[2023-06-08 20:36:31,340] [INFO] DFAST_QC pipeline started.
[2023-06-08 20:36:31,343] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 20:36:31,343] [INFO] DQC Reference Directory: /var/lib/cwl/stgc563d896-1c63-43da-ab96-0d57e4713231/dqc_reference
[2023-06-08 20:36:32,588] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 20:36:32,589] [INFO] Task started: Prodigal
[2023-06-08 20:36:32,589] [INFO] Running command: gunzip -c /var/lib/cwl/stg600cbe60-73f9-4bba-bec7-6b56f35f1b1c/GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 20:36:37,298] [INFO] Task succeeded: Prodigal
[2023-06-08 20:36:37,298] [INFO] Task started: HMMsearch
[2023-06-08 20:36:37,298] [INFO] Running command: hmmsearch --tblout GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc563d896-1c63-43da-ab96-0d57e4713231/dqc_reference/reference_markers.hmm GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 20:36:37,540] [INFO] Task succeeded: HMMsearch
[2023-06-08 20:36:37,541] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg600cbe60-73f9-4bba-bec7-6b56f35f1b1c/GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 20:36:37,572] [INFO] Query marker FASTA was written to GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 20:36:37,573] [INFO] Task started: Blastn
[2023-06-08 20:36:37,573] [INFO] Running command: blastn -query GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc563d896-1c63-43da-ab96-0d57e4713231/dqc_reference/reference_markers.fasta -out GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:36:38,132] [INFO] Task succeeded: Blastn
[2023-06-08 20:36:38,136] [INFO] Selected 20 target genomes.
[2023-06-08 20:36:38,136] [INFO] Target genome list was writen to GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 20:36:38,137] [INFO] Task started: fastANI
[2023-06-08 20:36:38,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg600cbe60-73f9-4bba-bec7-6b56f35f1b1c/GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 20:36:49,843] [INFO] Task succeeded: fastANI
[2023-06-08 20:36:49,843] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc563d896-1c63-43da-ab96-0d57e4713231/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 20:36:49,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc563d896-1c63-43da-ab96-0d57e4713231/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 20:36:49,846] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 20:36:49,846] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 20:36:49,846] [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 20:36:49,848] [INFO] DFAST Taxonomy check result was written to GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 20:36:49,849] [INFO] ===== Taxonomy check completed =====
[2023-06-08 20:36:49,849] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 20:36:49,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc563d896-1c63-43da-ab96-0d57e4713231/dqc_reference/checkm_data
[2023-06-08 20:36:49,852] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 20:36:49,880] [INFO] Task started: CheckM
[2023-06-08 20:36:49,880] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 20:37:11,311] [INFO] Task succeeded: CheckM
[2023-06-08 20:37:11,312] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.93%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 20:37:11,334] [INFO] ===== Completeness check finished =====
[2023-06-08 20:37:11,335] [INFO] ===== Start GTDB Search =====
[2023-06-08 20:37:11,335] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 20:37:11,335] [INFO] Task started: Blastn
[2023-06-08 20:37:11,335] [INFO] Running command: blastn -query GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc563d896-1c63-43da-ab96-0d57e4713231/dqc_reference/reference_markers_gtdb.fasta -out GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:37:12,067] [INFO] Task succeeded: Blastn
[2023-06-08 20:37:12,071] [INFO] Selected 18 target genomes.
[2023-06-08 20:37:12,071] [INFO] Target genome list was writen to GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 20:37:12,073] [INFO] Task started: fastANI
[2023-06-08 20:37:12,073] [INFO] Running command: fastANI --query /var/lib/cwl/stg600cbe60-73f9-4bba-bec7-6b56f35f1b1c/GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 20:37:19,549] [INFO] Task succeeded: fastANI
[2023-06-08 20:37:19,563] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 20:37:19,563] [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_017621075.1	s__Acetatifactor sp017621075	77.5838	89	526	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017476665.1	s__Acetatifactor sp017476665	77.4693	105	526	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056885.1	s__Acetatifactor sp015056885	77.4464	69	526	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900766575.1	s__Acetatifactor sp900766575	77.3436	64	526	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003584705.1	s__Acetatifactor sp900066565	77.2678	116	526	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	98.01	97.56	0.88	0.80	26	-
GCA_900771995.1	s__Acetatifactor sp900771995	77.1568	120	526	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003447295.1	s__Acetatifactor sp003447295	77.1499	75	526	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	97.04	96.84	0.74	0.71	4	-
GCA_018385425.1	s__Acetatifactor sp018385425	77.0625	80	526	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	99.11	99.11	0.86	0.86	2	-
GCA_900772845.1	s__Acetatifactor sp900772845	77.057	81	526	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	95.92	95.92	0.80	0.80	2	-
GCA_016293615.1	s__Acetatifactor sp016293615	77.047	85	526	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009695995.1	s__Acetatifactor intestinalis	77.0371	110	526	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	96.98	96.46	0.81	0.76	18	-
GCA_016286555.1	s__AC2028 sp016286555	77.0132	58	526	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__AC2028	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002368865.1	s__Acetatifactor sp002368865	76.9684	65	526	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017480445.1	s__Acetatifactor sp017480445	76.9351	70	526	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056915.1	s__Acetatifactor sp015056915	76.8207	77	526	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 20:37:19,565] [INFO] GTDB search result was written to GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 20:37:19,566] [INFO] ===== GTDB Search completed =====
[2023-06-08 20:37:19,569] [INFO] DFAST_QC result json was written to GCA_945831795.1_SRR5976185_bin.24_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 20:37:19,569] [INFO] DFAST_QC completed!
[2023-06-08 20:37:19,569] [INFO] Total running time: 0h0m48s