[2023-06-08 13:17:58,432] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:17:58,435] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:17:58,435] [INFO] DQC Reference Directory: /var/lib/cwl/stg13ef6fcb-4140-4980-891d-1d405d01fdc5/dqc_reference
[2023-06-08 13:17:59,660] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:17:59,661] [INFO] Task started: Prodigal
[2023-06-08 13:17:59,661] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b54ad25-e41d-4452-8ed2-cfc38ac574dc/GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:18:04,975] [INFO] Task succeeded: Prodigal
[2023-06-08 13:18:04,976] [INFO] Task started: HMMsearch
[2023-06-08 13:18:04,976] [INFO] Running command: hmmsearch --tblout GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13ef6fcb-4140-4980-891d-1d405d01fdc5/dqc_reference/reference_markers.hmm GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:18:05,217] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:18:05,219] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3b54ad25-e41d-4452-8ed2-cfc38ac574dc/GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-08 13:18:05,250] [INFO] Query marker FASTA was written to GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 13:18:05,251] [INFO] Task started: Blastn
[2023-06-08 13:18:05,251] [INFO] Running command: blastn -query GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg13ef6fcb-4140-4980-891d-1d405d01fdc5/dqc_reference/reference_markers.fasta -out GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:18:05,851] [INFO] Task succeeded: Blastn
[2023-06-08 13:18:05,856] [INFO] Selected 25 target genomes.
[2023-06-08 13:18:05,857] [INFO] Target genome list was writen to GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 13:18:05,860] [INFO] Task started: fastANI
[2023-06-08 13:18:05,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b54ad25-e41d-4452-8ed2-cfc38ac574dc/GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 13:18:18,524] [INFO] Task succeeded: fastANI
[2023-06-08 13:18:18,525] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13ef6fcb-4140-4980-891d-1d405d01fdc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 13:18:18,526] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13ef6fcb-4140-4980-891d-1d405d01fdc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 13:18:18,528] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 13:18:18,528] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 13:18:18,528] [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
--------------------------------------------------------------------------------
[2023-06-08 13:18:18,531] [INFO] DFAST Taxonomy check result was written to GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 13:18:18,531] [INFO] ===== Taxonomy check completed =====
[2023-06-08 13:18:18,532] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:18:18,532] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13ef6fcb-4140-4980-891d-1d405d01fdc5/dqc_reference/checkm_data
[2023-06-08 13:18:18,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:18:18,567] [INFO] Task started: CheckM
[2023-06-08 13:18:18,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 13:18:41,150] [INFO] Task succeeded: CheckM
[2023-06-08 13:18:41,151] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 13:18:41,178] [INFO] ===== Completeness check finished =====
[2023-06-08 13:18:41,178] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:18:41,178] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 13:18:41,179] [INFO] Task started: Blastn
[2023-06-08 13:18:41,179] [INFO] Running command: blastn -query GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg13ef6fcb-4140-4980-891d-1d405d01fdc5/dqc_reference/reference_markers_gtdb.fasta -out GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:18:42,049] [INFO] Task succeeded: Blastn
[2023-06-08 13:18:42,054] [INFO] Selected 22 target genomes.
[2023-06-08 13:18:42,054] [INFO] Target genome list was writen to GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:18:42,064] [INFO] Task started: fastANI
[2023-06-08 13:18:42,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b54ad25-e41d-4452-8ed2-cfc38ac574dc/GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:18:53,696] [INFO] Task succeeded: fastANI
[2023-06-08 13:18:53,712] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 13:18:53,712] [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_910589105.1	s__1XD42-69 sp910589105	99.3999	701	764	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910586355.1	s__1XD42-69 sp910586355	79.404	330	764	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586645.1	s__1XD42-69 sp910586645	77.6098	214	764	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011959925.1	s__1XD42-69 sp011959925	77.5344	165	764	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	98.99	98.99	0.83	0.83	2	-
GCA_910588565.1	s__1XD42-69 sp910588565	77.1429	151	764	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585825.1	s__1XD42-69 sp910585825	77.0995	188	764	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586725.1	s__1XD42-69 sp910586725	76.9981	195	764	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000364225.1	s__Eubacterium_J plexicaudatum	76.3396	59	764	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_J	95.0	99.29	99.29	0.93	0.93	2	-
GCA_910578885.1	s__RUG115 sp910578885	76.2781	61	764	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586045.1	s__Eubacterium_J sp910586045	76.2545	56	764	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017625255.1	s__1XD42-69 sp017625255	76.1677	85	764	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577225.1	s__Eubacterium_J sp910577225	75.8675	54	764	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910580075.1	s__Eubacterium_J sp910580075	75.7057	57	764	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_J	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 13:18:53,714] [INFO] GTDB search result was written to GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 13:18:53,714] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:18:53,717] [INFO] DFAST_QC result json was written to GCA_947574295.1_SRR15730549_bin.1_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 13:18:53,717] [INFO] DFAST_QC completed!
[2023-06-08 13:18:53,718] [INFO] Total running time: 0h0m55s