[2023-06-08 13:17:22,203] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:17:22,205] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:17:22,206] [INFO] DQC Reference Directory: /var/lib/cwl/stg75ac0f0f-b720-402b-98a2-9cf6961e273e/dqc_reference
[2023-06-08 13:17:23,488] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:17:23,489] [INFO] Task started: Prodigal
[2023-06-08 13:17:23,489] [INFO] Running command: gunzip -c /var/lib/cwl/stg12cc9453-63ce-4064-aa9c-dd93ba98b525/GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:17:28,645] [INFO] Task succeeded: Prodigal
[2023-06-08 13:17:28,646] [INFO] Task started: HMMsearch
[2023-06-08 13:17:28,646] [INFO] Running command: hmmsearch --tblout GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75ac0f0f-b720-402b-98a2-9cf6961e273e/dqc_reference/reference_markers.hmm GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:17:28,905] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:17:28,906] [INFO] Found 6/6 markers.
[2023-06-08 13:17:28,932] [INFO] Query marker FASTA was written to GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 13:17:28,932] [INFO] Task started: Blastn
[2023-06-08 13:17:28,933] [INFO] Running command: blastn -query GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg75ac0f0f-b720-402b-98a2-9cf6961e273e/dqc_reference/reference_markers.fasta -out GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:17:29,540] [INFO] Task succeeded: Blastn
[2023-06-08 13:17:29,557] [INFO] Selected 18 target genomes.
[2023-06-08 13:17:29,558] [INFO] Target genome list was writen to GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 13:17:29,562] [INFO] Task started: fastANI
[2023-06-08 13:17:29,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg12cc9453-63ce-4064-aa9c-dd93ba98b525/GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 13:17:41,365] [INFO] Task succeeded: fastANI
[2023-06-08 13:17:41,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75ac0f0f-b720-402b-98a2-9cf6961e273e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 13:17:41,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75ac0f0f-b720-402b-98a2-9cf6961e273e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 13:17:41,370] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2023-06-08 13:17:41,371] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 13:17:41,371] [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
Phascolarctobacterium faecium	strain=DSM 14760	GCA_003269275.1	33025	33025	type	True	98.9779	686	757	95	conclusive
Phascolarctobacterium succinatutens	strain=YIT 12067	GCA_000188175.1	626940	626940	type	True	77.4154	91	757	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 13:17:41,373] [INFO] DFAST Taxonomy check result was written to GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 13:17:41,373] [INFO] ===== Taxonomy check completed =====
[2023-06-08 13:17:41,374] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:17:41,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75ac0f0f-b720-402b-98a2-9cf6961e273e/dqc_reference/checkm_data
[2023-06-08 13:17:41,375] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:17:41,406] [INFO] Task started: CheckM
[2023-06-08 13:17:41,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 13:18:04,733] [INFO] Task succeeded: CheckM
[2023-06-08 13:18:04,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 13:18:04,756] [INFO] ===== Completeness check finished =====
[2023-06-08 13:18:04,757] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:18:04,757] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 13:18:04,758] [INFO] Task started: Blastn
[2023-06-08 13:18:04,758] [INFO] Running command: blastn -query GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg75ac0f0f-b720-402b-98a2-9cf6961e273e/dqc_reference/reference_markers_gtdb.fasta -out GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:18:05,631] [INFO] Task succeeded: Blastn
[2023-06-08 13:18:05,635] [INFO] Selected 11 target genomes.
[2023-06-08 13:18:05,635] [INFO] Target genome list was writen to GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:18:05,639] [INFO] Task started: fastANI
[2023-06-08 13:18:05,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg12cc9453-63ce-4064-aa9c-dd93ba98b525/GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:18:10,121] [INFO] Task succeeded: fastANI
[2023-06-08 13:18:10,140] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 13:18:10,140] [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_003269275.1	s__Phascolarctobacterium faecium	98.9779	686	757	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium	95.0	98.58	98.24	0.93	0.90	33	conclusive
GCA_900551745.1	s__Phascolarctobacterium sp900551745	94.5349	414	757	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium	95.0	98.93	98.93	0.62	0.62	2	-
GCA_900545535.1	s__Phascolarctobacterium sp900545535	85.7175	583	757	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium	95.0	97.61	97.37	0.85	0.81	3	-
GCA_900544795.1	s__Phascolarctobacterium sp900544795	81.9647	492	757	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium	95.0	99.13	98.29	0.95	0.93	3	-
GCA_900541915.1	s__Phascolarctobacterium_A sp900541915	78.1064	123	757	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	96.75	96.74	0.90	0.89	3	-
GCA_900545025.1	s__Phascolarctobacterium_A sp900545025	77.7413	129	757	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552005.1	s__Phascolarctobacterium_A sp900552005	77.2209	85	757	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017452325.1	s__Phascolarctobacterium_A sp017452325	77.1761	64	757	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757795.1	s__Phascolarctobacterium_A sp900757795	76.9955	79	757	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	97.50	97.50	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-08 13:18:10,142] [INFO] GTDB search result was written to GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 13:18:10,143] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:18:10,146] [INFO] DFAST_QC result json was written to GCA_945918445.1_SRR15057927_bin.12_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 13:18:10,146] [INFO] DFAST_QC completed!
[2023-06-08 13:18:10,146] [INFO] Total running time: 0h0m48s