicoccus_A stercorigallinarum	83.2395	229	290	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002449635.1	s__Butyricicoccus_A sp002449635	80.6892	153	290	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A	95.0	99.64	99.40	0.85	0.80	8	-
GCA_004555915.1	s__Butyricicoccus_A sp004555915	80.0405	183	290	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A	95.0	99.18	99.18	0.98	0.98	2	-
GCA_016293155.1	s__JAEDEU01 sp016293155	79.7007	98	290	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__JAEDEU01	95.0	98.88	98.88	0.85	0.85	2	-
GCF_018918345.1	s__Butyricicoccus_A sp002395695	79.6797	150	290	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A	95.0	98.08	98.03	0.91	0.78	6	-
--------------------------------------------------------------------------------
[2023-06-08 09:54:25,322] [INFO] GTDB search result was written to GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 09:54:25,322] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:54:25,325] [INFO] DFAST_QC result json was written to GCA_945827415.1_SRR5976182_bin.19_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 09:54:25,325] [INFO] DFAST_QC completed!
[2023-06-08 09:54:25,325] [INFO] Total running time: 0h0m40s