[2023-06-13 06:34:01,350] [INFO] DFAST_QC pipeline started.
[2023-06-13 06:34:01,353] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 06:34:01,353] [INFO] DQC Reference Directory: /var/lib/cwl/stg3676ca1c-4324-48b9-814d-00f52b3b29e1/dqc_reference
[2023-06-13 06:34:02,612] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 06:34:02,613] [INFO] Task started: Prodigal
[2023-06-13 06:34:02,613] [INFO] Running command: gunzip -c /var/lib/cwl/stg87a39ace-1759-4573-b3d4-6a0da4690303/GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna/cds.fna -a GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 06:34:08,234] [INFO] Task succeeded: Prodigal
[2023-06-13 06:34:08,235] [INFO] Task started: HMMsearch
[2023-06-13 06:34:08,235] [INFO] Running command: hmmsearch --tblout GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3676ca1c-4324-48b9-814d-00f52b3b29e1/dqc_reference/reference_markers.hmm GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 06:34:08,483] [INFO] Task succeeded: HMMsearch
[2023-06-13 06:34:08,484] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg87a39ace-1759-4573-b3d4-6a0da4690303/GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna.gz]
[2023-06-13 06:34:08,509] [INFO] Query marker FASTA was written to GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 06:34:08,510] [INFO] Task started: Blastn
[2023-06-13 06:34:08,510] [INFO] Running command: blastn -query GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg3676ca1c-4324-48b9-814d-00f52b3b29e1/dqc_reference/reference_markers.fasta -out GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:34:09,146] [INFO] Task succeeded: Blastn
[2023-06-13 06:34:09,150] [INFO] Selected 24 target genomes.
[2023-06-13 06:34:09,150] [INFO] Target genome list was writen to GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 06:34:09,152] [INFO] Task started: fastANI
[2023-06-13 06:34:09,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg87a39ace-1759-4573-b3d4-6a0da4690303/GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 06:34:21,932] [INFO] Task succeeded: fastANI
[2023-06-13 06:34:21,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3676ca1c-4324-48b9-814d-00f52b3b29e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 06:34:21,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3676ca1c-4324-48b9-814d-00f52b3b29e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 06:34:21,937] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 06:34:21,938] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 06:34:21,938] [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
Anaeromassilibacillus senegalensis	strain=mt9	GCA_001261775.1	1673717	1673717	type	True	77.0643	77	690	95	below_threshold
Clostridium jeddahense	strain=JCD	GCA_000577335.1	1414721	1414721	type	True	76.8695	74	690	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 06:34:21,940] [INFO] DFAST Taxonomy check result was written to GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 06:34:21,940] [INFO] ===== Taxonomy check completed =====
[2023-06-13 06:34:21,941] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 06:34:21,941] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3676ca1c-4324-48b9-814d-00f52b3b29e1/dqc_reference/checkm_data
[2023-06-13 06:34:21,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 06:34:21,973] [INFO] Task started: CheckM
[2023-06-13 06:34:21,973] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna/checkm_input GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 06:34:44,913] [INFO] Task succeeded: CheckM
[2023-06-13 06:34:44,914] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 06:34:44,932] [INFO] ===== Completeness check finished =====
[2023-06-13 06:34:44,932] [INFO] ===== Start GTDB Search =====
[2023-06-13 06:34:44,933] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 06:34:44,933] [INFO] Task started: Blastn
[2023-06-13 06:34:44,934] [INFO] Running command: blastn -query GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg3676ca1c-4324-48b9-814d-00f52b3b29e1/dqc_reference/reference_markers_gtdb.fasta -out GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:34:45,936] [INFO] Task succeeded: Blastn
[2023-06-13 06:34:45,941] [INFO] Selected 15 target genomes.
[2023-06-13 06:34:45,941] [INFO] Target genome list was writen to GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 06:34:45,946] [INFO] Task started: fastANI
[2023-06-13 06:34:45,946] [INFO] Running command: fastANI --query /var/lib/cwl/stg87a39ace-1759-4573-b3d4-6a0da4690303/GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 06:34:53,438] [INFO] Task succeeded: fastANI
[2023-06-13 06:34:53,454] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 06:34:53,454] [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_018712265.1	s__Gallacutalibacter pullicola	97.9895	603	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Gallacutalibacter	95.0	98.09	98.02	0.89	0.86	4	conclusive
GCF_002160025.1	s__Caccousia stercoris	77.7321	109	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caccousia	95.0	99.23	99.23	0.95	0.95	2	-
GCA_018712435.1	s__Caccousia avicola	77.726	111	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caccousia	95.0	98.29	98.29	0.88	0.88	2	-
GCF_002159845.1	s__Anaeromassilibacillus stercoravium	77.3356	93	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Anaeromassilibacillus	95.0	98.79	98.27	0.94	0.87	13	-
GCF_015667585.1	s__Anaeromassilibacillus sp015667585	77.24	97	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Anaeromassilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001261775.1	s__Anaeromassilibacillus senegalensis	77.0643	77	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Anaeromassilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018710915.1	s__Heritagella pullistercoris	76.798	56	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Heritagella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002305575.1	s__UBA1417 sp002305575	76.7871	59	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	98.68	98.68	0.86	0.86	2	-
GCA_902810075.1	s__Clostridium_E sp002397665	76.6617	91	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Clostridium_E	95.0	97.21	97.21	0.87	0.87	2	-
GCA_012517675.1	s__Caproiciproducens sp012517675	76.6317	78	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproiciproducens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215105.1	s__Heritagella sp905215105	76.6282	56	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Heritagella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000752215.1	s__Caproiciproducens sp000752215	76.5952	84	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproiciproducens	95.0	98.70	97.09	0.94	0.88	5	-
--------------------------------------------------------------------------------
[2023-06-13 06:34:53,456] [INFO] GTDB search result was written to GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 06:34:53,457] [INFO] ===== GTDB Search completed =====
[2023-06-13 06:34:53,462] [INFO] DFAST_QC result json was written to GCA_930971555.1_ERR3414576_bin.106_metaWRAP_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 06:34:53,462] [INFO] DFAST_QC completed!
[2023-06-13 06:34:53,462] [INFO] Total running time: 0h0m52s